New Phytol , IF:10.151 , 2024 Nov , V244 (3) : P1057-1073 doi: 10.1111/nph.20059
Spatiotemporal transcriptome atlas reveals gene regulatory patterns during the organogenesis of the rapid growing bamboo shoots.
Jiangxi Provincial Key Laboratory for Bamboo Germplasm Resources and Utilization, Forestry College, Jiangxi Agricultural University, Nanchang, 330045, China.; State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China.
Bamboo with its remarkable growth rate and economic significance, offers an ideal system to investigate the molecular basis of organogenesis in rapidly growing plants, particular in monocots, where gene regulatory networks governing the maintenance and differentiation of shoot apical and intercalary meristems remain a subject of controversy. We employed both spatial and single-nucleus transcriptome sequencing on 10x platform to precisely dissect the gene functions in various tissues and early developmental stages of bamboo shoots. Our comprehensive analysis reveals distinct cell trajectories during shoot development, uncovering critical genes and pathways involved in procambium differentiation, intercalary meristem formation, and vascular tissue development. Spatial and temporal expression patterns of key regulatory genes, particularly those related to hormone signaling and lipid metabolism, strongly support the hypothesis that intercalary meristem origin from surrounded parenchyma cells. Specific gene expressions in intercalary meristem exhibit regular and dispersed distribution pattern, offering clues for understanding the intricate molecular mechanisms that drive the rapid growth of bamboo shoots. The single-nucleus and spatial transcriptome analysis reveal a comprehensive landscape of gene activity, enhancing the understanding of the molecular architecture of organogenesis and providing valuable resources for future genomic and genetic studies relying on identities of specific cell types.
PMID: 39140996
Bioresour Technol , IF:9.642 , 2024 Dec , V413 : P131484 doi: 10.1016/j.biortech.2024.131484
Microbial community dynamics in different floc size aggregates during nitrogen removal process upgrading in a full-scale landfill leachate treatment plant.
School of Basic Medical Sciences, Guangdong Pharmaceutical University, Guangzhou 510006, PR China. Electronic address: shengbb@gdpu.edu.cn.; School of Basic Medical Sciences, Guangdong Pharmaceutical University, Guangzhou 510006, PR China.; School of Life Sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou 510006, PR China.; School of Life Sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou 510006, PR China; Guangdong Provincial Key Laboratory of Advanced Drug Delivery, Guangdong Provincial Engineering Center of Topical Precise Drug Delivery System, Guangdong Pharmaceutical University, Guangzhou 510006, PR China. Electronic address: rxzhang@gdpu.edu.cn.
Upgrading processes to reduce biodegradable organic substance addition is crucial for treating landfill leachate with high pollutant concentrations, aiding carbon emission reduction. Aggregate size in activated sludge processes impacts pollutant removal and sludge/water separation. This study investigated microbial community succession and driving mechanisms in different floc-size aggregates during nitrogen removal progress upgrade from conventional to partial nitrification-denitrification in a full-scale landfill leachate treatment plant (LLTP) using 16S rRNA gene sequencing. The upgrade and floc sizes significantly influenced microbial diversity and composition. After upgrading, ammonia-oxidizing bacteria were enriched while nitrite-oxidizing bacteria suppressed in small flocs with homogeneity and high mass transfer efficiency. Larger flocs enriched Defluviicoccus, Thauera, and Truepera, while smaller flocs enriched Nitrosomonas, suggesting their potential as biomarkers. Multi-network analyses revealed microbial interactions. A deep learning model with convolutional neural networks predicted nitrogen removal efficiency. These findings guide optimizing LLTP processes and understanding microbial community dynamics based on floc size.
PMID: 39277056
Elife , IF:8.14 , 2024 Oct , V13 doi: 10.7554/eLife.94558
A metabolic modeling-based framework for predicting trophic dependencies in native rhizobiomes of crop plants.
Department of Natural Resources, Newe Ya'ar Research Center, Agricultural Research Organization (Volcani Institute), Ramat Ishay, Israel.; Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel.; Bioinformatics Unit, Newe Ya'ar Research Center, Agricultural Research Organization (Volcani Institute), Ramat Yishay, Israel.; Institute of Plant Sciences, Agricultural Research Organization (ARO), The Volcani Center, Beit Dagan, Israel.; Migal-Galilee Research Institute, Kiryat Shmona, Israel.; Faculty of Sciences and Technology, Tel-Hai Academic College, Qiryat Shemona, Israel.; Kinneret Limnological Laboratory, Israel Oceanographic and Limnological Research, Migdal, Israel.; Department of Postharvest Sciences, Agricultural Research Organization (ARO), The Volcani Center, Rishon LeZion, Israel.; United States Department of Agriculture-Agricultural Research Service Tree Fruits Research Lab, Wenatchee, United States.; Department of Plant Pathology, Stellenbosch University, Stellenbosch, South Africa.
The exchange of metabolites (i.e., metabolic interactions) between bacteria in the rhizosphere determines various plant-associated functions. Systematically understanding the metabolic interactions in the rhizosphere, as well as in other types of microbial communities, would open the door to the optimization of specific predefined functions of interest, and therefore to the harnessing of the functionality of various types of microbiomes. However, mechanistic knowledge regarding the gathering and interpretation of these interactions is limited. Here, we present a framework utilizing genomics and constraint-based modeling approaches, aiming to interpret the hierarchical trophic interactions in the soil environment. 243 genome scale metabolic models of bacteria associated with a specific disease-suppressive vs disease-conducive apple rhizospheres were drafted based on genome-resolved metagenomes, comprising an in silico native microbial community. Iteratively simulating microbial community members' growth in a metabolomics-based apple root-like environment produced novel data on potential trophic successions, used to form a network of communal trophic dependencies. Network-based analyses have characterized interactions associated with beneficial vs non-beneficial microbiome functioning, pinpointing specific compounds and microbial species as potential disease supporting and suppressing agents. This framework provides a means for capturing trophic interactions and formulating a range of testable hypotheses regarding the metabolic capabilities of microbial communities within their natural environment. Essentially, it can be applied to different environments and biological landscapes, elucidating the conditions for the targeted manipulation of various microbiomes, and the execution of countless predefined functions.
PMID: 39417540
Environ Pollut , IF:8.071 , 2024 Nov , V361 : P124849 doi: 10.1016/j.envpol.2024.124849
One-year monitoring of grass-type architectural waterscapes with long-term operation: Water quality and microorganism.
Shenzhen Institute of Building Research Co., Ltd., 518049 Shenzhen, Guangdong, China; School of Civil and Environmental Engineering, Harbin Institute of Technology (Shenzhen), 518055 Shenzhen, Guangdong, China. Electronic address: tmmdh2@163.com.; Shenzhen Jianyan Testing Co., Ltd., 518031 Shenzhen, Guangdong, China.; Shenzhen Institute of Building Research Co., Ltd., 518049 Shenzhen, Guangdong, China.; School of Civil and Environmental Engineering, Harbin Institute of Technology (Shenzhen), 518055 Shenzhen, Guangdong, China.
Grass-type architectural waterscapes (GAWs) utilize submerged plants to enhance self-purification ability and maintain a clear-water state. However, knowledge about their long-term water quality and microbial community dynamics remains limited. This study monitored the water quality, microbial community composition, and networks in two GAWs. GAW1 consisted solely Hydrilla verticillata with a water depth of 0.70 m, while GAW2 primarily contained Vallisneria natans, Microsorum pteropus, and Aquarius grisebachii with a water depth of 0.30 m. Results show that both water depth and submerged plant species play crucial roles in GAW establishment. The water depth of 0.7 m enabled Hydrilla verticillata to thrive underwater despite temperature variations, which demonstrated excellent nutrient uptake capacity. Thus, GAW1 exhibited superior self-purification ability, consistently meeting Class III standard for surface water in China. In contrast, GAW2 had a shallow water depth and contained ornamental plants, only meeting Class V standard. Furthermore, microbial communities were shaped by water quality, with distinct enriched genera serving as potential "microbial indicators". Enrichment of the hgcI clade and Sporichthyaceae_unclassified indicated superior water quality in GAW1, while prevalence of Comamonadaceae_unclassified, Flavobacterium, Rhodoluna, and Pseudarcicella suggested poor water quality in GAW2. Additionally, highly complex and connected microbial networks suggested elevated pollutant levels in GAWs. This study emphasized the significance of submerged plant species and water depth in GAWs construction and highlighted microbial communities and networks as potential indicators of water quality.
PMID: 39214442
Food Chem , IF:7.514 , 2024 Dec , V460 (Pt 3) : P140771 doi: 10.1016/j.foodchem.2024.140771
Transcriptome and metabolome analyses provide insights into the fruit softening disorder of papaya fruit under postharvest heat stress.
Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center for Postharvest Technology of Horticultural Crops in South China, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou, Guangdong, 510642, China.; Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center for Postharvest Technology of Horticultural Crops in South China, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou, Guangdong, 510642, China. Electronic address: xiaoyang_zhu@scau.edu.cn.
Heat stress in summer causes softening disorder in papaya but the molecular mechanism is not clear. In this study, papaya fruit stored at 35 degrees C showed a softening disorder termed rubbery texture. Analysis of the transcriptome and metabolome identified numerous differentially expressed genes (DEGs) and differentially accumulated metabolites (DAMs) between the fruit stored at 25 degrees C and 35 degrees C. The DEGs and DAMs related to lignin biosynthesis were upregulated, while those related to ethylene biosynthesis, sucrose metabolism, and cell wall degradation were downregulated under heat stress. Co-expression network analysis highlighted the correlation between the DEGs and metabolites associated with lignin biosynthesis, ethylene biosynthesis, and cell wall degradation under heat stress. Finally, the correlation analysis identified the key factors regulating softening disorder under heat stress. The study's findings reveal that heat stress inhibited papaya cell wall degradation and ethylene production, delaying fruit ripening and softening and ultimately resulting in a rubbery texture.
PMID: 39128369
J Integr Plant Biol , IF:7.061 , 2024 Oct , V66 (10) : P2226-2241 doi: 10.1111/jipb.13753
Proteomic dynamics revealed sex-biased responses to combined heat-drought stress in Marchantia.
Department of Organisms and, Systems Biology, Faculty of Biology/Biotechnology, Institute of Asturias, University of Oviedo, Oviedo, 33071, Asturias, Spain.
Recent studies have documented plant responses to climate change extensively, particularly to single-stress exposures. However, critical factors for stress survival, such as sexual differentiation, are not often considered. The dioicous Marchantia polymorpha stands as an evolutionary milestone, potentially preserving ancestral traits from the early colonizers. In this study, we employed proteomic analyses complemented with physiological monitoring to investigate combined heat and drought responses in Tak-1 (male) and Tak-2 (female) accessions of this liverwort. Additionally, targeted transcriptomics was conducted using different natural populations from contrasting environments. Our findings revealed sex-biased dynamics among natural accessions, particularly evident under control conditions and during early stress responses. Although Tak-2 exhibited greater diversity than Tak-1 under control conditions, male accession demonstrated distinct and more rapid stress sensing and signaling. These differences in stress response appeared to be strongly related to sex-specific plasticity influenced by geoclimatic origin. Furthermore, we established distinct protein gene ages and genomic distribution trends, underscoring the importance of protein diversification over time. This study provides an evolutionary perspective on sexual divergence and stress emergence employing a systems biology approach, which allowed for the establishment of global and sex-specific interaction networks in the stress response.
PMID: 39109947
J Environ Manage , IF:6.789 , 2024 Oct , V370 : P122726 doi: 10.1016/j.jenvman.2024.122726
Microbial inoculants using spent mushroom substrates as carriers improve soil multifunctionality and plant growth by changing soil microbial community structure.
Co-Innovation Center for Sustainable Forestry in Southern China, Jiangsu Province Key Laboratory of Soil and Water Conservation and Ecological Restoration, Nanjing Forestry University, 159 Longpan Road, Nanjing, Jiangsu, 210037, China. Electronic address: nh1263179511@njfu.edu.cn.; Co-Innovation Center for Sustainable Forestry in Southern China, Jiangsu Province Key Laboratory of Soil and Water Conservation and Ecological Restoration, Nanjing Forestry University, 159 Longpan Road, Nanjing, Jiangsu, 210037, China; Institute of Plant Ecology, Justus-Liebig University Giessen, Heinrich-Buff-Ring 26, 35392, Giessen, Germany. Electronic address: cli5104@njfu.edu.cn.; Co-Innovation Center for Sustainable Forestry in Southern China, Jiangsu Province Key Laboratory of Soil and Water Conservation and Ecological Restoration, Nanjing Forestry University, 159 Longpan Road, Nanjing, Jiangsu, 210037, China. Electronic address: zhjia2018@njfu.edu.cn.; Co-Innovation Center for Sustainable Forestry in Southern China, Jiangsu Province Key Laboratory of Soil and Water Conservation and Ecological Restoration, Nanjing Forestry University, 159 Longpan Road, Nanjing, Jiangsu, 210037, China. Electronic address: xuef0117@gmail.com.; Co-Innovation Center for Sustainable Forestry in Southern China, Jiangsu Province Key Laboratory of Soil and Water Conservation and Ecological Restoration, Nanjing Forestry University, 159 Longpan Road, Nanjing, Jiangsu, 210037, China. Electronic address: liuxinswc@njfu.edu.cn.; Co-Innovation Center for Sustainable Forestry in Southern China, Jiangsu Province Key Laboratory of Soil and Water Conservation and Ecological Restoration, Nanjing Forestry University, 159 Longpan Road, Nanjing, Jiangsu, 210037, China. Electronic address: lqq77@njfu.edu.cn.; Co-Innovation Center for Sustainable Forestry in Southern China, Jiangsu Province Key Laboratory of Soil and Water Conservation and Ecological Restoration, Nanjing Forestry University, 159 Longpan Road, Nanjing, Jiangsu, 210037, China. Electronic address: chenmeiling@njfu.edu.cn.; Co-Innovation Center for Sustainable Forestry in Southern China, Jiangsu Province Key Laboratory of Soil and Water Conservation and Ecological Restoration, Nanjing Forestry University, 159 Longpan Road, Nanjing, Jiangsu, 210037, China. Electronic address: dingyong252027@163.com.; Co-Innovation Center for Sustainable Forestry in Southern China, Jiangsu Province Key Laboratory of Soil and Water Conservation and Ecological Restoration, Nanjing Forestry University, 159 Longpan Road, Nanjing, Jiangsu, 210037, China. Electronic address: zhangjc8811@gmail.com.
Peat is typically used as a carrier for microbial inoculants; however, due to its non-renewable nature alternatives need to be identified as reliable and renewable carriers for mineral-solubilizing inoculants. In pot experiments, solid microbial inoculants were comprised of peat (P), biochar (BC), and spent mushroom substrates (SMS) using Medicago sativa L. as experimental materials, and the purpose of this study is to assess the effect of solid microbial inoculants on soil multifunctionality and plant growth. The results revealed that the SMS microbial inoculant had the greatest positive impact on plant biomass and significantly stimulated soil multifunctionality which is typically managed or assessed based on various soil functions or processes that are crucial for sustaining productivity, in contrast to the peat microbial inoculant, particularly at a supply level of 100 g/pot. There was no significant correlation between soil multifunctionality and bacterial/fungal microbial diversity. However, according to the co-occurrence network of bacteria and fungi, soil multifunctionality was intimately correlated with the biodiversity of the main ecological clusters (modules) of bacteria and fungi, rather than to the entire soil microbial community structure. The keystone species of module hubs and connectors play critical roles in maintaining the stability of ecological clusters of microbial co-occurrence networks and linkages between ecological clusters. Soil pH is a major predictor of changes in plant biomass, and leads to changes therein by affecting the major ecological clusters of bacterial and fungal co-occurrence networks. These results suggested that SMS may serve as a good alternative to peat as a carrier of mineral-solubilizing microorganisms to maintain soil multifunctionality and promote plant growth.
PMID: 39366236
Sci Rep , IF:4.379 , 2024 Oct , V14 (1) : P24557 doi: 10.1038/s41598-024-76195-2
Microbial community composition and co-occurrence network analysis of the rhizosphere soil of the main constructive tree species in Helan Mountain of Northwest China.
College of Life Science and Technology, Inner Mongolia Normal University, Huhhot, 010022, China.; Key Laboratory of Biodiversity Conservation and Sustainable Utilization for the College, University of Inner Mongolia Autonomous Region, Hohhot, China.; College of Life Science and Technology, Inner Mongolia Normal University, Huhhot, 010022, China. limin_8123@126.com.; Key Laboratory of Biodiversity Conservation and Sustainable Utilization for the College, University of Inner Mongolia Autonomous Region, Hohhot, China. limin_8123@126.com.; School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, China.
To understand the microbial diversity and community composition within the main constructive tree species, Picea crassifolia, Betula platyphylla, and Pinus tabuliformis, in Helan Mountain and their response to changes in soil physicochemical factors, a high throughput sequencing technology was used to analyze the bacterial and fungal diversity and community structure. RDA (Redundancy Analysis) and Pearson correlation analysis were used to explore the influence of soil physicochemical factors on microbial community construction, and co-occurrence network analysis was conducted on the microbial communities. The results showed that the fungal and bacterial diversity was highest in B. platyphylla, and lowest in P. crassifolia. Additionally, the fungal/bacterial richness was greatest in the rhizosphere soils of P. tabuliformis and B. platyphylla. RDA and Pearson correlation analysis revealed that NN (nitrate nitrogen) and AP (available phosphorus) were the main determining factors of the bacterial community, while NN and SOC (soil water content) were the main determining factors of the fungal community. Pearson correlation analysis between soil physicochemical factors and the alpha diversity of the microbial communities revealed a significant positive correlation between pH and the bacterial and fungal diversity, while SOC, TN (total nitrogen), AP, and AN (available nitrogen) were significantly negatively correlated with the bacterial and fungal diversity. Co-occurrence network analysis revealed that the soil bacterial communities exhibit richer network nodes, edges, greater diversity, and greater network connectivity. Indicating that bacterial communities exhibit more complex and stable interaction patterns in soil. This study reveals the complex interactive relationship between microbial communities and soil physicochemical factors in forest ecosystems. By analyzing the response of rhizosphere microbial communities of major tree species in Helan Mountain to nutrient dynamics and pH changes, we can deepen our understanding of the role of microorganisms in regulating ecosystem functions and provide theoretical basis for soil improvement and ecological restoration strategies.
PMID: 39427091
Plant Physiol Biochem , IF:4.27 , 2024 Sep , V216 : P109176 doi: 10.1016/j.plaphy.2024.109176
Regulatory network analysis reveals gene-metabolite relationships in pear fruit treated with methyl jasmonate.
Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, China.; Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, China. Electronic address: slzhang@njau.edu.cn.; Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, China. Electronic address: wuxiao@njau.edu.cn.
The economic value of pear is determined by its intrinsic qualities, which are influenced by metabolites produced during the ripening process. Methyl jasmonate (MeJA), a hormone, plays an important role in plant metabolism. To date, few studies have investigated the molecular mechanism underlying the changes in metabolic pathways related to the internal quality of pear fruit after MeJA treatment. In this study, ultrahigh-performance liquid chromatography‒Q Exactive Orbitrap mass spectrometry (UHPLC‒QE‒MS) was used to determine the changes in metabolite contents in pear after MeJA treatment. MeJA treatment primarily activated carbohydrate metabolism and amino acid metabolism pathways. Through combined analysis of UHPLC‒QE‒MS data and whole-transcriptome data, the abovementioned pathways and each metabolite were analysed separately, and competitive endogenous RNA (ceRNA) and microRNA-transcription factor-target (miRNA-TF-target) regulatory networks were constructed. The core nodes of three genes (PEA, Pbr022732.1; GAA, Pbr035655.1; and miR8033-x) and two genes (SDS, Pbr031708.1; and novel-m6796-3p) were associated with the carbohydrate metabolism and amino acid metabolism pathways, respectively. The core mRNA nodes TCONS_00048038 and Pbr019584.1, the core miRNA node miR4993-x, the core lncRNA node TCONS_0004356, the core circRNA node novel_circ_001967 and the core transcription factor node TSO1 (Pbr025407.1) were identified via separate metabolite analyses. These findings elucidate the changes in metabolites related to fruit quality in 'Nanguo' pear and the relationships between the metabolites and genes, reveal the molecular mechanism underlying the response of MeJA treatment in pear fruit, and provide a theoretical basis for improving the internal quality of 'Nanguo' pear.
PMID: 39378644
Environ Sci Pollut Res Int , IF:4.223 , 2024 Oct , V31 (46) : P57114-57128 doi: 10.1007/s11356-024-32207-2
The social network perspective on power system co-evolution: responses to "double carbon target" realization in China.
School of Management, Lanzhou University, Lanzhou, 730000, China.; School of Economics, Lanzhou University, Lanzhou, 730000, China. niey@lzu.edu.cn.; School of Information, Renmin University of China, Beijing, 100872, China.
The introduction of dual carbon targets will significantly impact power system development. Despite this, there is currently limited research on achieving system evolution and transition while ensuring safety, low-carbon output, and efficiency, as well as quantitatively analyzing the resulting changes dual carbon targets will have on the power system. Co-evolution of the power system offers a solution to balance the impact of dual carbon goals and enhance interaction among system entities, thereby facilitating the achievement of these goals. Our study focuses on constructing an evolutionary topological network by analyzing the dynamic evolution rule of power systems. We investigate the co-evolution pattern of power systems by analyzing the relationship between the role of power system agents and their dynamic structures. Furthermore, we analyze the future structural changes of power systems, which can provide theoretical support for achieving dual carbon goals in the power system. Our findings highlight key measures to promote synergistic evolution, including increasing energy storage capabilities, stabilizing renewable energy supply, breaking inter-provincial barriers in electricity transmission, and developing a multi-level intelligent power system. Through link analysis, we discover that future power systems will maintain a mild coordination among agents rather than implementing large-scale realignment and reconfiguration. We posit that overcoming obstacles can be achieved by fostering cohesion between the network and agents through technological innovation and widespread market diffusion to drive co-evolution.
PMID: 38321285
BMC Plant Biol , IF:4.215 , 2024 Oct , V24 (1) : P982 doi: 10.1186/s12870-024-05690-5
Comprehensive analysis of PLATZ family genes and their responses to abiotic stresses in Barley.
The Characteristic Laboratory of Crop Germplasm Innovation and Application, Provincial Department of Education, College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, China.; The Characteristic Laboratory of Crop Germplasm Innovation and Application, Provincial Department of Education, College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, China. liuwx@qau.edu.cn.; The Key Laboratory of the Plant Development and Environmental Adaptation Biology, School of Life Sciences, Ministry of Education, Shandong University, Qingdao, Shandong Province, 266237, China. liuwx@qau.edu.cn.
BACKGROUND: Plant A/T-rich protein and zinc-binding protein (PLATZ) transcription factors are pivotal regulators in various aspects of plant biology, including growth, development, and responses to environmental stresses. While PLATZ genes have been extensively studied and functionally characterized in various plants, limited information is available for these genes in barley. RESULTS: Here, we discovered a total of 11 PLATZ genes distributed across seven chromosomes in barley. Based on phylogenetic and conserved motif analysis, we classified PLATZ into five subfamilies, comprising 3, 1, 2, 1 and 4 genes, respectively. Analysis of gene structure demonstrated that these 11 HvPLATZ genes typically possessed two to four exons. Most HvPLATZ genes were found to possess at least one ABRE cis-element in their promoter regions, and a few of them also contained LTR, CAT-box, MRE, and DRE cis-elements. Then, we conducted an exploration of the expression patterns of HvPLATZs, which displayed notable differences across various tissues and in response to abiotic stresses. Functional analysis of HvPLATZ6 and HvPLATZ8 in yeast cells showed that they may be involved in drought tolerance. Additionally, we constructed a regulatory network including miRNA-targeted gene predictions and identified two miRNAs targeting two HvPLATZs, such as hvu-miR5053 and hvu-miR6184 targeting HvPLATZ2, hvu-miR6184 targeting HvPLATZ10. CONCLUSION: In summary, these findings provide valuable insights for future functional verification of HvPLATZs and contribute to a deeper understanding of the role of HvPLATZs in response to stress conditions in barley.
PMID: 39420254
Phytopathology , IF:4.025 , 2024 Oct doi: 10.1094/PHYTO-08-24-0269-FI
An integrated analysis of the Passifloraceae virome using public-domain data.
Universidad Nacional de Colombia Facultad de Ciencias Sede Medellin, Biociencias, Medellin, Colombia; mmhiguit@unal.edu.co.; Universidad Nacional de Colombia Facultad de Ciencias Sede Medellin, Biociencias, Medellin, Colombia; jsanchezy@unal.edu.co.; Universidad Nacional de Colombia Facultad de Ciencias Sede Medellin, Biociencias, Medellin, Colombia; alperezp@unal.edu.co.; Universidad Nacional de Colombia Facultad de Ciencias Sede Medellin, Biociencias, Medellin, Colombia; enariasm@unal.edu.co.; Universidad Nacional de Colombia Facultad de Ciencias Sede Medellin, Biociencias, Carrera 65 Nro. 59A - 110,, Medellin, Colombia, 50034; paguties@unal.edu.co.
Passifloraceae is a plant family that includes several species of interest in the food, medicinal, and ornamental industries. The most relevant species are the purple and yellow varieties of P. edulis, which are among the most highly prized tropical fruits in the international markets. Unfortunately, the rapid expansion of this crop worldwide has resulted in the emergence of several viral diseases that endangered the productivity of this crop. In this work, we performed an integrated analysis of the Passifloraceae virome using public data. We investigated Pubmed and Genbank records and analyzed all the transcriptome data available for members of this plant family. This analysis resulted in the identification of six novel virus associations and six putative new viral species. We also used RNAseq to inspect virus accumulation levels and mixed infections. Using network analysis, we also examined the global distribution of Passiflora viruses and their associations with alternative hosts, which is valuable information in implementing viral disease management strategies. Our data suggest that a large diversity of viruses remains to be discovered. Finally, we used the information gathered in this work to estimate the cross-transmission risk of viruses in Colombian Passiflora fields.
PMID: 39387526
BMC Genomics , IF:3.969 , 2024 Sep , V25 (1) : P897 doi: 10.1186/s12864-024-10798-x
Transcriptomic insights into the epigenetic modulation of turnip mosaic virus evolution in Arabidopsis thaliana.
Instituto de Biologia Integrativa de Sistemas (I 2 SysBio), CSIC-Universitat de Valencia, Catedratico Agustin Escardino 9, Paterna, Valencia, 46980, Spain.; Departmento de Genetica, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.; Instituto de Biologia Integrativa de Sistemas (I 2 SysBio), CSIC-Universitat de Valencia, Catedratico Agustin Escardino 9, Paterna, Valencia, 46980, Spain. santiago.elena@csic.es.; Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM, 87501, USA. santiago.elena@csic.es.
BACKGROUND: Plant-virus interaction models propose that a virus's ability to infect a host genotype depends on the compatibility between virulence and resistance genes. Recently, we conducted an evolution experiment in which lineages of turnip mosaic virus (TuMV) were passaged in Arabidopsis thaliana genotypes carrying mutations in components of the DNA methylation and the histone demethylation epigenetic pathways. All evolved lineages increased infectivity, virulence and viral load in a host genotype-dependent manner. RESULTS: To better understand the underlying reasons for these evolved relationships, we delved into the transcriptomic responses of mutant and WT plant genotypes in mock conditions and infected with either the ancestral or evolved viruses. Such a comparison allowed us to classify every gene into nine basic expression profiles. Regarding the targets of viral adaptation, our analyses allowed the identification of common viral targets as well as host genotype-specific genes and categories of biological processes. As expected, immune response-related genes were found to be altered upon infection. However, we also noticed the pervasive over-representation of other functional groups, suggesting that viral adaptation was not solely driven by the level of expression of plant resistance genes. In addition, a significant association between the presence of transposable elements within or upstream the differentially expressed genes was observed. Finally, integration of transcriptomic data into a virus-host protein-protein interaction network highlighted the most impactful interactions. CONCLUSIONS: These findings shed extra light on the complex dynamics between plants and viruses, indicating that viral infectivity depends on various factors beyond just the plant's resistance genes.
PMID: 39350047
Plants (Basel) , IF:3.935 , 2024 Oct , V13 (20) doi: 10.3390/plants13202927
A Model for the Gene Regulatory Network Along the Arabidopsis Fruit Medio-Lateral Axis: Rewiring the Pod Shatter Process.
Instituto de Biologia Molecular y Celular de Plantas, Consejo Superior de Investigaciones Cientificas-Universidad Politecnica de Valencia, 46022 Valencia, Spain.; Instituto de Hortofruticultura Subtropical y Mediterranea, Universidad de Malaga-Consejo Superior de Investigaciones Cientificas (IHSM-UMA-CSIC), Campus de Teatinos, 29071 Malaga, Spain.; Departamento de Ciencias Naturales, Unidad Cuajimalpa, Universidad Autonoma Metropolitana, Mexico City 05348, Mexico.; Laboratorio de Genetica Molecular, Epigenetica, Desarrollo y Evolucion de Plantas, Instituto de Ecologia, Universidad Nacional Autonoma de Mexico, Mexico City 04510, Mexico.
Different convergent evolutionary strategies adopted by angiosperm fruits lead to diverse functional seed dispersal units. Dry dehiscent fruits are a common type of fruit, characterized by their lack of fleshy pericarp and the release of seeds at maturity through openings (dehiscence zones, DZs) in their structure. In previous decades, a set of core players in DZ formation have been intensively characterized in Arabidopsis and integrated in a gene regulatory network (GRN) that explains the morphogenesis of these tissues. In this work, we compile all the experimental data available to date to build a discrete Boolean model as a mechanistic approach to validate the network and, if needed, to identify missing components of the GRN and/or propose new hypothetical regulatory interactions, but also to provide a new formal framework to feed further work in Brassicaceae fruit development and the evolution of seed dispersal mechanisms. Hence, by means of exhaustive in-silico validations and experimental evidence, we are able to incorporate both the NO TRANSMITTING TRACT (NTT) transcription factor as a new additional node, and a new set of regulatory hypothetical rules to uncover the dynamics of Arabidopsis DZ specification.
PMID: 39458874
Gene , IF:3.688 , 2024 Oct , V933 : P148994 doi: 10.1016/j.gene.2024.148994
Genome‑wide identification of circular RNAs and MAPKs reveals the regulatory networks in response to green peach aphid infestation in peach (Prunus persica).
School of Horticulture Landscape Architecture, Henan Institute of Science and Technology, 453003, PR China; Henan Province Engineering Research Center of Horticultural Plant Resource Utilization and Germplasm Enhancement, Xinxiang, PR China. Electronic address: wangxianyou@hist.edu.cn.; School of Horticulture Landscape Architecture, Henan Institute of Science and Technology, 453003, PR China; Henan Province Engineering Research Center of Horticultural Plant Resource Utilization and Germplasm Enhancement, Xinxiang, PR China.
The green peach aphid (GPA), Myzus persicae (Sulzer), is a serious agricultural pest with a worldwide distribution and a vector of over 100 plant viruses. Various pathways, such as the mitogen-activated protein kinase (MAPK) cascades, play pivotal roles in signaling plant defense against pest attack, and circular RNAs (circRNAs) regulate the expression of mRNAs in response to pest attack. However, the mechanism underlying peach (Prunus persica) response to GPA attack remains unclear. The present study initially identified and characterized 316 circRNAs and 18 PpMAPKs from healthy and GPA-infested peach leaves by whole-transcriptome sequencing and predicted the differentially expressed circRNAs (DECs) after GPA infestation. PCR and Sanger sequencing confirmed the presence of six DECs in peach samples. Besides, RNA sequencing analysis detected 13 DECs, including 5 upregulated and 8 downregulated ones, in peach in response to the GPA attack. Gene ontology (GO) enrichment analysis indicated that specific DECs play crucial roles in the MAPK signaling pathway, and qRT-PCR revealed that GPA infestation altered the expression patterns of PpMAPKs. Finally, five circRNAs, three microRNA (miRNAs), and two MAPK target genes were identified to interact as a network and perform critical roles in modulating the MAPK pathway in the peach during GPA infestation.
PMID: 39395730
Gene , IF:3.688 , 2024 Dec , V931 : P148899 doi: 10.1016/j.gene.2024.148899
Multiple functions and regulatory networks of WRKY33 and its orthologs.
School of Life Sciences, Nantong University, Nantong, China; Key Laboratory of Landscape Plant Genetics and Breeding, Nantong, China. Electronic address: chenyh@ntu.edu.cn.; School of Life Sciences, Nantong University, Nantong, China; Key Laboratory of Landscape Plant Genetics and Breeding, Nantong, China.
Arabidopsis thaliana WRKY33 is currently one of the most studied members of the Group I WRKY transcription factor family. Research has confirmed that WRKY33 is involved in the regulation of various biological and abiotic stresses and occupies a central position in the regulatory network. The functional studies of orthologous genes of WRKY33 from other species are also receiving increasing attention. In this article, we summarized thirty-eight orthologous genes of AtWKRY33 from twenty-five different species. Their phylogenetic relationship and conserved WRKY domain were analyzed and compared. Similar to AtWKRY33, the well-studied orthologous gene members from rice and tomato also have multiple functions. In addition to playing important regulatory roles in responding to their specific pathogens, they are also involved in regulating various abiotic stresses and development. AtWKRY33 exerts its multiple functions through a complex regulatory network. Upstream transcription factors or other regulatory factors activate or inhibit the expression of AtWKRY33 at the chromatin and transcriptional levels. Interacting proteins affect the transcriptional activity of AtWKRY33 through phosphorylation, ubiquitination, SUMOylation, competition, or cooperation. The downstream genes are diverse and include three major categories: transcription factors, synthesis, metabolism, and signal transduction of various hormones, and disease resistance genes. In the regulatory network of AtWRKY33 orthologs, many conserved regulatory characteristics have been discovered, such as self-activation and phosphorylation by MAP kinases. This can provide a comparative reference for further studying the functions of other orthologous genes of AtWKRY33.
PMID: 39209179
AoB Plants , IF:3.276 , 2024 Oct , V16 (5) : Pplae053 doi: 10.1093/aobpla/plae053
Molecular mechanism of flower colour formation in Rhododendron simsii Planchon revealed by integration of microRNAome and RNAomics.
College of Biology and Agricultural Resources, Huanggang Normal University, Huanggang, Hubei Province, 438000, China.
Systems-wide understanding of gene expression profile regulating flower colour formation in Rhododendron simsii Planchon is insufficient. In this research, integration analysis of ribonucleic acid (RNA)omics and microRNAome were performed to reveal the molecular mechanism of flower colour formation in three R. simsii varieties with red, pink and crimson flowers, respectively. Totally, 3129, 5755 and 5295 differentially expressed gene (DEG)s were identified through comparative transcriptome analysis between 'Red variety' and 'Pink variety' (1507 up-regulated and 1622 down-regulated), 'Red variety' and 'Crimson variety' (2148 up-regulated 3607 down-regulated), as well as 'Pink variety' and 'Crimson variety' (2089 up-regulated and 3206 down-regulated), which were involved in processes of 'catalytic activity', 'binding', 'metabolic process' and 'cellular process', as well as pathways of 'metabolic pathways', 'biosynthesis of secondary metabolites', 'plant-pathogen interaction' and 'phenylpropanoid biosynthesis'. A total of 215 miRNAs, containing 153 known miRNAs belonging to 57 families and 62 novel miRNA, were involved in flower colour formation. In particular, 55 miRNAs were significantly differently expressed. Based on miRNA-mRNA regulatory network, ath-miR5658 could affect the synthesis of pelargonidin, cyanidin and delphinidin through downregulating accumulation of anthocyanidin 3-O-glucosyltransferase; ath-miR868-3p could regulate isoflavonoid biosynthesis through downregulating expression of CYP81E1/E7; ath-miR156g regulated the expression of flavonoid 3',5'-hydroxylase; and ath-miR829-5p regulated flavonol synthasein flavonoid biosynthesis process. This research will provide important roles in breeding new varieties with rich flower colour.
PMID: 39430437
J Evol Biol , IF:2.411 , 2024 Oct , V37 (10) : P1205-1214 doi: 10.1093/jeb/voae096
The improbability of detecting trade-offs and some practical solutions.
Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada.
Trade-offs are a fundamental concept in evolutionary biology because they are thought to explain much of nature's biological diversity, from variation in life-histories to differences in metabolism. Despite the predicted importance of trade-offs, they are notoriously difficult to detect. Here we contribute to the existing rich theoretical literature on trade-offs by examining how the shape of the distribution of resources or metabolites acquired in an allocation pathway influences the strength of trade-offs between traits. We further explore how variation in resource distribution interacts with two aspects of pathway complexity (i.e., the number of branches and hierarchical structure) affects tradeoffs. We simulate variation in the shape of the distribution of a resource by sampling 106 individuals from a beta distribution with varying parameters to alter the resource shape. In a simple "Y-model" allocation of resources to two traits, any variation in a resource leads to slopes less than -1, with left skewed and symmetrical distributions leading to negative relationships between traits, and highly right skewed distributions associated with positive relationships between traits. Adding more branches further weakens negative and positive relationships between traits, and the hierarchical structure of pathways typically weakens relationships between traits, although in some contexts hierarchical complexity can strengthen positive relationships between traits. Our results further illuminate how variation in the acquisition and allocation of resources, and particularly the shape of a resource distribution and how it interacts with pathway complexity, makes its challenging to detect trade-offs. We offer several practical suggestions on how to detect trade-offs given these challenges.
PMID: 39110030