Mol Biol Evol , IF:16.24 , 2023 Jul , V40 (7) doi: 10.1093/molbev/msad141
Whole-genome Duplications and the Long-term Evolution of Gene Regulatory Networks in Angiosperms.
Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.; VIB Center for Plant Systems Biology, VIB, Ghent, Belgium.; Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa.; College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, China.
Angiosperms have a complex history of whole-genome duplications (WGDs), with varying numbers and ages of WGD events across clades. These WGDs have greatly affected the composition of plant genomes due to the biased retention of genes belonging to certain functional categories following their duplication. In particular, regulatory genes and genes encoding proteins that act in multiprotein complexes have been retained in excess following WGD. Here, we inferred protein-protein interaction (PPI) networks and gene regulatory networks (GRNs) for seven well-characterized angiosperm species and explored the impact of both WGD and small-scale duplications (SSDs) in network topology by analyzing changes in frequency of network motifs. We found that PPI networks are enriched in WGD-derived genes associated with dosage-sensitive intricate systems, and strong selection pressures constrain the divergence of WGD-derived genes at the sequence and PPI levels. WGD-derived genes in network motifs are mostly associated with dosage-sensitive processes, such as regulation of transcription and cell cycle, translation, photosynthesis, and carbon metabolism, whereas SSD-derived genes in motifs are associated with response to biotic and abiotic stress. Recent polyploids have higher motif frequencies than ancient polyploids, whereas WGD-derived network motifs tend to be disrupted on the longer term. Our findings demonstrate that both WGD and SSD have contributed to the evolution of angiosperm GRNs, but in different ways, with WGD events likely having a more significant impact on the short-term evolution of polyploids.
PMID: 37405949
New Phytol , IF:10.151 , 2023 Aug , V239 (3) : P992-1004 doi: 10.1111/nph.18788
A gene regulatory network in Arabidopsis roots reveals features and regulators of the plant response to elevated CO(2).
IPSiM, Univ. Montpellier, CNRS, INRAE, Institut Agro, 34000, Montpellier, France.; IMAG, Univ. Montpellier, CNRS, 34000, Montpellier, France.; Universite Paul-Valery-Montpellier 3, 34000, Montpellier, France.
The elevation of CO(2) in the atmosphere increases plant biomass but decreases their mineral content. The genetic and molecular bases of these effects remain mostly unknown, in particular in the root system, which is responsible for plant nutrient uptake. To gain knowledge about the effect of elevated CO(2) on plant growth and physiology, and to identify its regulatory in the roots, we analyzed genome expression in Arabidopsis roots through a combinatorial design with contrasted levels of CO(2) , nitrate, and iron. We demonstrated that elevated CO(2) has a modest effect on root genome expression under nutrient sufficiency, but by contrast leads to massive expression changes under nitrate or iron deficiencies. We demonstrated that elevated CO(2) negatively targets nitrate and iron starvation modules at the transcriptional level, associated with a reduction in high-affinity nitrate uptake. Finally, we inferred a gene regulatory network governing the root response to elevated CO(2) . This network allowed us to identify candidate transcription factors including MYB15, WOX11, and EDF3 which we experimentally validated for their role in the stimulation of growth by elevated CO(2) . Our approach identified key features and regulators of the plant response to elevated CO(2) , with the objective of developing crops resilient to climate change.
PMID: 36727308
Crit Rev Biotechnol , IF:8.429 , 2023 Dec , V43 (5) : P716-733 doi: 10.1080/07388551.2022.2058460
Systems seed biology to understand and manipulate rice grain quality and nutrition.
Consumer-Driven Grain Quality and Nutrition Unit, International Rice Research Institute (IRRI), Manila, Philippines.; Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Australia.
Rice is one of the most essential crops since it meets the calorific needs of 3 billion people around the world. Rice seed development initiates upon fertilization, leading to the establishment of two distinct filial tissues, the endosperm and embryo, which accumulate distinct seed storage products, such as starch, storage proteins, and lipids. A range of systems biology tools deployed in dissecting the spatiotemporal dynamics of transcriptome data, methylation, and small RNA based regulation operative during seed development, influencing the accumulation of storage products was reviewed. Studies of other model systems are also considered due to the limited information on the rice transcriptome. This review highlights key genes identified through a holistic view of systems biology targeted to modify biochemical composition and influence rice grain quality and nutritional value with the target of improving rice as a functional food.
PMID: 35723584
Elife , IF:8.14 , 2023 Jul , V12 doi: 10.7554/eLife.79743
Integrating analog and digital modes of gene expression at Arabidopsis FLC.
Department of Computational and Systems Biology, John Innes Centre, Norwich, United Kingdom.; School of Molecular Biosciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom.; Swedish University of Agricultural Sciences, Plant Biology Department, Uppsala, Sweden.; Department of Cell and Developmental Biology, John Innes Centre, Norwich, United Kingdom.; EMBL Australia Node in Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney, Australia.; State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.; Faculty of Medicine and Health Sciences, Norwich Medical School, University of East Anglia, Norwich, United Kingdom.; College of Life Sciences, Wuhan University, Wuhan, China.; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, United Kingdom.
Quantitative gene regulation at the cell population level can be achieved by two fundamentally different modes of regulation at individual gene copies. A 'digital' mode involves binary ON/OFF expression states, with population-level variation arising from the proportion of gene copies in each state, while an 'analog' mode involves graded expression levels at each gene copy. At the Arabidopsis floral repressor FLOWERING LOCUS C (FLC), 'digital' Polycomb silencing is known to facilitate quantitative epigenetic memory in response to cold. However, whether FLC regulation before cold involves analog or digital modes is unknown. Using quantitative fluorescent imaging of FLC mRNA and protein, together with mathematical modeling, we find that FLC expression before cold is regulated by both analog and digital modes. We observe a temporal separation between the two modes, with analog preceding digital. The analog mode can maintain intermediate expression levels at individual FLC gene copies, before subsequent digital silencing, consistent with the copies switching OFF stochastically and heritably without cold. This switch leads to a slow reduction in FLC expression at the cell population level. These data present a new paradigm for gradual repression, elucidating how analog transcriptional and digital epigenetic memory pathways can be integrated.
PMID: 37466633
Sci Total Environ , IF:7.963 , 2023 Jul , V897 : P165441 doi: 10.1016/j.scitotenv.2023.165441
Prevalence of antibiotic resistance genes and virulence factors in the sediment of WWTP effluent-dominated rivers.
The National Key Laboratory of Water Disaster Prevention, Yangtze Institute for Conservation and Development, Hohai University, Nanjing 210098, PR China.; The National Key Laboratory of Water Disaster Prevention, Dayu College, Hohai University, Nanjing 210098, PR China.; Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, PR China.; Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, PR China. Electronic address: envly@hhu.edu.cn.
In the context of increasing aridity due to climate changes, effluent from wastewater treatment plants (WWTPs) became dominant in some rivers. However, the prevalence of antibiotic resistance genes (ARGs) and virulence factors (VFs) in effluent-dominated rivers was rarely investigated. In this study, the profiles of ARGs and VFs in the sediment of two effluent-dominated rivers were revealed through the metagenomic sequencing technique. In each river, samples from the effluent discharge point (P site) and approximately 500 m downstream (D site) were collected. Results showed that the abundances of ARGs and VFs were both higher in D sites than those in P sites, indicating higher risks in the downstream areas. The compositions of ARGs were similar in the P sites of two rivers while being distinct in the D sites. The same was true for changes in the VFs compositions. Microbial community structure variations were the main driver for the changes in ARGs and VFs. Network analysis revealed that the interaction of ARGs and VF genes (VFGs) in sediment was intense. Two VFGs and eleven ARGs were identified to play important roles in the network. Metagenome-assembled genomes (MAGs) were generated to evaluate the coexistence of ARGs and VFGs at the single genome level. It was found that 38.4 % of the MAGs contained both ARGs and VFGs, and two MAGs were from pathogenic genera. These results suggested that high microbiological risks existed in effluent-dominated rivers, and necessary measures should be taken to prevent the potential threat to public health.
PMID: 37437635
Sci Total Environ , IF:7.963 , 2023 Jul , V896 : P165249 doi: 10.1016/j.scitotenv.2023.165249
Response of heavy-metal and antibiotic resistance genes and their related microbe in rice paddy irrigated with treated municipal wastewaters.
China National Rice Research Institute, Hangzhou 310006, PR China; Rice Product Quality Inspection and Supervision Testing Center of Ministry of Agriculture and Rural Affairs, China National Rice Research Institute, Hangzhou 310006, PR China.; China National Rice Research Institute, Hangzhou 310006, PR China.; China National Rice Research Institute, Hangzhou 310006, PR China; Rice Product Quality Inspection and Supervision Testing Center of Ministry of Agriculture and Rural Affairs, China National Rice Research Institute, Hangzhou 310006, PR China. Electronic address: qyan2005@hotmail.com.
Paddy irrigation with secondary effluents from municipal wastewater treatment plants (MWTPs) is a well-established practice to alleviate water scarcity. However, the reuse might lead to more complicated contamination caused by interactions between residual antibiotics in effluents and heavy metals in paddy soil. To date, no information is available for the potential effects of dual stress of heavy metals and antibiotics on heavy-metal resistance genes (MRGs) and antibiotic resistance genes (ARGs). Here, this study investigated the response of heavy metal and antibiotic resistance genes, and related microorganisms to the dual threat of antibiotics and heavy metals under the long-term MWTP effluent irrigation for rice paddy using metagenome. The results showed that there was not a negative effect on rice consumption if MWTP effluent was used to irrigate rice for a long time. The concentration of antibiotics could reshape the ARGs and MRG profiles in rice paddy soil. The findings revealed the co-occurrence of ARGs and MRGs in rice paddy soils, thus highlighting the need for simultaneous elimination of antibiotics and heavy metals to effectively reduce ARGs and MRGs. Acn and sul1 genes encoding Iron and sulfonamides resistance mechanisms are the most abundant MRG and ARG, respectively. Network analysis revealed the possibility that IntI1 plays a role in the co-transmission of MRG and ARG to host microbes, and that Proteobacteria are the most dominant hosts for MRG, ARG, and integrons. The presence of antibiotics in irrigated MWTP effluents has been found to stimulate the proliferation of heavy metal and antibiotic resistances by altering soil microbial communities. This study will enhance our comprehension of the co-selection between ARGs and MRGs, as well as reveal the concealed environmental impacts of combined pollution. The obtained results have important implications for food safety and human health in rice.
PMID: 37406708
Sci Total Environ , IF:7.963 , 2023 Jun , V895 : P165099 doi: 10.1016/j.scitotenv.2023.165099
Spatial and molecular variations in forest topsoil dissolved organic matter as revealed by FT-ICR mass spectrometry.
Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin, 300072, China.; Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin, 300072, China. Electronic address: liucongqiang@tju.edu.cn.; School of Environment Studies, China University of Geosciences, Wuhan 430074, China.; LAPC, Institute of Atmospheric Physics, Chinese Academy of Sciences, Beijing 100029, China.; Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.; Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin, 300072, China. Electronic address: fupingqing@tju.edu.cn.
Forest soils cover about 30 % of the Earth's land surface and play a fundamental role in the global cycle of organic matter. Dissolved organic matter (DOM), the largest active pool of terrestrial carbon, is essential for soil development, microbial metabolism and nutrient cycling. However, forest soil DOM is a highly complex mixture of tens of thousands of individual compounds, which is largely composed of organic matter from primary producers, residues from microbial process and the corresponding chemical reactions. Therefore, we need a detailed picture of molecular composition in forest soil, especially the pattern of large-scale spatial distribution, which can help us understand the role of DOM in the carbon cycle. To explore the spatial and molecular variations of DOM in forest soil, we choose six major forest reserves located in different latitudes ranging in China, which were investigated by Fourier transform-ion cyclotron resonance mass spectrometry (FT-ICR MS). Results show that aromatic-like molecules are preferentially enriched in DOM at high latitude forest soils, while aliphatic/peptide-like, carbohydrate-like, and unsaturated hydrocarbon molecules are preferentially enriched in DOM at low latitude forest soils, besides, lignin-like compounds account for the highest proportion in all forest soil DOM. High latitude forest soils have higher aromatic equivalents and aromatic indices than low latitude forest soils, which suggest that organic matter at higher latitude forest soils preferentially contain plant-derived ingredients and are refractory to degradation while microbially derived carbon is dominant in organic matter at low latitudes. Besides, we found that CHO and CHON compounds make up the majority in all forest soil samples. Finally, we visualized the complexity and diversity of soil organic matter molecules through network analysis. Our study provides a molecular-level understanding of forest soil organic matter at large scales, which may contribute to the conservation and utilization of forest resources.
PMID: 37379928
Sci Total Environ , IF:7.963 , 2023 Sep , V892 : P164506 doi: 10.1016/j.scitotenv.2023.164506
Diversity of fungal microbiome obtained from plant rhizoplanes.
Department of Biology and Biochemistry, University of Houston, Houston, TX 77004, USA.; Department of Civil and Environmental Engineering, University of Houston, Houston, TX 77004, USA.; Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.; Department of Biology and Biochemistry, University of Houston, Houston, TX 77004, USA; Department of Civil and Environmental Engineering, University of Houston, Houston, TX 77004, USA. Electronic address: dfrigirodrigues@uh.edu.
Microbial communities, and their ecological importance, have been investigated in several habitats. However, so far, most studies could not describe the closest microbial interactions and their functionalities. This study investigates the co-occurring interactions between fungi and bacteria in plant rhizoplanes and their potential functions. The partnerships were obtained using fungal-highway columns with four plant-based media. The fungi and associated microbiomes isolated from the columns were identified by sequencing the ITS (fungi) and 16S rRNA genes (bacteria). Statistical analyses including Exploratory Graph and Network Analysis were used to visualize the presence of underlying clusters in the microbial communities and evaluate the metabolic functions associated with the fungal microbiome (PICRUSt2). Our findings characterize the presence of both unique and complex bacterial communities associated with different fungi. The results showed that Bacillus was associated as exo-bacteria in 80 % of the fungi but occurred as putative endo-bacteria in 15 %. A shared core of putative endo-bacterial genera, potentially involved in the nitrogen cycle was found in 80 % of the isolated fungi. The comparison of potential metabolic functions of the putative endo- and exo-communities highlighted the potential essential factors to establish an endosymbiotic relationship, such as the loss of pathways associated with metabolites obtained from the host while maintaining pathways responsible for bacterial survival within the hypha.
PMID: 37295515
Sci Total Environ , IF:7.963 , 2023 Jun , V879 : P163244 doi: 10.1016/j.scitotenv.2023.163244
Response of soil fungal community to chromium contamination in agricultural soils with different physicochemical properties.
State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; School of Environment Science and Spatial Information, China University of Mining and Technology, Xuzhou, Jiangsu 221116, China.; School of Environment Science and Spatial Information, China University of Mining and Technology, Xuzhou, Jiangsu 221116, China.; State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; RDFZ Chaoyang School, Beijing 100028, China.; State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.; State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.; State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China. Electronic address: xinzhang@rcees.ac.cn.
Chromium (Cr) contamination has been of great concern in agricultural soil health due to its persistence, toxicity and bioaccumulation. Fungi, as an essential regulator of soil remediation and biochemical processes, had an unclear response to Cr contamination. In this study, the composition, diversity and interaction mechanisms of fungal communities in agricultural soils from ten different provinces of China were investigated in order to elucidate the fungal community response to varying soil properties and Cr concentrations. The results showed that high concentrations of Cr led to substantial alterations in the fungal community composition. The complex soil properties had a far greater impact on the fungal community structure than the single factor of Cr concentration, with soil available phosphorus (AP) and pH being most influential. Function predictions based on FUNGuild indicated that high concentrations of Cr have a significant impact on certain functional groups of fungi, including mycorrhizal fungi and plant saprotroph. The fungal community tended to resist Cr stress by enhancing interactions and clustering among network modules, while generating new keystone taxa. This study allowed insights into the response of soil fungal community to Cr contamination in different agricultural soils from different provinces and provided a theoretical basis for soil Cr ecological risk assessment and the development of bioremediation techniques for Cr-contaminated soils.
PMID: 37004770
Plant Cell Environ , IF:7.228 , 2023 Sep , V46 (9) : P2909-2927 doi: 10.1111/pce.14647
Integrative time-scale and multi-omics analysis of host responses to viroid infection.
Department of Molecular Interactions and Regulation, Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Cientificas (CSIC), Universitat de Valencia (UV), Parc Cientific, Paterna, Spain.; Department of Virologia Molecular y Evolutiva de Plantas, Instituto de Biologia Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Cientificas (CSIC), Universitat Politecnica de Valencia, Valencia, Spain.
Viroids are circular RNAs of minimal complexity compelled to subvert plant-regulatory networks to accomplish their infectious process. Studies focused on the response to viroid-infection have mostly addressed specific regulatory levels and considered specifics infection-times. Thus, much remains to be done to understand the temporal evolution and complex nature of viroid-host interactions. Here we present an integrative analysis of the temporal evolution of the genome-wide alterations in cucumber plants infected with hop stunt viroid (HSVd) by integrating differential host transcriptome, sRNAnome and methylome. Our results support that HSVd promotes the redesign of the cucumber regulatory-pathways predominantly affecting specific regulatory layers at different infection-phases. The initial response was characterised by a reconfiguration of the host-transcriptome by differential exon-usage, followed by a progressive transcriptional downregulation modulated by epigenetic changes. Regarding endogenous small RNAs, the alterations were limited and mainly occurred at the late stage. Significant host-alterations were predominantly related to the downregulation of transcripts involved in plant-defence mechanisms, the restriction of pathogen-movement and the systemic spreading of defence signals. We expect that these data constituting the first comprehensive temporal-map of the plant-regulatory alterations associated with HSVd infection could contribute to elucidate the molecular basis of the yet poorly known host-response to viroid-induced pathogenesis.
PMID: 37378473
Plant Cell Environ , IF:7.228 , 2023 Jul doi: 10.1111/pce.14672
Dynamic gene regulatory networks improving spike fertility through regulation of floret primordia fate in wheat.
College of Agronomy and Biotechnology, China Agricultural University, Beijing, China.; College of Biological Sciences, China Agricultural University, Beijing, China.; Texas A&M AgriLife Research and Extension Center at Amarillo, Amarillo, Texas, USA.; Engineering Technology Research Center for Agriculture in Low Plain Areas, Hebei Province, China.
The developmental process of spike is critical for spike fertility through affecting floret primordia fate in wheat; however, the genetic regulation of this dynamic and complex developmental process remains unclear. Here, we conducted a high temporal-resolution analysis of spike transcriptomes and monitored the number and morphology of floret primordia within spike. The development of all floret primordia in a spike was clearly separated into three distinct phases: differentiation, pre-dimorphism and dimorphism. Notably, we identified that floret primordia with meiosis ability at the pre-dimorphism phase usually develop into fertile floret primordia in the next dimorphism phase. Compared to control, increasing plant space treatment achieved the maximum increasement range (i.e., 50%) in number of fertile florets by accelerating spike development. The process of spike fertility improvement was directed by a continuous and dynamic regulatory network involved in transcription factor and genes interaction. This was based on the coordination of genes related to heat shock protein and jasmonic acid biosynthesis during differentiation phase, and genes related to lignin, anthocyanin and chlorophyll biosynthesis during dimorphism phase. The multi-dimensional association with high temporal-resolution approach reported here allows rapid identification of genetic resource for future breeding studies to realise the maximum spike fertility potential in more cereal crops.
PMID: 37485926
Genes Dis , IF:7.103 , 2023 Sep , V10 (5) : P2049-2063 doi: 10.1016/j.gendis.2022.09.009
The transcriptional regulators of virulence for Pseudomonas aeruginosa: Therapeutic opportunity and preventive potential of its clinical infections.
College of Plant Protection, Laboratory of Plant Immunity, Key Laboratory of Integrated Management of Crop Diseases and Pests, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China.; Department of Biomedical Sciences, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China.; School of Pharmaceutical Sciences, Sun Yat-Sen University, University Town, Guangzhou, Guangdong 510006, China.; Tung Biomedical Sciences Centre, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China.; Shenzhen Research Institute, City University of Hong Kong, Shenzhen, Guangdong 518057, China.
In Pseudomonas aeruginosa (P. aeruginosa), transcription factors (TFs) are important mediators in the genetic regulation of adaptability and pathogenicity to respond to multiple environmental stresses and host defences. The P. aeruginosa genome harbours 371 putative TFs; of these, about 70 have been shown to regulate virulence-associated phenotypes by binding to the promoters of their target genes. Over the past three decades, several techniques have been applied to identify TF binding sites on the P. aeruginosa genome, and an atlas of TF binding patterns has been mapped. The virulence-associated regulons of TFs show complex crosstalk in P. aeruginosa's regulatory network. In this review, we summarise the recent literature on TF regulatory networks involved in the quorum-sensing system, biofilm formation, pyocyanin synthesis, motility, the type III secretion system, the type VI secretion system, and oxidative stress responses. We discuss future perspectives that could provide insights and targets for preventing clinical infections caused by P. aeruginosa based on the global regulatory network of transcriptional regulators.
PMID: 37492705
J Exp Bot , IF:6.992 , 2023 Aug , V74 (15) : P4503-4519 doi: 10.1093/jxb/erad178
Deciphering transcriptional mechanisms of maize internodal elongation by regulatory network analysis.
State Key Laboratory of Plant Physiology and Biochemistry, Engineering Research Center of Plant Growth Regulator, Ministry of Education & College of Agronomy and Biotechnology, China Agricultural University, No.2 Yuanmingyuan West Road, Haidian, Beijing 100193, China.; North China Key Laboratory for Crop Germplasm Resources, Ministry of Education, State Key Laboratory of North China Crop Improvement and Regulation & College of Agronomy, Hebei Agricultural University, Baoding, Hebei 071001, China.; College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China.
The lengths of the basal internodes is an important factor for lodging resistance of maize (Zea mays). In this study, foliar application of coronatine (COR) to 10 cultivars at the V8 growth stage had different suppression effects on the length of the eighth internode, with three being categorized as strong-inhibition cultivars (SC), five as moderate (MC), and two as weak (WC). RNA-sequencing of the eighth internode of the cultivars revealed a total of 7895 internode elongation-regulating genes, including 777 transcription factors (TFs). Genes related to the hormones cytokinin, gibberellin, auxin, and ethylene in the SC group were significantly down-regulated compared to WC, and more cell-cycle regulatory factors and cell wall-related genes showed significant changes, which severely inhibited internode elongation. In addition, we used EMSAs to explore the direct regulatory relationship between two important TFs, ZmABI7 and ZmMYB117, which regulate the cell cycle and cell wall modification by directly binding to the promoters of their target genes ZmCYC1, ZmCYC3, ZmCYC7, and ZmCPP1. The transcriptome reported in this study will provide a useful resource for studying maize internode development, with potential use for targeted genetic control of internode length to improve the lodging resistance of maize.
PMID: 37170764
J Exp Bot , IF:6.992 , 2023 Aug , V74 (14) : P3933-3950 doi: 10.1093/jxb/erad135
An evo-devo view of the gynoecium.
International Research Organization for Advanced Science and Technology (IROAST), Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555, Japan.; Laboratorio de Genetica Molecular, Epigenetica, Desarrollo y Evolucion de Plantas, Instituto de Ecologia, Universidad Nacional Autonoma de Mexico, Ciudad Universitaria, Av. Universidad 3000, Coyoacan, Mexico DF 04510, Mexico.; Faculty of Advanced Science and Technology (FAST), Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555, Japan.; Unidad de Genomica Avanzada (LANGEBIO), Centro de Investigacion y de Estudios Avanzados del Instituto Politecnico Nacional (CINVESTAV-IPN), Irapuato 36824, Guanajuato, Mexico.
The appearance of the flower marks a key event in the evolutionary history of plants. Among the four types of floral organs, the gynoecium represents the major adaptive advantage of the flower. The gynoecium is an enclosing structure that protects and facilitates the fertilization of the ovules, which then mature as seeds. Upon fertilization, in many species, the gynoecium itself eventually becomes the fruit, which contributes to the dispersal of the seeds. However, despite its importance and the recent advances in our understanding of the genetic regulatory network guiding early gynoecium development, many questions remain to be resolved regarding the extent of the conservation of the molecular mechanisms for gynoecium development among different taxa, and how these mechanisms give origin and diversification to the gynoecium. In this review, we compile the existing knowledge about the evolution, development, and molecular mechanisms involved in the origin and evolution of the gynoecium.
PMID: 37075814
Int J Biol Macromol , IF:6.953 , 2023 Jul , V242 (Pt 3) : P124834 doi: 10.1016/j.ijbiomac.2023.124834
Comparative transcriptome analysis reveals the core molecular network in pattern-triggered immunity in Sorghum bicolor.
Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang 550025, PR China.; National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, PR China.; Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang 550025, PR China. Electronic address: ippxiexin@163.com.
Pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI) is the first line of defense in plant disease resistance. However, the molecular mechanisms of plant PTI vary across species, making it challenging to identify a core set of trait-associated genes. This study aimed to investigate key factors that influence PTI and identify the core molecular network in Sorghum bicolor, a C4 plant. We performed comprehensive weighted gene co-expression network analysis and temporal expression analysis of large-scale transcriptome data from various sorghum cultivars under different PAMP treatments. Our results revealed that the type of PAMP had a stronger influence on the PTI network than did the sorghum cultivar. Following PAMP treatment, 30 genes with stable downregulated expression and 158 genes with stable upregulated expression were identified, including genes encoding potential pattern recognition receptors whose expression was upregulated within 1 h of treatment. PAMP treatment altered the expression of resistance-related, signaling, salt-sensitive, heavy metal-related, and transporter genes. These findings provide novel insights into the core genes involved in plant PTI and are expected to facilitate the identification and application of resistance genes in plant breeding studies.
PMID: 37207754
Int J Biol Macromol , IF:6.953 , 2023 Aug , V246 : P125633 doi: 10.1016/j.ijbiomac.2023.125633
Morphology, sucrose metabolism and gene network reveal the molecular mechanism of seed fiber development in poplar.
State Key Laboratory for Efficient Production of Forest Resources, Key Laboratory of Silviculture and Conservation of the Ministry of Education, National Energy R&D Center for Non-food Biomass, Engineering Research Center for Carbon Sequestration and Sink Enhancement by Forestry and Grass of the Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China.; National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China.; State Key Laboratory for Efficient Production of Forest Resources, Key Laboratory of Silviculture and Conservation of the Ministry of Education, National Energy R&D Center for Non-food Biomass, Engineering Research Center for Carbon Sequestration and Sink Enhancement by Forestry and Grass of the Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China. Electronic address: zhongchen@bjfu.edu.cn.
Poplar is an important tree species for ecological protection, wood production, bioenergy and urban greening; it has been widely planted worldwide. However, the catkin fibers produced by female poplars can cause environmental pollution and safety hazards during spring. This study focused on Populus tomentosa, and revealed the sucrose metabolism regulatory mechanism of catkin fibers development from morphological, physiological and molecular aspects. Paraffin section suggested that poplar catkin fibers were not seed hairs and produced from the epidermal cells of funicle and placenta. Sucrose degradation via invertase and sucrose synthase played the dominant role during poplar catkin fibers development. The expression patterns revealed that sucrose metabolism-related genes played important roles during catkin fibers development. Y1H analysis indicated that there was a potential interaction between sucrose synthase 2 (PtoSUS2)/vacuolar invertase 3 (PtoVIN3) and trichome-regulating MYB transcription factors in poplar. Finally, the two key genes, PtoSUS2 and PtoVIN3, had roles in Arabidopsis trichome density, indicating that sucrose metabolism is important in poplar catkin fibers development. This study is not only helpful for clarifying the mechanism of sucrose regulation during trichome development in perennial woody plants, but also establishes a foundation to solve poplar catkin fibers pollution through genetic engineering methods.
PMID: 37406903
Environ Res , IF:6.498 , 2023 Jul , V234 : P116499 doi: 10.1016/j.envres.2023.116499
Community recovery of benthic macroinvertebrates in a stream influenced by mining activity: Importance of microhabitat monitoring.
Freshwater Biodiversity Research Bureau, Nakdonggang National Institute of Biological Resources (NNIBR), Sangju, 37242, South Korea. Electronic address: mjbae@nnibr.re.kr.; Freshwater Biodiversity Research Bureau, Nakdonggang National Institute of Biological Resources (NNIBR), Sangju, 37242, South Korea.; Freshwater Biodiversity Research Bureau, Nakdonggang National Institute of Biological Resources (NNIBR), Sangju, 37242, South Korea. Electronic address: ejkim@nnibr.re.kr.
The decrease in freshwater biodiversity owing to anthropogenic disturbances such as mining activity is a global challenge; hence, there is an urgent need for systematic approaches to continuously monitor such disturbances and/or the recovery of biodiversity in freshwater habitats. The Hwangjicheon Stream is the source of South Korea's longest river and has been subjected to runoff from coal mining. We investigated changes in the diversity of the benthic macroinvertebrate community in various microhabitats, including riffle, run, and pool, to monitor the recovery of biodiversity in the stream following the improvement of a mining water treatment plant in 2019. The dataset comprised 111 samples obtained from four types of microhabitats (riffle, run, pool, and riparian) over a four-year period from 2018 to 2021. The mining-affected sites had lower macroinvertebrate community complexities according to a network analysis, and grouped into the same cluster based on self-organizing map (SOM) analysis. Moreover, 51 taxa selected as indicator species represented each cluster obtained through the SOM analysis. Among them, only Limnodrilus gotoi and Radix auricularia were included as indicator species at the mining-affected sites. However, after 2020, the benthic macroinvertebrate community complexity increased, and some of the microhabitats at the mining-affected sites were included in the same cluster as the reference sites in the SOM analysis, indicating that the recovery of benthic macroinvertebrate communities had initiated in certain microhabitats (e.g., riparian). Further analysis confirmed that the macroinvertebrate community clearly differed according to the survey year, even in different microhabitats at the same sites. This suggests that more acute microhabitat monitoring may be necessary to quickly confirm biodiversity restoration when assessing the degree of the recovery in river biodiversity from anthropogenic disturbances.
PMID: 37429394
mSystems , IF:6.496 , 2023 Jul : Pe0044023 doi: 10.1128/msystems.00440-23
Paired associated SARS-CoV-2 spike variable positions: a network analysis approach to emerging variants.
Department of Microbiology, Medical School, National and Kapodistrian University of Athens , Athens, Greece.; ELGO-Demeter, Plant Protection Division of Patras, Laboratory of Virology , Patras, Greece.; Department of Medicine, Stanford University , Stanford, California, USA.; Departments of Epidemiology and Population Health, Stanford University , Stanford, California, USA.; Department of Biomedical Data Science, Stanford University , Stanford, California, USA.; Department of Statistics, Stanford University , Stanford, California, USA.
Amino acids in variable positions of proteins may be correlated, with potential structural and functional implications. Here, we apply exact tests of independence in R x C contingency tables to examine noise-free associations between variable positions of the SARS-CoV-2 spike protein, using as a paradigm sequences from Greece deposited in GISAID (N = 6,683/1,078 full length) for the period 29 February 2020 to 26 April 2021 that essentially covers the first three pandemic waves. We examine the fate and complexity of these associations by network analysis, using associated positions (exact P /= 2) as links and the corresponding positions as nodes. We found a temporal linear increase of positional differences and a gradual expansion of the number of position associations over time, represented by a temporally evolving intricate web, resulting in a non-random complex network of 69 nodes and 252 links. Overconnected nodes corresponded to the most adapted variant positions in the population, suggesting a direct relation between network degree and position functional importance. Modular analysis revealed 25 k-cliques comprising 3 to 11 nodes. At different k-clique resolutions, one to four communities were formed, capturing epistatic associations of circulating variants (Alpha, Beta, B.1.1.318), but also Delta, which dominated the evolutionary landscape later in the pandemic. Cliques of aminoacidic positional associations tended to occur in single sequences, enabling the recognition of epistatic positions in real-world virus populations. Our findings provide a novel way of understanding epistatic relationships in viral proteins with potential applications in the design of virus control procedures. IMPORTANCE Paired positional associations of adapted amino acids in virus proteins may provide new insights for understanding virus evolution and variant formation. We investigated potential intramolecular relationships between variable SARS-CoV-2 spike positions by exact tests of independence in R x C contingency tables, having applied Average Product Correction (APC) to eliminate background noise. Associated positions (exact P /= 2) formed a non-random, epistatic network of 25 cliques and 1-4 communities at different clique resolutions, revealing evolutionary ties between variable positions of circulating variants and a predictive potential of previously unknown network positions. Cliques of different sizes represented theoretical combinations of changing residues in sequence space, allowing the identification of significant aminoacidic combinations in single sequences of real-world populations. Our analytic approach that links network structural aspects to mutational aminoacidic combinations in the spike sequence population offers a novel way to understand virus epidemiology and evolution.
PMID: 37432011
Food Res Int , IF:6.475 , 2023 Aug , V170 : P112950 doi: 10.1016/j.foodres.2023.112950
Aroma profiling of Shine Muscat grape provides detailed insights into the regulatory effect of gibberellic acid and N-(2-chloro-4-pyridinyl)-N-phenylurea applications on aroma quality.
Shandong Academy of Grape, Shandong Academy of Agricultural Sciences, Jinan 250100, China.; Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai 200240, China.; Shandong Academy of Grape, Shandong Academy of Agricultural Sciences, Jinan 250100, China. Electronic address: sdtalibo@163.com.; Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai 200240, China. Electronic address: fruit@sjtu.edu.cn.
As plant growth regulators, gibberellic acid (GA(3)) and CPPU [forchlorfenuron, N-(2-chloro-4-pyridinyl)-N-phenylurea] are widely used in the production of table grapes. However, how these compounds regulate the aroma quality remains unclear. By measuring free and bound aroma compounds in Shine Muscat grapes from eight groups during whole growth period, GA(3) and CPPU were both found to significantly promote the synthesis of acyclic monoterpenes and (E)-2-hexenal, and double applications were found to further increase the aroma compound contents. On the other hand, GA(3) and CPPU obviously promoted the expansion of berries, and the effect of promoting the synthesis of aroma compounds was largely diminished. In conclusion, free compound concentrations in berry were almost unaffected by GA(3) and CPPU. From the perspective of aroma compounds, a highly concerted interplay was observed for terpenes, and bound compounds exhibited higher correlations than those of free compounds. In addition, 17 compounds could be used as markers that indicated the developmental timing of berries.
PMID: 37316003
Plant J , IF:6.417 , 2023 Aug , V115 (3) : P772-787 doi: 10.1111/tpj.16260
Gene expression and expression quantitative trait loci analyses uncover natural variations underlying the improvement of important agronomic traits during modern maize breeding.
Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.; Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, Inner Mongolia University, Hohhot, 010070, China.; State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China.; Maize Research Institute, Jilin Academy of Agricultural Sciences, Gongzhuling, 136100, China.; HainanYazhou Bay Seed Lab, Sanya, 572025, China.; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China.
Maize (Zea mays L.) is a major staple crop worldwide, and during modern maize breeding, cultivars with increased tolerance to high-density planting and higher yield per plant have contributed significantly to the increased yield per unit land area. Systematically identifying key agronomic traits and their associated genomic changes during modern maize breeding remains a significant challenge because of the complexity of genetic regulation and the interactions of the various agronomic traits, with most of them being controlled by numerous small-effect quantitative trait loci (QTLs). Here, we performed phenotypic and gene expression analyses for a set of 137 elite inbred lines of maize from different breeding eras in China. We found four yield-related traits are significantly improved during modern maize breeding. Through gene-clustering analyses, we identified four groups of expressed genes with distinct trends of expression pattern change across the historical breeding eras. In combination with weighted gene co-expression network analysis, we identified several candidate genes regulating various plant architecture- and yield-related agronomic traits, such as ZmARF16, ZmARF34, ZmTCP40, ZmPIN7, ZmPYL10, ZmJMJ10, ZmARF1, ZmSWEET15b, ZmGLN6 and Zm00001d019150. Further, by combining expression quantitative trait loci (eQTLs) analyses, correlation coefficient analyses and population genetics, we identified a set of candidate genes that might have been under selection and contributed to the genetic improvement of various agronomic traits during modern maize breeding, including a number of known key regulators of plant architecture, flowering time and yield-related traits, such as ZmPIF3.3, ZAG1, ZFL2 and ZmBES1. Lastly, we validated the functional variations in GL15, ZmPHYB2 and ZmPYL10 that influence kernel row number, flowering time, plant height and ear height, respectively. Our results demonstrates the effectiveness of our combined approaches for uncovering key candidate regulatory genes and functional variation underlying the improvement of important agronomic traits during modern maize breeding, and provide a valuable genetic resource for the molecular breeding of maize cultivars with tolerance for high-density planting.
PMID: 37186341
Plant J , IF:6.417 , 2023 Aug , V115 (3) : P614-626 doi: 10.1111/tpj.16248
Co-expression network analysis of diverse wheat landraces reveals markers of early thermotolerance and a candidate master regulator of thermotolerance genes.
Department of Biology, Centre for Novel Agricultural Products (CNAP), University of York, Wentworth Way, YO10 5DD, UK.
Triticum aestivum L. (bread wheat) is a crop relied upon by billions of people around the world, as a major source of both income and calories. Rising global temperatures, however, pose a genuine threat to the livelihood of these people, as wheat growth and yields are extremely vulnerable to damage by heat stress. Here we present the YoGI wheat landrace panel, comprising 342 accessions that show remarkable phenotypic and genetic diversity thanks to their adaptation to different climates. We quantified the abundance of 110 790 transcripts from the panel and used these data to conduct weighted co-expression network analysis and to identify hub genes in modules associated with abiotic stress tolerance. We found that the expression of three hub genes, all heat-shock proteins (HSPs), were significantly correlated with early thermotolerance in a validation panel of landraces. These hub genes belong to the same module, with one (TraesCS4D01G207500.1) being a candidate master-regulator potentially controlling the expression of the other two hub genes, as well as a suite of other HSPs and heat-stress transcription factors (HSFs). In this work, therefore, we identify three validated hub genes, the expression of which can serve as markers of thermotolerance during early development, and suggest that TraesCS4D01G207500.1 is a potential master regulator of HSP and HSF expression - presenting the YoGI landrace panel as an invaluable tool for breeders wishing to determine and introduce novel alleles into modern varieties, for the production of climate-resilient crops.
PMID: 37077043
Plant J , IF:6.417 , 2023 Aug doi: 10.1111/tpj.16416
Organ-enriched gene expression during floral morphogenesis in wild barley.
Institute of Crop Science, National Agriculture and Food Research Organization (NARO), 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan.; Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo, Chiba, 271-8510, Japan.; Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing, 100141, China.; Crop Research Institute, Shandong Academy of Agricultural Sciences/National Engineering Research Center of Wheat and Maize/Shandong Technology Innovation Center of Wheat, Jinan, 252100, China.
Floral morphology varies considerably between dicots and monocots. The ABCDE model explaining how floral organ development is controlled was formulated using core eudicots and applied to grass crops. Barley (Hordeum. vulgare) has unique floral morphogenesis. Wild barley (H. vulgare ssp. spontaneum), which is the immediate ancestor of cultivated barley (H. vulgare ssp. vulgare), contains a rich reservoir of genetic diversity. However, the wild barley genes involved in floral organ development are still relatively uncharacterized. In this study, we generated an organ-specific transcriptome atlas for wild barley floral organs. Genome-wide transcription profiles indicated that 22 838 protein-coding genes were expressed in at least one organ. These genes were grouped into seven clusters according to the similarities in their expression patterns. Moreover, 5619 genes exhibited organ-enriched expression, 677 of which were members of 47 transcription factor families. Gene ontology analyses suggested that the functions of the genes with organ-enriched expression influence the biological processes in floral organs. The co-expression regulatory network showed that the expression of 690 genes targeted by MADS-box proteins was highly positively correlated with the expression of ABCDE model genes during floral morphogenesis. Furthermore, the expression of 138 genes was specific to the wild barley OUH602 genome and not the Morex genome; most of these genes were highly expressed in the glume, awn, lemma, and palea. This study revealed the global gene expression patterns underlying floral morphogenesis in wild barley. On the basis of the study findings, a molecular mechanism controlling floral morphology in barley was proposed.
PMID: 37548103
Plant J , IF:6.417 , 2023 Jul , V115 (2) : P351-368 doi: 10.1111/tpj.16229
The ALOG family members OsG1L1 and OsG1L2 regulate inflorescence branching in rice.
Dipartimento di Bioscienze, Universita degli Studi di Milano, Via Celoria 26, 20133, Milano, Italy.; Plant and Microbial Biology Department, North Carolina State University, Raleigh, NC, 27695, USA.; DIADE, University of Montpellier, IRD, CIRAD, Montpellier, France.
The architecture of the rice inflorescence is an important determinant of crop yield. The length of the inflorescence and the number of branches are among the key factors determining the number of spikelets, and thus grains, that a plant will develop. In particular, the timing of the identity transition from indeterminate branch meristem to determinate spikelet meristem governs the complexity of the inflorescence. In this context, the ALOG gene TAWAWA1 (TAW1) has been shown to delay the transition to determinate spikelet development in Oryza sativa (rice). Recently, by combining precise laser microdissection of inflorescence meristems with RNA-seq, we observed that two ALOG genes, OsG1-like 1 (OsG1L1) and OsG1L2, have expression profiles similar to that of TAW1. Here, we report that osg1l1 and osg1l2 loss-of-function CRISPR mutants have similar phenotypes to the phenotype of the previously published taw1 mutant, suggesting that these genes might act on related pathways during inflorescence development. Transcriptome analysis of the osg1l2 mutant suggested interactions of OsG1L2 with other known inflorescence architecture regulators and the data sets were used for the construction of a gene regulatory network (GRN), proposing interactions among genes potentially involved in controlling inflorescence development in rice. In this GRN, we selected the homeodomain-leucine zipper transcription factor encoding the gene OsHOX14 for further characterization. The spatiotemporal expression profiling and phenotypical analysis of CRISPR loss-of-function mutants of OsHOX14 suggests that the proposed GRN indeed serves as a valuable resource for the identification of new proteins involved in rice inflorescence development.
PMID: 37009647
Int J Mol Sci , IF:5.923 , 2023 Jul , V24 (14) doi: 10.3390/ijms241411323
Comparative Transcriptomics of Multi-Stress Responses in Pachycladon cheesemanii and Arabidopsis thaliana.
School of Natural Sciences, Massey University, Tennent Drive, Palmerston North 4474, New Zealand.; Department Molecular Biology, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Strasse 24-25, Haus 20, 14476 Potsdam, Germany.; School of Agriculture & Environment, Massey University, Palmerston North 4442, New Zealand.; School of Biological Sciences, University of Auckland, Auckland 1142, New Zealand.; Biochemistry Department, School of Biomedical Sciences, University of Otago, Dunedin 9016, New Zealand.; Center of Plant Systems Biology and Biotechnology (CPSBB), 139 Ruski Blvd., 4000 Plovdiv, Bulgaria.; Department of Plant Physiology and Plant Molecular Biology, University of Plovdiv, 24 Tsar Assen Str., 4000 Plovdiv, Bulgaria.; Max Planck Institute of Molecular Plant Physiology, Am Muhlenberg 1, 14476 Potsdam, Germany.
The environment is seldom optimal for plant growth and changes in abiotic and biotic signals, including temperature, water availability, radiation and pests, induce plant responses to optimise survival. The New Zealand native plant species and close relative to Arabidopsis thaliana, Pachycladon cheesemanii, grows under environmental conditions that are unsustainable for many plant species. Here, we compare the responses of both species to different stressors (low temperature, salt and UV-B radiation) to help understand how P. cheesemanii can grow in such harsh environments. The stress transcriptomes were determined and comparative transcriptome and network analyses discovered similar and unique responses within species, and between the two plant species. A number of widely studied plant stress processes were highly conserved in A. thaliana and P. cheesemanii. However, in response to cold stress, Gene Ontology terms related to glycosinolate metabolism were only enriched in P. cheesemanii. Salt stress was associated with alteration of the cuticle and proline biosynthesis in A. thaliana and P. cheesemanii, respectively. Anthocyanin production may be a more important strategy to contribute to the UV-B radiation tolerance in P. cheesemanii. These results allowed us to define broad stress response pathways in A. thaliana and P. cheesemanii and suggested that regulation of glycosinolate, proline and anthocyanin metabolism are strategies that help mitigate environmental stress.
PMID: 37511083
J Fungi (Basel) , IF:5.816 , 2023 Jul , V9 (7) doi: 10.3390/jof9070740
Secretome Analysis for a New Strain of the Blackleg Fungus Plenodomus lingam Reveals Candidate Proteins for Effectors and Virulence Factors.
Department of Biology, College of Science, Taibah University, P.O. Box 344, Al Madinah Al Munawwarah 42317-8599, Saudi Arabia.; Department of Microbiology, Faculty of Science, Ain Shams University, Cairo 11566, Egypt.
The fungal secretome is the main interface for interactions between the pathogen and its host. It includes the most important virulence factors and effector proteins. We integrated different bioinformatic approaches and used the newly drafted genome data of P. lingam isolate CAN1 (blackleg of rapeseed fungus) to predict the secretion of 217 proteins, including many cell-wall-degrading enzymes. All secretory proteins were identified; 85 were classified as CAZyme families and 25 were classified as protease families. Moreover, 49 putative effectors were predicted and identified, where 39 of them possessed at least one conserved domain. Some pectin-degrading enzymes were noticeable as a clustering group according to STRING web analysis. The secretome of P. lingam CAN1 was compared to the other two blackleg fungal species (P. lingam JN3 and P. biglobosus CA1) secretomes and their CAZymes and effectors were identified. Orthologue analysis found that P. lingam CAN1 shared 14 CAZy effectors with other related species. The Pathogen-Host Interaction database (PHI base) classified the effector proteins in several categories where most proteins were assigned as reduced virulence and two of them termed as hypervirulence. Nowadays, in silico approaches can solve many ambiguous issues about the mechanism of pathogenicity between fungi and plant host with well-designed bioinformatics tools.
PMID: 37504729
Front Plant Sci , IF:5.753 , 2023 , V14 : P1210309 doi: 10.3389/fpls.2023.1210309
Metabolomic and transcriptomice analyses of flavonoid biosynthesis in apricot fruits.
College of Horticulture, Xinjiang Agricultural University, Urumqi, China.; Postdoctoral Research Station of Crop Science, Xinjiang Agricultural University, Urumqi, China.; Luntai Fruit Tree Resource Nursery, Xinjiang Academy of Agricultural Sciences, Luntai, China.
INTRODUCTION: Flavonoids, as secondary metabolites in plants, play important roles in many biological processes and responses to environmental factors. METHODS: Apricot fruits are rich in flavonoid compounds, and in this study, we performed a combined metabolomic and transcriptomic analysis of orange flesh (JN) and white flesh (ZS) apricot fruits. RESULTS AND DISCUSSION: A total of 222 differentially accumulated flavonoids (DAFs) and 15855 differentially expressed genes (DEGs) involved in flavonoid biosynthesis were identified. The biosynthesis of flavonoids in apricot fruit may be regulated by 17 enzyme-encoding genes, namely PAL (2), 4CL (9), C4H (1), HCT (15), C3'H (4), CHS (2), CHI (3), F3H (1), F3'H (CYP75B1) (2), F3'5'H (4), DFR (4), LAR (1), FLS (3), ANS (9), ANR (2), UGT79B1 (6) and CYP81E (2). A structural gene-transcription factor (TF) correlation analysis yielded 3 TFs (2 bHLH, 1 MYB) highly correlated with 2 structural genes. In addition, we obtained 26 candidate genes involved in the biosynthesis of 8 differentially accumulated flavonoids metabolites in ZS by weighted gene coexpression network analysis. The candidate genes and transcription factors identified in this study will provide a highly valuable molecular basis for the in-depth study of flavonoid biosynthesis in apricot fruits.
PMID: 37534290
Front Plant Sci , IF:5.753 , 2023 , V14 : P1212559 doi: 10.3389/fpls.2023.1212559
Transcriptomic and co-expression network analyses on diverse wheat landraces identifies candidate master regulators of the response to early drought.
Centre for Novel Agricultural Products (CNAP), Department of Biology, University of York, York, United Kingdom.
INTRODUCTION: Over four billion people around the world rely on bread wheat (Triticum aestivum L.) as a major constituent of their diet. The changing climate, however, threatens the food security of these people, with periods of intense drought stress already causing widespread wheat yield losses. Much of the research into the wheat drought response has centred on the response to drought events later in development, during anthesis or grain filling. But as the timing of periods of drought stress become increasingly unpredictable, a more complete understanding of the response to drought during early development is also needed. METHODS: Here, we utilized the YoGI landrace panel to identify 10,199 genes which were differentially expressed under early drought stress, before weighted gene co-expression network analysis (WGCNA) was used to construct a co-expression network and identify hub genes in modules particularly associated with the early drought response. RESULTS: Of these hub genes, two stood out as novel candidate master regulators of the early drought response - one as an activator (TaDHN4-D1; TraesCS5D02G379200) and the other as a repressor (uncharacterised gene; TraesCS3D02G361500). DISCUSSION: As well as appearing to coordinate the transcriptional early drought response, we propose that these hub genes may be able to regulate the physiological early drought response due to potential control over the expression of members of gene families well-known for their involvement in the drought response in many plant species, namely dehydrins and aquaporins, as well as other genes seemingly involved in key processes such as, stomatal opening, stomatal closing, stomatal morphogenesis and stress hormone signalling.
PMID: 37426985
Front Plant Sci , IF:5.753 , 2023 , V14 : P1200139 doi: 10.3389/fpls.2023.1200139
STOP1 and STOP1-like proteins, key transcription factors to cope with acid soil syndrome.
Hainan Yazhou Bay Seed Lab, Sanya, Hainan, China.; Center for Advanced Bioindustry Technologies, and Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
Acid soil syndrome leads to severe yield reductions in various crops worldwide. In addition to low pH and proton stress, this syndrome includes deficiencies of essential salt-based ions, enrichment of toxic metals such as manganese (Mn) and aluminum (Al), and consequent phosphorus (P) fixation. Plants have evolved mechanisms to cope with soil acidity. In particular, STOP1 (Sensitive to proton rhizotoxicity 1) and its homologs are master transcription factors that have been intensively studied in low pH and Al resistance. Recent studies have identified additional functions of STOP1 in coping with other acid soil barriers: STOP1 regulates plant growth under phosphate (Pi) or potassium (K) limitation, promotes nitrate (NO(3) (-)) uptake, confers anoxic tolerance during flooding, and inhibits drought tolerance, suggesting that STOP1 functions as a node for multiple signaling pathways. STOP1 is evolutionarily conserved in a wide range of plant species. This review summarizes the central role of STOP1 and STOP1-like proteins in regulating coexisting stresses in acid soils, outlines the advances in the regulation of STOP1, and highlights the potential of STOP1 and STOP1-like proteins to improve crop production on acid soils.
PMID: 37416880
J Agric Food Chem , IF:5.279 , 2023 Jun , V71 (25) : P9573-9598 doi: 10.1021/acs.jafc.2c07741
Root Hair Development and Adaptation to Abiotic Stress.
Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Sciences, Shandong Normal University, Shandong 250014, China.; Dongying Institute, Shandong Normal University, Dongying 257000, China.
Root hairs tie the root system to the soil substrate, facilitate water and nutrient absorption, and enable the interaction with microbes in the soil. Root hair development can be classified into three main development types (I-III). Root hair development type III has been extensively studied, mainly represented using the model plant Arabidopsis thaliana. Transcription factors, plant hormones, and proteins are involved at different root hair developmental stages. The mechanisms underlying development in types I and II have been examined using other representative plant species but have not been studied as intensively. Many key developmental genes in types I and II are highly homologous with those in type III, exhibiting conservation of related mechanisms. Root hairs are also involved in the regulation of plant response to abiotic stress by altering developmental patterns. Abiotic stress, regulatory genes, and plant hormones jointly regulate root hair development and growth; however, few studies have focused on how root hair recognizes abiotic stress signals. This review examines the molecular mechanisms of root hair development and adaptations under stress, and prospective future developments in root hair research are also discussed.
PMID: 37314142
Front Genet , IF:4.599 , 2023 , V14 : P1184704 doi: 10.3389/fgene.2023.1184704
Comprehensive analysis of the progression mechanisms of CRPC and its inhibitor discovery based on machine learning algorithms.
College of Basic Medical Sciences, Dali University, Dali, Yunnan, China.; The First Affiliated Hospital of Dali University, Dali, Yunnan, China.; Yunnan Key Laboratory of Screening and Research on Anti-pathogenic Plant Resources from West Yunnan (Cultivation), Dali, Yunnan, China.; Princess Margaret Cancer Centre, TMDT-MaRS Centre, University Health Network, Toronto, ON, Canada.
Background: Almost all patients treated with androgen deprivation therapy (ADT) eventually develop castration-resistant prostate cancer (CRPC). Our research aims to elucidate the potential biomarkers and molecular mechanisms that underlie the transformation of primary prostate cancer into CRPC. Methods: We collected three microarray datasets (GSE32269, GSE74367, and GSE66187) from the Gene Expression Omnibus (GEO) database for CRPC. Differentially expressed genes (DEGs) in CRPC were identified for further analyses, including Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and gene set enrichment analysis (GSEA). Weighted gene coexpression network analysis (WGCNA) and two machine learning algorithms were employed to identify potential biomarkers for CRPC. The diagnostic efficiency of the selected biomarkers was evaluated based on gene expression level and receiver operating characteristic (ROC) curve analyses. We conducted virtual screening of drugs using AutoDock Vina. In vitro experiments were performed using the Cell Counting Kit-8 (CCK-8) assay to evaluate the inhibitory effects of the drugs on CRPC cell viability. Scratch and transwell invasion assays were employed to assess the effects of the drugs on the migration and invasion abilities of prostate cancer cells. Results: Overall, a total of 719 DEGs, consisting of 513 upregulated and 206 downregulated genes, were identified. The biological functional enrichment analysis indicated that DEGs were mainly enriched in pathways related to the cell cycle and metabolism. CCNA2 and CKS2 were identified as promising biomarkers using a combination of WGCNA, LASSO logistic regression, SVM-RFE, and Venn diagram analyses. These potential biomarkers were further validated and exhibited a strong predictive ability. The results of the virtual screening revealed Aprepitant and Dolutegravir as the optimal targeted drugs for CCNA2 and CKS2, respectively. In vitro experiments demonstrated that both Aprepitant and Dolutegravir exerted significant inhibitory effects on CRPC cells (p < 0.05), with Aprepitant displaying a superior inhibitory effect compared to Dolutegravir. Discussion: The expression of CCNA2 and CKS2 increases with the progression of prostate cancer, which may be one of the driving factors for the progression of prostate cancer and can serve as diagnostic biomarkers and therapeutic targets for CRPC. Additionally, Aprepitant and Dolutegravir show potential as anti-tumor drugs for CRPC.
PMID: 37476415
Plant Physiol Biochem , IF:4.27 , 2023 Aug , V201 : P107920 doi: 10.1016/j.plaphy.2023.107920
Transcriptomic and genetic approaches reveal that the pipecolate biosynthesis pathway simultaneously regulates tomato fruit ripening and quality.
Hainan Institute, Zhejiang University, Yazhou Bay Science and Technology City, Sanya, 572025, China; Department of Horticulture, Zhejiang University, Hangzhou, China.; Department of Horticulture, Zhejiang University, Hangzhou, China.; Hainan Institute, Zhejiang University, Yazhou Bay Science and Technology City, Sanya, 572025, China; Department of Horticulture, Zhejiang University, Hangzhou, China. Electronic address: kaishi@zju.edu.cn.
Pipecolic acid (Pip) and N-hydroxypipecolic acid (NHP) have been found to accumulate during the ripening of multiple types of fruits; however, the function and mechanism of pipecolate pathway in fruits remain unclear. Here study was conducted on fruits produced by the model plant tomato, wherein the NHP biosynthesis-related genes, Slald1 and Slfmo1, were mutated. The results showed that the fruits of both the Slald1 and the Slfmo1 mutants exhibited a delayed onset of ripening, decreased fruit size, nutrition and flavor. Exogenous treatment with Pip and NHP promoted fruit ripening and improved fruit quality. Transcriptomic analysis combined with weighted gene co-expression network analysis revealed that the genes involved in the biosynthesis of amino acids, carbon metabolism, photosynthesis, starch and sucrose metabolism, flavonoid biosynthesis, and plant hormone signal transduction were affected by SlFMO1 gene mutation. Transcription factor prediction analysis revealed that the NAC and AP2/ERF-ERF family members are notably involved in the regulation pathway. Overall, our results suggest that the pipecolate biosynthesis pathway is involved in the simultaneous regulation of fruit ripening and quality and indicate that a regulatory mechanism at the transcriptional level exists. However, possible roles of endogenously synthesized Pip and NHP in these processes remain to be determined. The biosynthesis pathway genes SlALD1 and SlFMO1 may be potential breeding targets for promoting fruit ripening and improving fruit quality with concomitant yield increases.
PMID: 37527607
Plant Physiol Biochem , IF:4.27 , 2023 Aug , V201 : P107859 doi: 10.1016/j.plaphy.2023.107859
Natural variation in photosynthesis and water use efficiency of locally adapted Persian walnut populations under drought stress and recovery.
Department of Horticulture, College of Aburaihan, University of Tehran, Tehran, Iran. Electronic address: mm.arab@ut.ac.ir.; Department of Plant Sciences and Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran. Electronic address: h_askari@sbu.ac.ir.; Photosynthesis Laboratory, Department of Horticulture, College of Aburaihan, University of Tehran, Tehran, Iran. Electronic address: aliniaeifard@ut.ac.ir.; Department of Agronomy, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran. Electronic address: mokhtassi@modares.ac.ir.; Department of Horticultural Sciences, Faculty of Agriculture, University of Vali-E-Asr, Rafsanjan, Iran. Electronic address: estaji1366@gmail.com.; Department of Horticulture, Faculty of Agriculture, University of Jiroft, Jiroft, Iran. Electronic address: m.hosseini@ujiroft.ac.ir.; Department of Plant Production and Genetic Engineering, Faculty of Agriculture, Lorestan University, Khorramabad, Iran. Electronic address: sohrabi.s@lu.ac.ir.; Department of Plant Sciences, University of California, Davis, CA, 95616, USA. Electronic address: mbmesgaran@ucdavis.edu.; Department of Plant Sciences, University of California, Davis, CA, 95616, USA. Electronic address: caleslie@ucdavis.edu.; Department of Plant Sciences, University of California, Davis, CA, 95616, USA. Electronic address: pjbrown@ucdavis.edu.; Department of Horticulture, College of Aburaihan, University of Tehran, Tehran, Iran. Electronic address: kvahdati@ut.ac.ir.
Persian walnut is a drought-sensitive species with considerable genetic variation in the photosynthesis and water use efficiency of its populations, which is largely unexplored. Here, we aimed to elucidate changes in the efficiency of photosynthesis and water content using a diverse panel of 60 walnut families which were submitted to a progressive drought for 24 days, followed by two weeks of re-watering. Severe water-withholding reduced leaf relative water content (RWC) by 20%, net photosynthetic rate (P(n)) by 50%, stomatal conductance (g(s)) by 60%, intercellular CO(2) concentration (C(i)) by 30%, and transpiration rate (T(r)) by 50%, but improved water use efficiency (WUE) by 25%. Severe water-withholding also inhibited photosystem II functionality as indicated by reduced quantum yield of intersystem electron transport (phi(Eo)) and transfer of electrons per reaction center (ET(0)/RC), also enhanced accumulation of Q(A) (V(J)) resulted in the reduction of the photosynthetic performance (PI(ABS)) and maximal quantum yield of PSII (F(V)/F(M)); while elevated quantum yield of energy dissipation (phi(Do)), energy fluxes for absorption (ABS/RC) and dissipated energy flux (DI(0)/RC) in walnut families. Cluster analysis classified families into three main groups (tolerant, moderately tolerant, and sensitive), with the tolerant group from dry climates exhibiting lesser alterations in assessed parameters than the other groups. Multivariate analysis of phenotypic data demonstrated that RWC and biophysical parameters related to the chlorophyll fluorescence such as F(V)/F(M), phi(Eo), phi(Do), PI(ABS), ABS/RC, ET(0)/RC, and DI(0)/RC represent fast, robust and non-destructive biomarkers for walnut performance under drought stress. Finally, phenotype-environment association analysis showed significant correlation of some photosynthetic traits with geoclimatic factors, suggesting a key role of climate and geography in the adaptation of walnut to its habitat conditions.
PMID: 37406405
Plant Physiol Biochem , IF:4.27 , 2023 Aug , V201 : P107894 doi: 10.1016/j.plaphy.2023.107894
Molecular regulation of lipid metabolism in Suaeda salsa.
College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, 163319, China; Heilongjiang Academy of Agricultural Sciences Postdoctoral Programme, Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin, China.; College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, 163319, China.; Harbin Academy of Agricultural Science, Harbin, 150028, China.; Heilongjiang Academy of Agricultural Sciences Postdoctoral Programme, Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin, China.; College of Food Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, 163319, China. Electronic address: zhulei@byau.edu.cn.; College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, 163319, China. Electronic address: xujingyu@byau.edu.cn.
Suaeda salsa is remarkable for its high oil content and abundant unsaturated fatty acids. In this study, the regulatory networks on fatty acid and lipid metabolism were constructed by combining the de novo transcriptome and lipidome data. Differentially expressed genes (DEGs) associated with lipids biosynthesis pathways were identified in the S. salsa transcriptome. DEGs involved in fatty acid and glycerolipids were generally up-regulated in leaf tissues. DEGs for TAG assembly were enriched in developing seeds, while DEGs in phospholipid metabolic pathways were enriched in root tissues. Polar lipids were extracted from S. salsa tissues and analyzed by lipidomics. The proportion of galactolipid MGDG was the highest in S. salsa leaves. The molar percentage of PG was high in the developing seeds, and the other main phospholipids had higher molar percentage in roots of S. salsa. The predominant C36:6 molecular species indicates that S. salsa is a typical 18:3 plant. The combined transcriptomic and lipidomic data revealed that different tissues of S. salsa were featured with DEGs associated with specific lipid metabolic pathways, therefore, represented unique lipid profiles. This study will be helpful on understanding lipid metabolism pathway and exploring the key genes involved in lipid synthesis in S. salsa.
PMID: 37482030
Plant Physiol Biochem , IF:4.27 , 2023 Aug , V201 : P107856 doi: 10.1016/j.plaphy.2023.107856
Integration of transcriptomic and metabolomic analysis unveils the response mechanism of sugar metabolism in Cyclocarya paliurus seedlings subjected to PEG-induced drought stress.
College of Forestry, Nanjing Forestry University, Nanjing, China.; College of Forestry, Nanjing Forestry University, Nanjing, China; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China.; College of Forestry, Nanjing Forestry University, Nanjing, China; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China. Electronic address: fangsz@njfu.edu.cn.
Cyclocarya paliurus (Batal.) Iljinskaja is a multiple function tree species used for functional food and valued timber production. Carbohydrates, especially water-soluble carbohydrates, play an important role in osmotic protection, signal transduction and carbon storage. Under the circumstance of global climate change the abiotic stress would restrict the development of C. paliurus plantation, whereas there is few knowledge on the regulatory mechanisms of sugar metabolism under drought stress in C. paliurus. To investigate the drought response of C. paliurus at molecular level, we conducted an integrated analysis of transcriptomic and metabolomic of C. paliurus at three PEG-induced drought stress levels (0%: control; 15%: moderate drought; 25%: severe drought) in short term. Both moderate and severe drought treatments activated the chemical defense with lowering relative water content, and enhancing the contents of soluble protein, proline and malondialdehyde in the leaves. Meanwhile, alterations in the expression of differentially expressed genes and carbohydrate metabolism profiles were observed among the treatments. Weighted gene co-expression network analysis (WGCNA) showed 3 key modules, 8 structural genes (such as genes encoding beta-fructofuranosidase (INV), sucrose synthase (SUS), raffinose synthase (RS)) and 14 regulatory transcription factors were closely linked to sugar metabolism. Our results provided the foundation to understand the response mechanism of sugar metabolism in C. paliurus under drought stress, and would drive progress in breeding of drought-tolerant varieties and plantation development of the species.
PMID: 37354727
Environ Sci Pollut Res Int , IF:4.223 , 2023 Aug , V30 (37) : P86741-86761 doi: 10.1007/s11356-023-28663-x
Municipal solid waste compost: a comprehensive bibliometric data-driven review of 50 years of research and identification of future research themes.
Agronomy Section, ICAR-National Dairy Research Institute, Karnal, Haryana, 132001, India.; Dairy Extension Division, ICAR-National Dairy Research Institute, Karnal, Haryana, India.; Agronomy Section, ICAR-National Dairy Research Institute, Karnal, Haryana, 132001, India. drdudi_rk@rediffmail.com.; Central Soil Salinity Research Institute, Karnal, Haryana, India.
This paper offers a thorough bibliometric review of the literature on municipal solid waste compost (MSWC), focusing on the past two decades. Using an extensive dataset of 827 documents, the research patterns are analyzed via the R-based Bibliometrix package, merging metadata from Web of Science and Scopus. The analysis reveals substantial global growth in MSWC research, with a particular surge in the last 20 years. Discipline-specific journals are the main publishers, while multidisciplinary environmental outlets gained more citations. The study identifies five major collaborative author clusters that dominate productivity and citation frequency. The thematic evolution over the past five decades shows a transition from waste disposal towards topics such as heavy metals, soil properties, and plant nutrition, with emerging themes like carbon sequestration, biochar, and microplastics signaling future research directions. Specifically, the field has experienced a 7.86% annual growth rate, with an average citation rate of 26.88 per article. The 827 publications emerged from 317 sources and 1910 authors, with an international co-authorship rate of 14.75%, reflecting the field's interdisciplinary character. Thirteen primary sources and twenty-two key authors were identified as major contributors. On the geographical front, Spain and Italy led with the most contributions and highest citation count, respectively. In terms of keywords, "heavy metals" and "sewage sludge" were the most recurrent, indicating the prevailing topics in MSWC research. This analysis hence provides key insights into the evolution and future trajectory of MSWC studies.
PMID: 37442933
BMC Genomics , IF:3.969 , 2023 Jul , V24 (1) : P421 doi: 10.1186/s12864-023-09436-9
Gene co-expression network analysis identifies hub genes associated with different tolerance under calcium deficiency in two peanut cultivars.
College of Agriculture, Hunan Agricultural University, No. 1 Nongda Road, Changsha, 410128, Hunan, China.; Arid Land Crop Research Institute, Hunan Agricultural University, No. 1 Nongda Road, Changsha, 410128, Hunan, China.; Hunan Peanut Engineering & Technology Research Center, No. 1 Nongda Road, Changsha, 410128, Hunan, China.; College of Plant Protection, Hunan Agricultural University, No.1 Nongda Road, Changsha, 410128, Hunan, China.; College of Agriculture, Hunan Agricultural University, No. 1 Nongda Road, Changsha, 410128, Hunan, China. zhanghaodsm@126.com.; Arid Land Crop Research Institute, Hunan Agricultural University, No. 1 Nongda Road, Changsha, 410128, Hunan, China. zhanghaodsm@126.com.; Hunan Peanut Engineering & Technology Research Center, No. 1 Nongda Road, Changsha, 410128, Hunan, China. zhanghaodsm@126.com.; College of Agriculture, Hunan Agricultural University, No. 1 Nongda Road, Changsha, 410128, Hunan, China. ldwtz@hunau.edu.cn.; Arid Land Crop Research Institute, Hunan Agricultural University, No. 1 Nongda Road, Changsha, 410128, Hunan, China. ldwtz@hunau.edu.cn.; Hunan Peanut Engineering & Technology Research Center, No. 1 Nongda Road, Changsha, 410128, Hunan, China. ldwtz@hunau.edu.cn.; College of Agriculture, Hunan Agricultural University, No. 1 Nongda Road, Changsha, 410128, Hunan, China. luozinan@hunau.edu.cn.; Arid Land Crop Research Institute, Hunan Agricultural University, No. 1 Nongda Road, Changsha, 410128, Hunan, China. luozinan@hunau.edu.cn.; Hunan Peanut Engineering & Technology Research Center, No. 1 Nongda Road, Changsha, 410128, Hunan, China. luozinan@hunau.edu.cn.
BACKGROUND: Peanut is an economically-important oilseed crop and needs a large amount of calcium for its normal growth and development. Calcium deficiency usually leads to embryo abortion and subsequent abnormal pod development. Different tolerance to calcium deficiency has been observed between different cultivars, especially between large and small-seed cultivars. RESULTS: In order to figure out different molecular mechanisms in defensive responses between two cultivars, we treated a sensitive (large-seed) and a tolerant (small-seed) cultivar with different calcium levels. The transcriptome analysis identified a total of 58 and 61 differentially expressed genes (DEGs) within small-seed and large-seed peanut groups under different calcium treatments, and these DEGs were entirely covered by gene modules obtained via weighted gene co-expression network analysis (WGCNA). KEGG enrichment analysis showed that the blue-module genes in the large-seed cultivar were mainly enriched in plant-pathogen attack, phenolic metabolism and MAPK signaling pathway, while the green-module genes in the small-seed cultivar were mainly enriched in lipid metabolism including glycerolipid and glycerophospholipid metabolisms. By integrating DEGs with WGCNA, a total of eight hub-DEGs were finally identified, suggesting that the large-seed cultivar concentrated more on plant defensive responses and antioxidant activities under calcium deficiency, while the small-seed cultivar mainly focused on maintaining membrane features to enable normal photosynthesis and signal transduction. CONCLUSION: The identified hub genes might give a clue for future gene validation and molecular breeding to improve peanut survivability under calcium deficiency.
PMID: 37501179
BMC Genomics , IF:3.969 , 2023 Jul , V24 (1) : P399 doi: 10.1186/s12864-023-09507-x
Identification of core genes associated with different phosphorus levels in quinoa seedlings by weighted gene co-expression network analysis.
College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China.; Institute of Agricultural Sciences of the Lixiache District, Yangzhou, 225007, China.; Yuxi Academy of Agricultural Sciences, Yuxi, 653100, China.; College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China. wheat-quinoa@ynau.edu.cn.
BACKGROUND: Quinoa is a highly nutritious and novel crop that is resistant to various abiotic stresses. However, its growth and development is restricted due to its limited utilization of soil phosphorus. Studies on the levels of phosphorus in quinoa seedlings are limited; therefore, we analyzed transcriptome data from quinoa seedlings treated with different concentrations of phosphorus. RESULTS: To identify core genes involved in responding to various phosphorus levels, the weighted gene co-expression network analysis method was applied. From the 12,085 expressed genes, an analysis of the gene co-expression network was done. dividing the expressed genes into a total of twenty-five different modules out of which two modules were strongly correlated with phosphorus levels. Subsequently we identified five core genes that correlated strongly either positively or negatively with the phosphorus levels. Gene ontology and assessments of the Kyoto Encyclopedia of Genes and Genomes have uncovered important biological processes and metabolic pathways that are involved in the phosphorus level response. CONCLUSIONS: We discovered crucial new core genes that encode proteins from various transcription factor families, such as MYB, WRKY, and ERF, which are crucial for abiotic stress resistance. This new library of candidate genes associated with the phosphorus level responses in quinoa seedlings will help in breeding varieties that are tolerant to phosphorus levels.
PMID: 37454047
Plants (Basel) , IF:3.935 , 2023 Jul , V12 (13) doi: 10.3390/plants12132574
Silicon Enhances Brassica napus Tolerance to Boron Deficiency by the Remobilisation of Boron and by Changing the Expression of Boron Transporters.
Plant Nutrition R&D Department, Centre Mondial de l'Innovation of Roullier Group, 35400 Saint Malo, France.; Phys-Chem and Bio-Analytics R&D Department, Centre Mondial de l'Innovation of Roullier Group, 35400 Saint-Malo, France.
Boron (B) is an essential micronutrient for plants, and its deficiency is a widespread nutritional disorder, particularly in high-demanding crops like Brassica napus. Over the past few decades, silicon (Si) has been shown to mitigate plant nutrient deficiencies of different macro- and micro-nutrients. However, the work on B and Si cross-talk has mostly been focused on the alleviation of B toxicity by Si application. In the present study, we investigated the effect of Si application on rapeseed plants grown hydroponically under long-term B deficiency (20 days at 0.1 microM B). In addition, a B-uptake labelling experiment was conducted, and the expression of the genes involved in B uptake were monitored between 2 and 15 days of B shortage. The results showed that Si significantly improved rapeseed plant growth under B deficiency by 34% and 49% in shoots and roots, respectively. It also increased the expression level of BnaNIP5;1 and BOR1;2c in both young leaves and roots. The uptake labelling experiment showed the remobilization of previously fixed (11)B from old leaves to new tissues. This study provides additional evidence of the beneficial effects of Si under conditions lacking B by changing the expression of the BnaNIP5;1 gene and by remobilizing (11)B to young tissues.
PMID: 37447134
G3 (Bethesda) , IF:3.154 , 2023 Aug doi: 10.1093/g3journal/jkad178
Cellular heterogeneity of the developing worker honey bee (Apis mellifera) pupa: a single cell transcriptomics analysis.
The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, UK, EH25 9RG.; Centre for Inflammation Research, University of Edinburgh, The Queen's Medical Research Institute, Edinburgh BioQuarter, Edinburgh, UK, EH16 4TJ.; Edinburgh Clinical Research Facility, University of Edinburgh, Western General Hospital, Edinburgh, UK, EH4 2XU.; Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK, EH4 2XU.; Beebytes Analytics CIC, The Roslin Innovation Centre, The Charnock Bradley Building, University of Edinburgh, Easter Bush, Midlothian, UK, EH25 9RG.
It is estimated that animals pollinate 87.5% of flowering plants worldwide and that managed honey bees (Apis mellifera) account for 30-50% of this ecosystem service to agriculture. In addition to their important role as pollinators, honey bees are well-established insect models for studying learning and memory, behaviour, caste differentiation, epigenetic mechanisms, olfactory biology, sex determination and eusociality. Despite their importance to agriculture, knowledge of honey bee biology lags behind many other livestock species. In this study we have used scRNA-Seq to map cell types to different developmental stages of the worker honey bee (prepupa at day 11 and pupa at day 15), and sought to determine their gene expression signatures. To identify cell type populations, we examined the cell-to-cell network based on the similarity of the single-cells' transcriptomic profiles. Grouping similar cells together we identified 63 different cell clusters of which 17 clusters were identifiable at both stages. To determine genes associated with specific cell populations or with a particular biological process involved in honey bee development, we used gene co-expression analysis. We combined this analysis with literature mining, the honey bee protein atlas and Gene Ontology analysis to determine cell cluster identity. Of the cell clusters identified, 17 were related to the nervous system and sensory organs, 7 to the fat body, 19 to the cuticle, 5 to muscle, 4 to compound eye, 2 to midgut, 2 to hemocytes and 1 to malpighian tubule/pericardial nephrocyte. To our knowledge, this is the first whole single cell atlas of honey bees at any stage of development and demonstrates the potential for further work to investigate their biology at the cellular level.
PMID: 37548242
J Mol Evol , IF:2.395 , 2023 Aug , V91 (4) : P424-440 doi: 10.1007/s00239-023-10109-0
Phylogenetic and Evolutionary Analysis of Plant Small RNA 2'-O-Methyltransferase (HEN1) Protein Family.
Department of Agricultural Biotechnology, College of Agriculture, Jahrom University, P.O. Box 74135-111, Jahrom, Islamic Republic of Iran. bheghrari@yahoo.com.; Institute of Biotechnology, School of Agriculture, Shiraz University, Shiraz, Islamic Republic of Iran.
HUA ENHANCER 1 (HEN1) is a pivotal mediator in protecting sRNAs from 3'-end uridylation and 3' to 5' exonuclease-mediated degradation in plants. Here, we investigated the pattern of the HEN1 protein family evolutionary history and possible relationships in the plant lineages using protein sequence analyses and conserved motifs composition, functional domain identification, architecture, and phylogenetic tree reconstruction and evolutionary history inference. According to our results, HEN1 protein sequences bear several highly conserved motifs in plant species retained during the evolution from their ancestor. However, several motifs are present only in Gymnosperms and Angiosperms. A similar trend showed for their domain architecture. At the same time, phylogenetic analysis revealed the grouping of the HEN1 proteins in the three main super clads. In addition, the Neighbor-net network analysis result provides some nodes have multiple parents indicating a few conflicting signals in the data, which is not the consequence of sampling error, the effect of the selected model, or the estimation method. By reconciling the protein and species tree, we considered the gene duplications in several given species and found 170 duplication events in the evolution of HEN1 in the plant lineages. According to our analysis, the main HEN1 superclass mostly showed orthologous sequences that illustrate the vertically transmitting of HEN1 to the main lines. However, in both orthologous and paralogs, we predicted insignificant structural deviations. Our analysis implies that small local structural changes that occur continuously during the folds can moderate the changes created in the sequence. According to our results, we proposed a hypothetical model and evolutionary trajectory for the HEN1 protein family in the plant kingdom.
PMID: 37191719
Plant Commun , 2023 Jul : P100645 doi: 10.1016/j.xplc.2023.100645
Systemic analysis of metabolome reconfiguration in Arabidopsis after abiotic stressors uncovers metabolites modulating defence against pathogens.
Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, C/Vall Moronta, Edifici CRAG, 08193, Bellaterra (Cerdanyola del Valles), Barcelona, Spain. Electronic address: antoni.garcia@cragenomica.es.; Departament of Biology, Biochemistry, and Natural Sciences, School of Technology and Experimental Sciences, Universitat Jaume I, 12006, Castello de la Plana, Spain.
Understanding plant immune responses is complex due to the high interdependence among biological processes in homeostatic networks. Hence, the integration of environmental cues causes network rewiring that interferes with defence responses. Similarly, plants retain molecular signatures configured under abiotic stress periods to rapidly respond to recurrent stress that can alter immunity. Metabolome changes imposed by abiotic stressors are persistent, although the impact on defence is elusive. In this study, we profiled metabolomes of Arabidopsis plants under several abiotic stress treatments applied individually or simultaneously to capture temporal trajectories in metabolite composition during adverse conditions and recovery. Further systemic analysis was conducted to address the relevance of metabolome changes and extract central features to be tested in planta. Our results demonstrate irreversibility in major fractions of metabolome changes as a general pattern in response to abiotic stress periods. Functional analysis of metabolomes and co-abundance networks points to convergences in the reconfiguration of the metabolism of organic acids and secondary metabolites. Arabidopsis mutant lines for components related to these metabolic pathways displayed altered defence capacities against different pathogens. Collectively, our data support that sustained metabolome changes configured during adverse environments can act as modulators of immune responses and provide evidence for a new layer of regulation in plant defence.
PMID: 37403356
Front Psychol , 2023 , V14 : P1112182 doi: 10.3389/fpsyg.2023.1112182
Free word association analysis of German laypeople's perception of biodiversity and its loss.
Biology Didactics, Department of Biology and Chemistry, Osnabruck University, Osnabruck, Germany.
Due to the dramatic biodiversity crisis, it is crucial to understand how people perceive biodiversity. Knowledge of how thoughts are organized around this concept can identify which ideas are best to focus on biodiversity conservation information campaigns. The primary aim of the present study was to identify social representations of the German public regarding the concept of biodiversity and its loss using a free word association test. Furthermore, unique association networks were analyzed. For this purpose, data collection was performed in September 2021 in Germany using an online questionnaire to assess participants' associations with the prompt "biodiversity" (n = 131) and "biodiversity loss" (n = 130). Additionally, we used the social network software Gephi to create biodiversity (loss) association networks. The five most commonly mentioned associations for biodiversity were "animal," "plant," "nature," "human," and "flower." For biodiversity loss, the five most commonly mentioned associations were "species extinction," "climate change," "plant," "insect," and "bee." Neither "land use change" nor "invasive species," as key drivers of biodiversity loss, were present in social representations of the German public. A difference was observed in the total number of mentioned associations between biodiversity and biodiversity loss. For both, the associations "plant" and "animal" were related. However, participants associated specific taxa only with animals, such as "insects" and "birds." For plants, no specific taxa were named. Based on the network analysis, the most commonly mentioned word pairs for biodiversity and biodiversity loss were "plant - animal" and "species loss - climate change," respectively. Based on our statistical network analysis, these associations were identified as the most central associations with the greatest influence in the network. Thus, they had the most connections and the function of predicting the flow in the network. In sum, the public's multifaceted views on biodiversity and its loss, as well as the aforementioned central associations, hold great potential to be utilized more for the communication and education of biodiversity conservation. In addition, our findings contribute to the scientific community's understanding of social representations and perceptions of biodiversity and its loss.
PMID: 37448712