Genome Biol , IF:13.583 , 2023 Mar , V24 (1) : P55 doi: 10.1186/s13059-023-02891-3
A role for heritable transcriptomic variation in maize adaptation to temperate environments.
Quantitative Life Sciences Initiative, University of Nebraska-Lincoln, Lincoln, USA.; Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, USA.; Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, USA.; School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, USA.; Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, USA.; Institute for Genomic Diversity, Cornell University, Ithaca, USA.; Quantitative Life Sciences Initiative, University of Nebraska-Lincoln, Lincoln, USA. schnable@unl.edu.; Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, USA. schnable@unl.edu.; Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, USA. schnable@unl.edu.
BACKGROUND: Transcription bridges genetic information and phenotypes. Here, we evaluated how changes in transcriptional regulation enable maize (Zea mays), a crop originally domesticated in the tropics, to adapt to temperate environments. RESULT: We generated 572 unique RNA-seq datasets from the roots of 340 maize genotypes. Genes involved in core processes such as cell division, chromosome organization and cytoskeleton organization showed lower heritability of gene expression, while genes involved in anti-oxidation activity exhibited higher expression heritability. An expression genome-wide association study (eGWAS) identified 19,602 expression quantitative trait loci (eQTLs) associated with the expression of 11,444 genes. A GWAS for alternative splicing identified 49,897 splicing QTLs (sQTLs) for 7614 genes. Genes harboring both cis-eQTLs and cis-sQTLs in linkage disequilibrium were disproportionately likely to encode transcription factors or were annotated as responding to one or more stresses. Independent component analysis of gene expression data identified loci regulating co-expression modules involved in oxidation reduction, response to water deprivation, plastid biogenesis, protein biogenesis, and plant-pathogen interaction. Several genes involved in cell proliferation, flower development, DNA replication, and gene silencing showed lower gene expression variation explained by genetic factors between temperate and tropical maize lines. A GWAS of 27 previously published phenotypes identified several candidate genes overlapping with genomic intervals showing signatures of selection during adaptation to temperate environments. CONCLUSION: Our results illustrate how maize transcriptional regulatory networks enable changes in transcriptional regulation to adapt to temperate regions.
PMID: 36964601
J Hazard Mater , IF:10.588 , 2023 May , V449 : P131026 doi: 10.1016/j.jhazmat.2023.131026
Exposure to cypermethrin pesticide disturbs the microbiome and disseminates antibiotic resistance genes in soil and the gut of Enchytraeus crypticus.
Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China.; College of Environment, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou 310032, China.; Centre for Environmental Policy, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, UK.; Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China.; Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China; State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China.; College of Environment, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou 310032, China. Electronic address: hfqian@zjut.edu.cn.; Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China; State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Beijing, China.
Worldwide, pyrethroids, such as cypermethrin, are the second most applied group of insecticides, however, their effects on the soil microbiome and non-target soil fauna remain largely unknown. Herein, we assessed the change of bacterial communities and antibiotic resistance genes (ARGs) of soil and in the gut of the model soil species Enchytraeus crypticus using a combination of 16S rRNA gene amplicon sequencing, and high-throughput qPCR of ARGs. Results indicate that cypermethrin exposure enriches potential pathogens (e.g. Bacillus anthracis) in the soil and gut microbiome of E. crypticus, heavily disrupting the latter's microbiome structure, and even disrupts activities of the E. crypticus immune system. The co-occurrence of potential pathogens (e.g. Acinetobacter baumannii), ARGs, and mobile genetic elements (MGEs) revealed the increased risk of pathogenicity as well as antibiotic resistance in potential pathogens. Moreover, structural equation modeling demonstrated that the dissemination of ARGs was not only promoted by MGEs, but also by the ratio of the core to non-core bacterial abundance. Collectively, these results provide an in-depth view of the previously unappreciated environmental risk of cypermethrin on the dissemination of ARGs in the soil and non-target soil fauna.
PMID: 36812731
New Phytol , IF:10.151 , 2023 Mar doi: 10.1111/nph.18885
A conserved gene regulatory network controls root epidermal cell patterning in superrosid species.
Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA.
In superrosid species, root epidermal cells differentiate into root hair cells and nonhair cells. In some superrosids, the root hair cells and nonhair cells are distributed randomly (Type I pattern), and in others, they are arranged in a position-dependent manner (Type III pattern). The model plant Arabidopsis (Arabidopsis thaliana) adopts the Type III pattern, and the gene regulatory network (GRN) that controls this pattern has been defined. However, it is unclear whether the Type III pattern in other species is controlled by a similar GRN as in Arabidopsis, and it is not known how the different patterns evolved. In this study, we analyzed superrosid species Rhodiola rosea, Boehmeria nivea, and Cucumis sativus for their root epidermal cell patterns. Combining phylogenetics, transcriptomics, and cross-species complementation, we analyzed homologs of the Arabidopsis patterning genes from these species. We identified R. rosea and B. nivea as Type III species and C. sativus as Type I species. We discovered substantial similarities in structure, expression, and function of Arabidopsis patterning gene homologs in R. rosea and B. nivea, and major changes in C. sativus. We propose that in superrosids, diverse Type III species inherited the patterning GRN from a common ancestor, whereas Type I species arose by mutations in multiple lineages.
PMID: 36932734
New Phytol , IF:10.151 , 2023 Jun , V238 (5) : P2064-2079 doi: 10.1111/nph.18840
A comprehensive metabolic map reveals major quality regulations in red-flesh kiwifruit (Actinidia chinensis).
Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China.; Key Laboratory of Breeding and Utilization of Kiwifruit in Sichuan Province, Sichuan Provincial Academy of Natural Resource Sciences, Chengdu, 610213, Sichuan, China.; GBF Laboratory, Universite de Toulouse, INRA, Castanet-Tolosan, 31320, France.; School of Life Sciences, University of Warwick, Warwick, CV4 7AL, UK.; School of Science and the Environment, University of Worcester, Worcester, WR2 6AJ, UK.; Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China.
Kiwifruit (Actinidia chinensis) is one of the popular fruits world-wide, and its quality is mainly determined by key metabolites (sugars, flavonoids, and vitamins). Previous works on kiwifruit are mostly done via a single omics approach or involve only limited metabolites. Consequently, the dynamic metabolomes during kiwifruit development and ripening and the underlying regulatory mechanisms are poorly understood. In this study, using high-resolution metabolomic and transcriptomic analyses, we investigated kiwifruit metabolic landscapes at 11 different developmental and ripening stages and revealed a parallel classification of 515 metabolites and their co-expressed genes into 10 distinct metabolic vs gene modules (MM vs GM). Through integrative bioinformatics coupled with functional genomic assays, we constructed a global map and uncovered essential transcriptomic and transcriptional regulatory networks for all major metabolic changes that occurred throughout the kiwifruit growth cycle. Apart from known MM vs GM for metabolites such as soluble sugars, we identified novel transcription factors that regulate the accumulation of procyanidins, vitamin C, and other important metabolites. Our findings thus shed light on the kiwifruit metabolic regulatory network and provide a valuable resource for the designed improvement of kiwifruit quality.
PMID: 36843264
Plant Biotechnol J , IF:9.803 , 2023 Mar , V21 (3) : P466-481 doi: 10.1111/pbi.13944
Multi-stress resilience in plants recovering from submergence.
State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.; Plant Stress Resilience, Institute of Environmental Biology, Utrecht University, Utrecht, The Netherlands.; Plant-Environment Signaling, Institute of Environmental Biology, Utrecht University, Utrecht, The Netherlands.
Submergence limits plants' access to oxygen and light, causing massive changes in metabolism; after submergence, plants experience additional stresses, including reoxygenation, dehydration, photoinhibition and accelerated senescence. Plant responses to waterlogging and partial or complete submergence have been well studied, but our understanding of plant responses during post-submergence recovery remains limited. During post-submergence recovery, whether a plant can repair the damage caused by submergence and reoxygenation and re-activate key processes to continue to grow, determines whether the plant survives. Here, we summarize the challenges plants face when recovering from submergence, primarily focusing on studies of Arabidopsis thaliana and rice (Oryza sativa). We also highlight recent progress in elucidating the interplay among various regulatory pathways, compare post-hypoxia reoxygenation between plants and animals and provide new perspectives for future studies.
PMID: 36217562
Elife , IF:8.14 , 2023 Mar , V12 doi: 10.7554/eLife.84488
The photosystem I supercomplex from a primordial green alga Ostreococcus tauri harbors three light-harvesting complex trimers.
Division of Environmental Photobiology, National Institute for Basic Biology, Okazaki, Japan.; National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.; College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.; Department of Basic Biology, School of Life Science, the Graduate University for Advanced Studies, Okazaki, Japan.; National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, Japan.; Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Japan.
As a ubiquitous picophytoplankton in the ocean and an early-branching green alga, Ostreococcus tauri is a model prasinophyte species for studying the functional evolution of the light-harvesting systems in photosynthesis. Here, we report the structure and function of the O. tauri photosystem I (PSI) supercomplex in low light conditions, where it expands its photon-absorbing capacity by assembling with the light-harvesting complexes I (LHCI) and a prasinophyte-specific light-harvesting complex (Lhcp). The architecture of the supercomplex exhibits hybrid features of the plant-type and the green algal-type PSI supercomplexes, consisting of a PSI core, an Lhca1-Lhca4-Lhca2-Lhca3 belt attached on one side and an Lhca5-Lhca6 heterodimer associated on the other side between PsaG and PsaH. Interestingly, nine Lhcp subunits, including one Lhcp1 monomer with a phosphorylated amino-terminal threonine and eight Lhcp2 monomers, oligomerize into three trimers and associate with PSI on the third side between Lhca6 and PsaK. The Lhcp1 phosphorylation and the light-harvesting capacity of PSI were subjected to reversible photoacclimation, suggesting that the formation of OtPSI-LHCI-Lhcp supercomplex is likely due to a phosphorylation-dependent mechanism induced by changes in light intensity. Notably, this supercomplex did not exhibit far-red peaks in the 77 K fluorescence spectra, which is possibly due to the weak coupling of the chlorophyll a603-a609 pair in OtLhca1-4.
PMID: 36951548
Elife , IF:8.14 , 2023 Feb , V12 doi: 10.7554/eLife.83398
Competitive interactions between culturable bacteria are highly non-additive.
Institute of Environmental Sciences, Hebrew University, Rehovot, Israel.
Microorganisms are found in diverse communities whose structure and function are determined by interspecific interactions. Just as single species seldom exist in isolation, communities as a whole are also constantly challenged and affected by external species. Though much work has been done on characterizing how individual species affect each other through pairwise interactions, the joint effects of multiple species on a single (focal) species remain underexplored. As such, it is still unclear how single-species effects combine to a community-level effect on a species of interest. To explore this relationship, we assayed thousands of communities of two, three, and four bacterial species, measuring the effect of single, pairs of, and trios of 61 affecting species on six different focal species. We found that when multiple species each have a negative effect on a focal species, their joint effect is typically not given by the sum of the effects of individual affecting species. Rather, they are dominated by the strongest individual-species effect. Therefore, while joint effects of multiple species are often non-additive, they can still be derived from the effects of individual species, making it plausible to map complex interaction networks based on pairwise measurements. This finding is important for understanding the fate of species introduced into an occupied environment and is relevant for applications in medicine and agriculture, such as probiotics and biocontrol agents, as well as for ecological questions surrounding migrating and invasive species.
PMID: 36852917
Sci Total Environ , IF:7.963 , 2023 Apr , 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
Sci Total Environ , IF:7.963 , 2023 Mar , V877 : P162517 doi: 10.1016/j.scitotenv.2023.162517
Gene co-expression network analysis for the selection of candidate early warning indicators of heat and nutrient stress in Posidonia oceanica.
Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, 80121 Naples, Italy. Electronic address: alex.santillan@szn.it.; Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, 80121 Naples, Italy; Department of Life Sciences, University of Trieste, Trieste, Italy.; Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, 80121 Naples, Italy.; Research Infrastructure for Marine Biological Resources Department, Stazione Zoologica Anton Dohrn, 80121 Naples, Italy.; Dead Sea and Arava Science Center (DSASC), Masada National Park, Mount Masada 8698000, Israel.; Eilat Campus, Ben-Gurion University of the Negev, Hatmarim Blv, Eilat 8855630, Israel.; Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, 80121 Naples, Italy; Seagrass Ecology Group, Oceanographic Center of Murcia, Spanish Institute of Oceanography (IEO-CSIC), Murcia, Spain.; Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, 80121 Naples, Italy. Electronic address: gpro@szn.it.
The continuous worldwide seagrasses decline calls for immediate actions in order to preserve this precious marine ecosystem. The main stressors that have been linked with decline in seagrasses are 1) the increasing ocean temperature due to climate change and 2) the continuous inputs of nutrients (eutrophication) associated with coastal human activities. To avoid the loss of seagrass populations, an "early warning" system is needed. We used Weighed Gene Co-expression Network Analysis (WGCNA), a systems biology approach, to identify potential candidate genes that can provide an early warning signal of stress in the Mediterranean iconic seagrass Posidonia oceanica, anticipating plant mortality. Plants were collected from both eutrophic (EU) and oligotrophic (OL) environments and were exposed to thermal and nutrient stress in a dedicated mesocosm. By correlating the whole-genome gene expression after 2-weeks exposure with the shoot survival percentage after 5-weeks exposure to stressors, we were able to identify several transcripts that indicated an early activation of several biological processes (BP) including: protein metabolic process, RNA metabolic process, organonitrogen compound biosynthetic process, catabolic process and response to stimulus, which were shared among OL and EU plants and among leaf and shoot apical meristem (SAM), in response to excessive heat and nutrients. Our results suggest a more dynamic and specific response of the SAM compared to the leaf, especially the SAM from plants coming from a stressful environment appeared more dynamic than the SAM from a pristine environment. A vast list of potential molecular markers is also provided that can be used as targets to assess field samples.
PMID: 36868282
Sci Total Environ , IF:7.963 , 2023 May , V871 : P162034 doi: 10.1016/j.scitotenv.2023.162034
Biodegradable mulch films significantly affected rhizosphere microbial communities and increased peanut yield.
Hebei Province Key Laboratory of Sustained Utilization and Development of Water Recourse, School of Water Resources and Environment, Hebei GEO University, Shijiazhuang 050031, China.; Hebei Province Key Laboratory of Sustained Utilization and Development of Water Recourse, School of Water Resources and Environment, Hebei GEO University, Shijiazhuang 050031, China; Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.; College of Resources and Environment, Hunan Agricultural University, Changsha 410128, China; Rural Energy and Environment Agency, Ministry of Agriculture and Rural Affairs, Beijing 100125, China.; Liaoning Academy of Agricultural Sciences, Shenyang 110161, China.; Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.; Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010 Graz, Austria.; Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China.; Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China. Electronic address: dcjin@rcees.ac.cn.
Biodegradable mulch films are widely used to replace conventional plastic films in agricultural fields. However, their ecological effects on different microbial communities that naturally inhabit agricultural fields are scarcely explored. Herein, differences in bacterial communities recovered from biofilms, bulk soil, and rhizosphere soil were comparatively assessed for polyethylene film (PE) and biodegradable mulch film (BDM) application in peanut planted fields. The results showed that the plastic film type significantly influenced the bacterial community in different ecological niches of agricultural fields (P < 0.001). Specifically, BDMs significantly increased the diversity and abundance of bacteria in the rhizosphere soil. The bacterial communities in each ecological niche were distinguishable from each other; bacterial communities in the rhizosphere soil showed the most pronounced response among different treatments. Acidobacteria and Pseudomonas were significantly enriched in the rhizosphere soil when BDMs were used. BDMs also increased the rhizosphere soil bacterial network complexity and stability. The enrichment of beneficial bacteria in the rhizosphere soil under BDMs may also have implications for the observed increase in peanut yield. Deepening analyses indicated that Pseudoxanthomonas and Glutamicibacter are biomarkers in biofilms of PE and BDMs respectively. Our study provides new insights into the consequences of the application of different types of plastic films on microbial communities in different ecological niches of agricultural fields.
PMID: 36754316
Food Chem , IF:7.514 , 2023 Mar , V404 (Pt A) : P134545 doi: 10.1016/j.foodchem.2022.134545
Controlled mechanical stimuli reveal novel associations between basil metabolism and sensory quality.
School of Science and Technology, Man-Technology-Environment Research Centre, Orebro University, 701 82 Orebro, Sweden.; School of Hospitality, Culinary Arts and Meal Science, Sweden. Electronic address: anders.herdenstam@oru.se.; School of Science and Technology, Centre for Applied Autonomous Sensor Systems, Orebro University, 701 82 Orebro, Sweden; Department of Radiation Sciences, Radiation Physics, Umea University, 901 87 Umea, Sweden.; School of Science and Technology, Centre for Applied Autonomous Sensor Systems, Orebro University, 701 82 Orebro, Sweden.; School of Science and Technology, Man-Technology-Environment Research Centre, Orebro University, 701 82 Orebro, Sweden. Electronic address: victor.castro-alves@oru.se.
There is an increasing interest in the use of automation in plant production settings. Here, we employed a robotic platform to induce controlled mechanical stimuli (CMS) aiming to improve basil quality. Semi-targeted UHPLC-qToF-MS analysis of organic acids, amino acids, phenolic acids, and phenylpropanoids revealed changes in basil secondary metabolism under CMS, which appear to be associated with changes in taste, as revealed by different means of sensory evaluation (overall liking, check-all-that-apply, and just-about-right analysis). Further network analysis combining metabolomics and sensory data revealed novel links between plant metabolism and sensory quality. Amino acids and organic acids including maleic acid were negatively associated with basil quality, while increased levels of secondary metabolites, particularly linalool glucoside, were associated with improved basil taste. In summary, by combining metabolomics and sensory analysis we reveal the potential of automated CMS on crop production, while also providing new associations between plant metabolism and sensory quality.
PMID: 36252376
Microbiol Spectr , IF:7.171 , 2023 Mar , V11 (2) : Pe0016623 doi: 10.1128/spectrum.00166-23
Unraveling the Gene Regulatory Networks of the Global Regulators VeA and LaeA in Aspergillus nidulans.
Department of Plant Pathology, University of Wisconsin-Madison, Madison, Wisconsin, USA.; Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA.; Biological Resource Center/Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, Republic of Korea.; Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA.; Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA.; Department of Systems Biotechnology, KonKuk University, Seoul, Republic of Korea.
In the filamentous fungus Aspergillus nidulans, the velvet family protein VeA and the global regulator of secondary metabolism LaeA govern development and secondary metabolism mostly by acting as the VelB/VeA/LaeA heterotrimeric complex. While functions of these highly conserved controllers have been well studied, the genome-wide regulatory networks governing cellular and chemical development remain to be uncovered. Here, by integrating transcriptomic analyses, protein-DNA interactions, and the known A. nidulans gene/protein interaction data, we have unraveled the gene regulatory networks governed by VeA and LaeA. Within the networks, VeA and LaeA directly control the expression of numerous genes involved in asexual/sexual development and primary/secondary metabolism in A. nidulans. Totals of 3,190 and 1,834 potential direct target genes of VeA and LaeA were identified, respectively, including several important developmental and metabolic regulators such as flbA.B.C, velB.C, areA, mpkB, and hogA. Moreover, by analyzing over 8,800 ChIP-seq peaks, we have revealed the predicted common consensus sequences 5'-TGATTGGCTG-3' and 5'-TCACGTGAC-3' that VeA and LaeA might bind to interchangeably. These findings further expand the biochemical and genomic studies of the VelB/VeA/LaeA complex functionality in the gene regulation. In summary, this study unveils genes that are under the regulation of VeA and LaeA, proposes the VeA- and LaeA-mediated gene regulatory networks, and demonstrates their genome-wide developmental and metabolic regulations in A. nidulans. IMPORTANCE Fungal development and metabolism are genetically programmed events involving specialized cellular differentiation, cellular communication, and temporal and spatial regulation of gene expression. In genus Aspergillus, the global regulators VeA and LaeA govern developmental and metabolic processes by affecting the expression of downstream genes, including multiple transcription factors and signaling elements. Due to their vital roles in overall biology, functions of VeA and LaeA have been extensively studied, but there still has been a lack of knowledge about their genome-wide regulatory networks. In this study, employing the model fungus A. nidulans, we have identified direct targets of VeA and LaeA and their gene regulatory networks by integrating transcriptome, protein-DNA interaction, and protein-protein interaction analyses. Our results demonstrate the genome-wide regulatory mechanisms of these global regulators, thereby advancing the knowledge of fungal biology and genetics.
PMID: 36920196
J Exp Bot , IF:6.992 , 2023 Apr 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 D.F. 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 fertilisation of the ovules, which then mature as seeds. Upon fertilisation, 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 (GRN) 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
Food Res Int , IF:6.475 , 2023 Mar , V165 : P112531 doi: 10.1016/j.foodres.2023.112531
Genome-wide transcriptome analysis uncovers gene networks regulating fruit quality and volatile compounds in mango cultivar 'Tainong' during postharvest.
Agro-Food Science and Technology Research Institute, Guangxi Academy of Agricultural Sciences, 530007 Nanning, China; Guangxi University, 530004 Nanning, China.; Agro-Food Science and Technology Research Institute, Guangxi Academy of Agricultural Sciences, 530007 Nanning, China; Key Laboratory of Agro-products Processing, Ministry of Agriculture and Rural Affairs, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, 100193 Beijing, China.; Guangxi Key Laboratory of Fruits and Vegetables Storage-processing Technology, Guangxi Academy of Agricultural Sciences, 530007 Nanning, China; Guangxi Academy of Agricultural Sciences, 530007 Nanning, China. Electronic address: jiansun@gxaas.net.; Agro-Food Science and Technology Research Institute, Guangxi Academy of Agricultural Sciences, 530007 Nanning, China.; Key Laboratory of Agro-products Processing, Ministry of Agriculture and Rural Affairs, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, 100193 Beijing, China.; Guangxi University, 530004 Nanning, China.; Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, 571101, Haikou, China.; Guangxi Key Laboratory of Fruits and Vegetables Storage-processing Technology, Guangxi Academy of Agricultural Sciences, 530007 Nanning, China.
Mango is one of the most economically important fruit; however, the gene regulatory mechanism associated with ripening and quality changes during storage remains largely unclear. This study explored the relationship between transcriptome changes and postharvest mango quality. Fruit quality patterns and volatile components were obtained using headspace gas chromatography and ion-mobility spectrometry (HS-GC-IMS). The changes in mango peel and pulp transcriptome were analyzed during four stages (pre-harvesting, harvesting, maturity, and overripe stages). Based on the temporal analysis, multiple genes involved in the biosynthesis of secondary metabolites were upregulated in both the peel and pulp during the mango ripening process. Moreover, cysteine and methionine metabolism related to ethylene synthesis were upregulated in the pulp over time. Weighted gene co-expression network analysis (WGCNA) further showed that the pathways of pyruvate metabolism, citrate cycle, propionate metabolism, autophagy, and SNARE interactions in vesicular transport were positively correlated with the ripening process. Finally, a regulatory network of important pathways from pulp to peel was constructed during the postharvest storage of mango fruit. The above findings provide a global insight into the molecular regulation mechanisms of postharvest mango quality and flavor changes.
PMID: 36869530
Plant J , IF:6.417 , 2023 Apr 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 Mar , V24 (7) doi: 10.3390/ijms24076185
Comprehensive Analysis of the INDETERMINATE DOMAIN (IDD) Gene Family and Their Response to Abiotic Stress in Zea mays.
The Characteristic Laboratory of Crop Germplasm Innovation and Application, Provincial Department of Education, College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China.; Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China.; State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Perth, WA 6150, Australia.; The Key Laboratory of the Plant Development and Environmental Adaptation Biology, School of Life Sciences, Ministry of Education, Shandong University, Qingdao 266237, China.
Transcription factors (TFs) are important regulators of numerous gene expressions due to their ability to recognize and combine cis-elements in the promoters of target genes. The INDETERMINATE DOMAIN (IDD) gene family belongs to a subfamily of C2H2 zinc finger proteins and has been identified only in terrestrial plants. Nevertheless, little study has been reported concerning the genome-wide analysis of the IDD gene family in maize. In total, 22 ZmIDD genes were identified, which can be distributed on 8 chromosomes in maize. On the basis of evolutionary relationships and conserved motif analysis, ZmIDDs were categorized into three clades (1, 2, and 3), each owning 4, 6, and 12 genes, respectively. We analyzed the characteristics of gene structure and found that 3 of the 22 ZmIDD genes do not contain an intron. Cis-element analysis of the ZmIDD promoter showed that most ZmIDD genes possessed at least one ABRE or MBS cis-element, and some ZmIDD genes owned the AuxRR-core, TCA-element, TC-rich repeats, and LTR cis-element. The Ka:Ks ratio of eight segmentally duplicated gene pairs demonstrated that the ZmIDD gene families had undergone a purifying selection. Then, the transcription levels of ZmIDDs were analyzed, and they showed great differences in diverse tissues as well as abiotic stresses. Furthermore, regulatory networks were constructed through the prediction of ZmIDD-targeted genes and miRNAs, which can inhibit the transcription of ZmIDDs. In total, 6 ZmIDDs and 22 miRNAs were discovered, which can target 180 genes and depress the expression of 9 ZmIDDs, respectively. Taken together, the results give us valuable information for studying the function of ZmIDDs involved in plant development and climate resilience in maize.
PMID: 37047154
Front Plant Sci , IF:5.753 , 2023 , V14 : P1154088 doi: 10.3389/fpls.2023.1154088
Recent insights into metabolic and signalling events of directional root growth regulation and its implications for sustainable crop production systems.
Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany, Czech Academy of Sciences, Prague, Czechia.; Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, Molecular Systems Biology (MoSys), University of Vienna, Wien, Austria.; Vienna Metabolomics Center (VIME), University of Vienna, Wien, Austria.
Roots are sensors evolved to simultaneously respond to manifold signals, which allow the plant to survive. Root growth responses, including the modulation of directional root growth, were shown to be differently regulated when the root is exposed to a combination of exogenous stimuli compared to an individual stress trigger. Several studies pointed especially to the impact of the negative phototropic response of roots, which interferes with the adaptation of directional root growth upon additional gravitropic, halotropic or mechanical triggers. This review will provide a general overview of known cellular, molecular and signalling mechanisms involved in directional root growth regulation upon exogenous stimuli. Furthermore, we summarise recent experimental approaches to dissect which root growth responses are regulated upon which individual trigger. Finally, we provide a general overview of how to implement the knowledge gained to improve plant breeding.
PMID: 37008498
Front Plant Sci , IF:5.753 , 2023 , V14 : P1125378 doi: 10.3389/fpls.2023.1125378
Short-term transcriptomic analysis at organ scale reveals candidate genes involved in low N responses in NUE-contrasting tomato genotypes.
Dipartimento Agraria, Universita Mediterranea di Reggio Calabria, Reggio Calabria, Italy.; National Research Council of Italy, Institute of Biosciences and Bioresources (CNR-IBBR), Palermo, Italy.; Dipartimento di Scienze Agrarie, Alimentari e Forestali, Universita degli Studi di Palermo, Viale delle Scienze, Palermo, Italy.
BACKGROUND: Understanding the complex regulatory network underlying plant nitrogen (N) responses associated with high Nitrogen Use Efficiency (NUE) is one of the main challenges for sustainable cropping systems. Nitrate (NO(3) (-)), acting as both an N source and a signal molecule, provokes very fast transcriptome reprogramming, allowing plants to adapt to its availability. These changes are genotype- and tissue-specific; thus, the comparison between contrasting genotypes is crucial to uncovering high NUE mechanisms. METHODS: Here, we compared, for the first time, the spatio-temporal transcriptome changes in both root and shoot of two NUE contrasting tomato genotypes, Regina Ostuni (high-NUE) and UC82 (low-NUE), in response to short-term (within 24 h) low (LN) and high (HN) NO(3) (-) resupply. RESULTS: Using time-series transcriptome data (0, 8, and 24 h), we identified 395 and 482 N-responsive genes differentially expressed (DEGs) between RO and UC82 in shoot and root, respectively. Protein kinase signaling plant hormone signal transduction, and phenylpropanoid biosynthesis were the main enriched metabolic pathways in shoot and root, respectively, and were upregulated in RO compared to UC82. Interestingly, several N transporters belonging to NRT and NPF families, such as NRT2.3, NRT2.4, NPF1.2, and NPF8.3, were found differentially expressed between RO and UC82 genotypes, which might explain the contrasting NUE performances. Transcription factors (TFs) belonging to several families, such as ERF, LOB, GLK, NFYB, ARF, Zinc-finger, and MYB, were differentially expressed between genotypes in response to LN. A complementary Weighted Gene Co-expression Network Analysis (WGCNA) allowed the identification of LN-responsive co-expression modules in RO shoot and root. The regulatory network analysis revealed candidate genes that might have key functions in short-term LN regulation. In particular, an asparagine synthetase (ASNS), a CBL-interacting serine/threonine-protein kinase 1 (CIPK1), a cytokinin riboside 5'-monophosphate phosphoribohydrolase (LOG8), a glycosyltransferase (UGT73C4), and an ERF2 were identified in the shoot, while an LRR receptor-like serine/threonine-protein kinase (FEI1) and two TFs NF-YB5 and LOB37 were identified in the root. DISCUSSION: Our results revealed potential candidate genes that independently and/or concurrently may regulate short-term low-N response, suggesting a key role played by cytokinin and ROS balancing in early LN regulation mechanisms adopted by the N-use efficient genotype RO.
PMID: 36938018
Front Plant Sci , IF:5.753 , 2023 , V14 : P1138415 doi: 10.3389/fpls.2023.1138415
Whole-transcriptome analyses identify key differentially expressed mRNAs, lncRNAs, and miRNAs associated with male sterility in watermelon.
State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China.; College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, Heilongjiang, China.; Vegetable Research Institute of Hainan Academy of Agricultural Sciences, Haikou, Hainan, China.; State Key Laboratory of Vegetable Germplasm Innovation, Tianjin, China.; College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, China.
Male sterility is a valuable trait for watermelon breeding, as watermelon hybrids exhibit obvious heterosis. However, the underlying regulatory mechanism is still largely unknown, especially regarding the related non-coding genes. In the present study, approximately 1035 differentially expressed genes (DEGs), as well as 80 DE-lncRNAs and 10 DE-miRNAs, were identified, with the overwhelming majority down-regulated in male-sterile floral buds. Enrichment analyses revealed that the general phenylpropanoid pathway as well as its related metabolisms was predicted to be altered in a mutant compared to its fertile progenitor. Meanwhile, the conserved genetic pathway DYT1-TDF1-AMS-MS188-MS1, as well as the causal gene ClAMT1 for the male-sterile mutant Se18, was substantially disrupted during male reproductive development. In addition, some targets of the key regulators AMS and MS188 in tapetum development were also down-regulated at a transcriptional level, such as ABCG26 (Cla004479), ACOS5 (Cla022956), CYP703A2 (Cla021151), PKSA (Cla021099), and TKPR1 (Cla002563). Considering lncRNAs may act as functional endogenous target mimics of miRNAs, competitive endogenous RNA networks were subsequently constructed, with the most complex one containing three DE-miRNAs, two DE-lncRNAs, and 21 DEGs. Collectively, these findings not only contribute to a better understanding of genetic regulatory networks underlying male sterility in watermelon, but also provide valuable candidates for future research.
PMID: 36938061
Plant Cell Physiol , IF:4.927 , 2023 Mar , V64 (3) : P274-283 doi: 10.1093/pcp/pcac161
Molecular Mechanisms Underlying the Establishment and Maintenance of Vascular Stem Cells in Arabidopsis thaliana.
Department of Biology, Graduate School of Science, Kobe University, 1-1 Rokkodai, Kobe, 657-8501 Japan.; Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-0033 Japan.; College of Life Sciences, Ritsumeikan University, 1-1-1 Noji-higashi, Kusatsu, 525-8577 Japan.
The vascular system plays pivotal roles in transporting water and nutrients throughout the plant body. Primary vasculature is established as a continuous strand, which subsequently initiates secondary growth through cell division. Key factors regulating primary and secondary vascular developments have been identified in numerous studies, and the regulatory networks including these factors have been elucidated through omics-based approaches. However, the vascular system is composed of a variety of cells such as xylem and phloem cells, which are commonly generated from vascular stem cells. In addition, the vasculature is located deep inside the plant body, which makes it difficult to investigate the vascular development while distinguishing between vascular stem cells and developing xylem and phloem cells. Recent technical advances in the tissue-clearing method, RNA-seq analysis and tissue culture system overcome these problems by enabling the cell-type-specific analysis during vascular development, especially with a special focus on stem cells. In this review, we summarize the recent findings on the establishment and maintenance of vascular stem cells.
PMID: 36398989
Plant Sci , IF:4.729 , 2023 Jun , V331 : P111689 doi: 10.1016/j.plantsci.2023.111689
Integrated analysis of smRNAome, transcriptome, and degradome data to decipher microRNAs regulating costunolide biosynthesis in Saussurea lappa.
Department of Biotechnology, Panjab University, BMS Block I, Sector 25, Chandigarh 160014, India. Electronic address: ravk14@gmail.com.; Department of Biotechnology, Panjab University, BMS Block I, Sector 25, Chandigarh 160014, India.
Saussurea lappa (S. lappa) has been known to synthesize medicinally important, costunolide. Due to its immense therapeutic importance, understanding of regulatory mechanism associated with its biosynthesis is crucial. The identification of genes and transcription factors (TFs) in S. lappa, created a clear picture of costunolide biosynthesis pathways. Further to understand the regulation of costunolide biosynthesis by miRNAs, an integrated study of transcriptome, miRNAs, and degradome was performed. Identified candidate miRNAs and associated feed-forward loops (FFLs) illustrates their regulatory role in secondary metabolite biosynthesis. Small RNA and degradome sequencing were performed for leaf and root tissues to determine miRNAs-targets pairs. A total of 711 and 525 such targets were obtained for novel and known miRNAs respectively. This data was used to generate costunolide-specific miRNA-TF-gene interactome to perform systematic analyses through graph theoretical approach. Interestingly, miR171c.1 and sla-miR121 were identified as key regulators to connect and co-regulate both mevalonate and sesquiterpenoid pathways to bio-synthesize costunolide. Tissue-specific FFLs were identified to be involved in costunolide biosynthesis which further suggests the evolutionary co-relation of root-specific networks in synthesis of secondary metabolites in addition to leaf-specific networks. This integrative approach allowed us to determine candidate miRNAs and associated tissue-specific motifs involved in the diversification of secondary metabolites. MiRNAs identified in present study can provide alternatives for bioengineering tool to enhance the synthesis of costunolide and other secondary metabolites in S. lappa.
PMID: 36965630
Molecules , IF:4.411 , 2023 Mar , V28 (5) doi: 10.3390/molecules28052404
Unraveling the Variability of Essential Oil Composition in Different Accessions of Bunium persicum Collected from Different Temperate Micro-Climates.
Advanced Research Station for Saffron and Seed Spices, SKUAST-Kashmir, Srinagar 192121, India.; Dryland Agricultural Research Station, SKUAST-Kashmir, Rangreth, Srinagar 191111, India.; Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Republic of Korea.; Botany and Microbiology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia.
The present investigation was performed to evaluate the variability of the essential oil composition present in the seed extract of Kala zeera (Bunium persicum Bioss.) obtained from different geographical zones of Northwestern-Himalayan using Gas Chromatography-Mass Spectrum (GC-MS). The results of the GC-MS analysis revealed significant differences in the essential oil content. Significant variability was observed in the chemical constituents of the essential oils mainly for p-cymene, D-limonene, Gamma-terpinene, Cumic aldehyde and 1, 4-p-menthadien-7-al. Among these compounds, the highest average percentage across the locations was observed for gamma-terpinene (32.08%) which was followed by cumic aldehyde (25.07%), and 1, 4-p-menthadien-7-al (15.45%). Principal component analysis (PCA) also grouped the 4 highly significant compounds i.e., p-Cymene, Gamma-Terpinene, Cumic aldehyde, and 1,4-p-Menthadien-7-al into same cluster which are mainly distributed in Shalimar Kalazeera-1, and Atholi Kishtwar zones. The highest value of gamma-terpinene was recorded in Atholi accession (40.66%). However, among climatic zones Zabarwan Srinagar and Shalimar Kalazeera-1 was found to have highly positive significant correlation (0.99). The cophenetic correlation coefficient (c) was found to be 0.8334 during hierarchical clustering for 12 essential oil compounds showing that our results are highly correlated. Network analysis also showed the overlapping pattern and similar interaction between the 12 compounds as shown by hierarchical clustering analysis. From the results, it could be concluded that existence of variability among the various bioactive compounds of B. persicum which are probably to be incorporated to the potential list of drugs and may serve as good genetic source for various modern breeding programs.
PMID: 36903647
Metabolomics , IF:4.29 , 2023 Mar , V19 (4) : P23 doi: 10.1007/s11306-023-01993-0
Unravelling the seasonal dynamics of the metabolome of white asparagus spears using untargeted metabolomics.
Laboratory of Plant Physiology, Wageningen University and Research, 6700 AA, Wageningen, The Netherlands.; Biometris, Wageningen Plant Research, Wageningen University and Research, 6700 AA, Wageningen, The Netherlands.; Bioscience, Wageningen Plant Research, Wageningen University and Research, 6700 AA, Wageningen, The Netherlands.; Laboratory of Plant Physiology, Wageningen University and Research, 6700 AA, Wageningen, The Netherlands. robert.hall@wur.nl.; Bioscience, Wageningen Plant Research, Wageningen University and Research, 6700 AA, Wageningen, The Netherlands. robert.hall@wur.nl.
INTRODUCTION: The white asparagus season lasts 4 months while the harvest period per field is 8 weeks. Different varieties are better suited for harvesting early or late in the season. Little is known of the dynamics of secondary metabolites of white asparagus during the production season. OBJECTIVE: Characterization of the metabolome of white asparagus spears covering volatile and non-volatile composition in relation to quality aspects. METHODS: Eight varieties, harvested repeatedly during two consecutive seasons were analysed following an untargeted metabolomics workflow using SPME GC-MS and LC-MS. Linear regression, cluster and network analyses were used to explore the profile dynamics, unravel patterns and study the influence of genotype and environment. RESULTS: The metabolite profiles were influenced by the harvest moment and genetic background. Metabolites that significantly changed over time were distributed across seven clusters based on their temporal patterns. Two clusters including monoterpenes, benzenoids and saponins showed the most prominent seasonal changes. The changes depicted by the other five clusters were mainly
PMID: 36971968
Plant Physiol Biochem , IF:4.27 , 2023 Apr , V197 : P107642 doi: 10.1016/j.plaphy.2023.107642
Comparative transcriptome analyses under individual and combined nutrient starvations provide insights into N/P/K interactions in rice.
College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China.; Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environment Sciences, Nanjing Agricultural University, Nanjing, 210095, China.; State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.; College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China. Electronic address: zenghq@hznu.edu.cn.
Crops often suffer from simultaneous limitations of multiple nutrients in soils, including nitrogen (N), phosphorus (P) and potassium (K), which are three major macronutrients essential for ensuring growth and yield. Although plant responses to individual N, P, and K deficiency have been well documented, our understanding of the responses to combined nutrient deficiencies and the crosstalk between nutrient starvation responses is still limited. Here, we compared the physiological responses in rice under seven kinds of single and multiple low nutrient stress of N, P and K, and used RNA sequencing approaches to compare their transcriptome changes. A total of 13,000 genes were found to be differentially expressed under all these single and multiple low N/P/K stresses, and 66 and 174 of them were shared by all these stresses in roots and shoots, respectively. Functional enrichment analyses of the DEGs showed that a group of biological and metabolic processes were shared by these low N/P/K stresses. Comparative analyses indicated that DEGs under multiple low nutrient stress was not the simple summation of single nutrient stress. N was found to be the predominant factor affecting the transcriptome under combined nutrient stress. N, P, or K availability exhibited massive influences on the transcriptomic responses to starvation of other nutrients. Many genes involved in nutrient transport, hormone signaling, and transcriptional regulation were commonly responsive to low N/P/K stresses. Some transcription factors were predicted to regulate the expression of genes that are commonly responsive to N, P, and K starvations. These results revealed the interactions between N, P, and K starvation responses, and will be helpful for further elucidation of the molecular mechanisms underlying nutrient interactions.
PMID: 36989993
Planta , IF:4.116 , 2023 Mar , V257 (4) : P72 doi: 10.1007/s00425-023-04104-4
Identification of circular RNAs of Cannabis sativa L. potentially involved in the biosynthesis of cannabinoids.
Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, People's Republic of China.; Guangxi Botanical Garden of Medicinal Plants, Nanning, 530023, People's Republic of China.; Natural Health Product Research Alliance, College of Biological Sciences, University of Guelph, Guelph, ON, N1G2W1, Canada.; International Climate Resilient Crop Genomics Consortium and International Phytomedomics and Nutriomics Consortium, Kolkata, 700094, India.; Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, People's Republic of China. bwu@implad.ac.cn.; Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, People's Republic of China. cliu@implad.ac.cn.
We identified circRNAs in the Cannabis sativa L. genome and examined their association with 28 cannabinoids in three tissues of C. sativa. Nine circRNAs are potentially involved in the biosynthesis of six cannabinoids. Cannabis sativa L. has been widely used in the production of medicine, textiles, and food for over 2500 years. The main bioactive compounds in C. sativa are cannabinoids, which have multiple important pharmacological actions. Circular RNAs (circRNAs) play essential roles in growth and development, stress resistance, and the biosynthesis of secondary metabolites. However, the circRNAs in C. sativa remain unknown. In this study, to explore the role of circRNAs in cannabinoid biosynthesis, we performed RNA-Seq and metabolomics analysis on the leaves, roots, and stems of C. sativa. We identified 741 overlapping circRNAs by three tools, of which 717, 16, and 8 circRNAs were derived from exonic, intronic, and intergenic, respectively. Functional enrichment analysis indicated that the parental genes (PGs) of circRNAs were enriched in many processes related to biological stress responses. We found that most of the circRNAs showed tissue-specific expression and 65 circRNAs were significantly correlated with their PGs (P < 0.05, |r|>/= 0.5). We also determined 28 cannabinoids by High-performance liquid chromatography-ESI-triple quadrupole-linear ion trap mass spectrometry. Ten circRNAs, including ciR0159, ciR0212, ciR0153, ciR0149, ciR0016, ciR0044, ciR0022, ciR0381, ciR0006, and ciR0025 were found to be associated with six cannabinoids by weighted gene co-expression network analysis. Twenty-nine of 53 candidate circRNAs, including 9 cannabinoids related were validated successfully using PCR amplification and Sanger sequencing. Taken together, all these results would help to enhance our acknowledge of the regulation of circRNAs, and lay the foundation for breeding new C. sativa cultivars with high cannabinoids through manipulating circRNAs.
PMID: 36862222
BMC Bioinformatics , IF:3.169 , 2023 Apr , V24 (1) : P163 doi: 10.1186/s12859-023-05253-9
A gene regulatory network inference model based on pseudo-siamese network.
School of Electrical and Information Engineering, Beijing University of Civil Engineering and Architecture, Beijing, China.; School of Electrical and Information Engineering, Beijing University of Civil Engineering and Architecture, Beijing, China. guomaozu@bucea.edu.cn.; College of Agronomy and Biotechnology, China Agricultural University, Beijing, China.
MOTIVATION: Gene regulatory networks (GRNs) arise from the intricate interactions between transcription factors (TFs) and their target genes during the growth and development of organisms. The inference of GRNs can unveil the underlying gene interactions in living systems and facilitate the investigation of the relationship between gene expression patterns and phenotypic traits. Although several machine-learning models have been proposed for inferring GRNs from single-cell RNA sequencing (scRNA-seq) data, some of these models, such as Boolean and tree-based networks, suffer from sensitivity to noise and may encounter difficulties in handling the high noise and dimensionality of actual scRNA-seq data, as well as the sparse nature of gene regulation relationships. Thus, inferring large-scale information from GRNs remains a formidable challenge. RESULTS: This study proposes a multilevel, multi-structure framework called a pseudo-Siamese GRN (PSGRN) for inferring large-scale GRNs from time-series expression datasets. Based on the pseudo-Siamese network, we applied a gated recurrent unit to capture the time features of each TF and target matrix and learn the spatial features of the matrices after merging by applying the DenseNet framework. Finally, we applied a sigmoid function to evaluate interactions. We constructed two maize sub-datasets, including gene expression levels and GRNs, using existing open-source maize multi-omics data and compared them to other GRN inference methods, including GENIE3, GRNBoost2, nonlinear ordinary differential equations, CNNC, and DGRNS. Our results show that PSGRN outperforms state-of-the-art methods. This study proposed a new framework: a PSGRN that allows GRNs to be inferred from scRNA-seq data, elucidating the temporal and spatial features of TFs and their target genes. The results show the model's robustness and generalization, laying a theoretical foundation for maize genotype-phenotype associations with implications for breeding work.
PMID: 37085776
Biosystems , IF:1.973 , 2023 Apr , V226 : P104872 doi: 10.1016/j.biosystems.2023.104872
Formal autopoiesis: Solutions of the classical and extended functional closure equations.
Departments of Mathematics and Computer Science, University of Dallas, United States of America. Electronic address: echastain@udallas.edu.
Formalization of autopoiesis is an ongoing effort among theoretical biologists. In this field, Letelier and co-authors proposed that Robert Rosen's (M,R)-systems theory be used as a formalism for autopoiesis. In (M,R)-systems theory, Rosen proposes that one solve a set of functional closure equations (FCEs) which account for all of the components of the system as coming from within the system itself. A key part of the functional closure equations is the repair of the metabolism component of the system. Rosen's theory gives the organizational closure of the components as well as their products, as found in autopoiesis. However, according to Razeto-Barry (M,R)-systems leaves out some of the messiness and approximation that we find in autopoiesis as he reformulates it. A related problem is that though FCEs have a long history, they are difficult in practice to solve due to their mathematical formulation. In this paper we give a novel exact solution for the FCEs for continuous real vector-valued functions which is nevertheless difficult to compute. In addition we propose an extended form of FCEs which both captures more of the messiness of autopoiesis and also helps to make the FCEs more solvable. Finally, we use our solution for the extended FCEs to give an extended repair function for a metabolism taken from a representative class of biological dynamics for gene expression (the repressilator). More generally we show that one can use our solution for the extended FCEs to get an extended repair function for continuous real vector-valued functions.
PMID: 36921792