New Phytol , IF:10.151 , 2024 Aug 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
New Phytol , IF:10.151 , 2024 Sep , V243 (5) : P1855-1869 doi: 10.1111/nph.19949
The biosynthesis of storage reserves and auxin is coordinated by a hierarchical regulatory network in maize endosperm.
State Key Laboratory of Maize Bio-breeding, Frontiers Science Center for Molecular Design Breeding, Joint International Research Laboratory of Crop Molecular Breeding, National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China.; State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.; Shanghai Key Laboratory of Bio-Energy Crops, Plant Science Center, School of Life Sciences, Shanghai University, Shanghai, 200444, China.
Grain filling in maize (Zea mays) is intricately linked to cell development, involving the regulation of genes responsible for the biosynthesis of storage reserves (starch, proteins, and lipids) and phytohormones. However, the regulatory network coordinating these biological functions remains unclear. In this study, we identified 1744 high-confidence target genes co-regulated by the transcription factors (TFs) ZmNAC128 and ZmNAC130 (ZmNAC128/130) through chromatin immunoprecipitation sequencing coupled with RNA-seq analysis in the zmnac128/130 loss-of-function mutants. We further constructed a hierarchical regulatory network using DNA affinity purification sequencing analysis of downstream TFs regulated by ZmNAC128/130. In addition to target genes involved in the biosynthesis of starch and zeins, we discovered novel target genes of ZmNAC128/130 involved in the biosynthesis of lipids and indole-3-acetic acid (IAA). Consistently, the number of oil bodies, as well as the contents of triacylglycerol, and IAA were significantly reduced in zmnac128/130. The hierarchical regulatory network centered by ZmNAC128/130 revealed a significant overlap between the direct target genes of ZmNAC128/130 and their downstream TFs, particularly in regulating the biosynthesis of storage reserves and IAA. Our results indicated that the biosynthesis of storage reserves and IAA is coordinated by a multi-TFs hierarchical regulatory network in maize endosperm.
PMID: 38962989
Cell Rep , IF:9.423 , 2024 Aug , V43 (8) : P114623 doi: 10.1016/j.celrep.2024.114623
Multi-omics analysis unravels chemical roadmap and genetic basis for peach fruit aroma improvement.
Laboratory of Fruit Quality Biology/Zhejiang Key Laboratory of Horticultural Crop Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou 310058, China.; Zhejiang Provincial Key Laboratory of Crop Genetic Resources, The Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 300058, China.; Institute of Pomology, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory of Horticultural Crop Genetic Improvement, Nanjing, Jiangsu 210014, China.; The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research) Mt Albert, Auckland Mail Centre, Private Bag 92169, Auckland 1142, New Zealand.; Institute of Pomology, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory of Horticultural Crop Genetic Improvement, Nanjing, Jiangsu 210014, China. Electronic address: zhangyuyan@jaas.ac.cn.; Laboratory of Fruit Quality Biology/Zhejiang Key Laboratory of Horticultural Crop Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou 310058, China; Hainan Institute of Zhejiang University, Sanya, Hainan 572000, China. Electronic address: bozhang@zju.edu.cn.
Selection of fruits with enhanced health benefits and superior flavor is an important aspect of peach breeding. Understanding the genetic interplay between appearance and flavor chemicals remains a major challenge. We identify the most important volatiles contributing to consumer preferences for peach, thus establishing priorities for improving flavor quality. We quantify volatiles of a peach population consisting of 184 accessions and demonstrate major reductions in the important flavor volatiles linalool and Z-3-hexenyl acetate in red-fleshed accessions. We identify 474 functional gene regulatory networks (GRNs), among which GRN05 plays a crucial role in controlling both red flesh and volatile content through the NAM/ATAF1/2/CUC (NAC) transcription factor PpBL. Overexpressing PpBL results in reduced expression of PpNAC1, a positive regulator for Z-3-hexenyl acetate and linalool synthesis. Additionally, we identify haplotypes for three tandem PpAATs that are significantly correlated with reduced gene expression and ester content. We develop genetic resources for improvement of fruit quality.
PMID: 39146179
Sci Total Environ , IF:7.963 , 2024 Aug , V937 : P173422 doi: 10.1016/j.scitotenv.2024.173422
The ethylene response factor gene, ThDRE1A, is involved in abscisic acid- and ethylene-mediated cadmium accumulation in Tamarix hispida.
State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, Northeast Forestry University, Harbin 150040, China.; State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China.; Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, Northeast Forestry University, Harbin 150040, China.; State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China. Electronic address: gaocaiqiu@nefu.edu.cn.
Tamarix hispida is highly tolerant to salt, drought and heavy metal stress and is a potential material for the remediation of cadmium (Cd)-contaminated soil under harsh conditions. In this study, T. hispida growth and chlorophyll content decreased, whereas flavonoid and carotenoid contents increased under long-term Cd stress (25 d). The aboveground components of T. hispida were collected for RNA-seq to investigate the mechanism of Cd accumulation. GO and KEGG enrichment analyses revealed that the differentially expressed genes (DEGs) were significantly enriched in plant hormone-related pathways. Exogenous hormone treatment and determination of Cd(2+) levels showed that ethylene (ETH) and abscisic acid (ABA) antagonists regulate Cd accumulation in T. hispida. Twenty-five transcription factors were identified as upstream regulators of hormone-related pathways. ThDRE1A, which was previously identified as an important regulatory factor, was selected for further analysis. The results indicated that ThABAH2.5 and ThACCO3.1 were direct target genes of ThDRE1A. The determination of Cd(2+), ABA, and ETH levels indicated that ThDRE1A plays an important role in Cd accumulation through the antagonistic regulation of ABA and ETH. In conclusion, these results reveal the molecular mechanism underlying Cd accumulation in plants and identify candidate genes for further research.
PMID: 38796019
Plant Cell Environ , IF:7.228 , 2024 Sep , V47 (9) : P3654-3667 doi: 10.1111/pce.14950
Regulatory networks of senescence-associated gene-transcription factors promote degradation in Moso bamboo shoots.
State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China.; College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao, China.; International Center for Bamboo and Rattan, Beijing, China.; Department of Forest and Conservation Sciences, Faculty of Forestry, Forest Sciences Centre, University of British Columbia, Vancouver, British Columbia, Canada.
Bamboo cultivation, particularly Moso bamboo (Phyllostachys edulis), holds significant economic importance in various regions worldwide. Bamboo shoot degradation (BSD) severely affects productivity and economic viability. However, despite its agricultural consequences, the molecular mechanisms underlying BSD remain unclear. Consequently, we explored the dynamic changes of BSD through anatomy, physiology and the transcriptome. Our findings reveal ruptured protoxylem cells, reduced cell wall thickness and the accumulation of sucrose and reactive oxygen species (ROS) during BSD. Transcriptomic analysis underscored the importance of genes related to plant hormone signal transduction, sugar metabolism and ROS homoeostasis in this process. Furthermore, BSD appears to be driven by the coexpression regulatory network of senescence-associated gene transcription factors (SAG-TFs), specifically PeSAG39, PeWRKY22 and PeWRKY75, primarily located in the protoxylem of vascular bundles. Yeast one-hybrid and dual-luciferase assays demonstrated that PeWRKY22 and PeWRKY75 activate PeSAG39 expression by binding to its promoter. This study advanced our understanding of the molecular regulatory mechanisms governing BSD, offering a valuable reference for enhancing Moso bamboo forest productivity.
PMID: 38752443
Microbiol Spectr , IF:7.171 , 2024 Aug , V12 (8) : Pe0421423 doi: 10.1128/spectrum.04214-23
Alternaria solani effectors AsCEP19 and AsCEP20 reveal novel functions in pathogenicity and conidiogenesis.
College of Plant Protection, Hebei Agricultural University, Baoding, Hebei, China.; Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, Baoding, Hebei, China.
Previous work identified a pair of specific effectors AsCEP19 and AsCEP20 in Alternaria solani as contributors to the virulence of A. solani. Here, we constructed AsCEP19 and AsCEP20 deletion mutants in A. solani strain HWC168 to further reveal the effects of these genes on the biology and pathogenicity of A. solani. Deletion of AsCEP19 and AsCEP20 did not affect vegetative growth but did affect conidial maturation, with an increase in the percentage of abnormal conidia produced. Furthermore, we determined the expression patterns of genes involved in the conidiogenesis pathway and found that the regulatory gene abaA was significantly upregulated and chsA, a positive regulator for conidiation, was significantly downregulated in the mutant strains compared to the wild-type strain. These results suggest that AsCEP19 and AsCEP20 indirectly affect the conidial development and maturation of A. solani. Pathogenicity assays revealed significantly impaired virulence of DeltaAsCEP19, DeltaAsCEP20, and DeltaAsCEP19 + AsCEP20 mutants on potato and tomato plants. Moreover, we performed localization assays with green fluorescent protein-tagged proteins in chili pepper leaves. We found that AsCEP19 can specifically localize to the chloroplasts of chili pepper epidermal cells, while AsCEP20 can localize to both chloroplasts and the plasma membrane. Weighted gene co-expression network analysis revealed enrichment of genes of this module in the photosynthesis pathway, with many hub genes associated with chloroplast structure and photosynthesis. These results suggest that chloroplasts are the targets for AsCEP19 and AsCEP20. IMPORTANCE: Alternaria solani is an important necrotrophic pathogen causing potato early blight. Previous studies have provide preliminary evidence that specific effectors AsCEP19 and AsCEP20 contribute to virulence, but their respective functions, localization, and pathogenic mechanisms during the infection process of A. solani remain unclear. Here, we have systematically studied the specific effectors AsCEP19 and AsCEP20 for the first time, which are essential for conidial maturation. The deletion of AsCEP19 and AsCEP20 can significantly impair fungal pathogenicity. Additionally, we preliminarily revealed that AsCEP19 and AsCEP20 target the chloroplasts of host cells. Our findings further enhance our understanding of the molecular mechanisms underlying the virulence of necrotrophic pathogens.
PMID: 38912810
Chemosphere , IF:7.086 , 2024 Aug , V364 : P143013 doi: 10.1016/j.chemosphere.2024.143013
Reutilization of post-adsorption lanthanum-loaded straw alleviates phosphorus pollution in rice-wheat system: Subsequent performance and underlying mechanisms.
Key Laboratory of Agricultural Environment of the Lower Reaches of the Yangtze River, Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China; Key Laboratory of Integrated Regulation and Resources Development of Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China. Electronic address: yangbeimail@126.com.; Key Laboratory of Agricultural Environment of the Lower Reaches of the Yangtze River, Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China.; Centro de Biotecnologia y Genomica de Plantas (UPM-INIA), Universidad Politecnica de Madrid, Madrid, 28223, Spain. Electronic address: qingnan.chu@upm.es.; Newcastle University, School of Engineering, Newcastle Upon Tyne, NE1 7RU, England, UK.; Nanjing Ningliang Biotechnology Co., Ltd, Nanjing, 211135, China.; Key Laboratory of Integrated Regulation and Resources Development of Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China.; Key Laboratory of Agricultural Environment of the Lower Reaches of the Yangtze River, Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China. Electronic address: njxuelihong@gmail.com.
Adsorption technology for phosphorus (P) removal is considered promising and reutilization of post-adsorbent can contribute to promoting sustainable agricultural production. However, the long-lasting impact of the post-adsorbent on crop growth and P remains unclear. This study assessed the effects of P-adsorbed lanthanum-modified straw (La@straw-P) on the rice yield, P fractionation and associated water quality parameters. The findings indicated that, compared with traditional fertilizer regimes, La@straw-P expedited the P reduction in the flooding water achieving a rate of decline to the tertiary standard for surface water (0.20 mg/L) 3.8 times faster and enhanced increased the P harvest index by 17.00 %. Economic estimation proved the positive benefits of La@straw-P in planting-breeding combination system. Redundancy analysis (RDA) and co-occurrence network analysis (CONA) revealed that electrical conductivity (EC) and dissolved Fe played primary roles in regulating total P. Fourier transform infrared spectra (FTIR), X-ray diffraction (XRD), X-ray photoelectron spectra (XPS), and soil P fractions collectively demonstrated that the abundant adsorption sites on La@straw-P could facilitate the transformation of active P into moderately Ca-bound P. This study proposes a strategy for recycling P-adsorbed materials to mitigate agricultural non-point P pollution.
PMID: 39111671
J Integr Plant Biol , IF:7.061 , 2024 Aug 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 Exp Bot , IF:6.992 , 2024 Aug , V75 (16) : P4960-4977 doi: 10.1093/jxb/erae251
Expression of dehydroshikimate dehydratase in poplar induces transcriptional and metabolic changes in the phenylpropanoid pathway.
Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA, USA.; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.; Recep Tayyip Erdogan University, Department of Chemistry, 53100, Rize, Turkiye.; Karadeniz Technical University, Department of Energy System Engineering, 61830, Trabzon, Turkiye.; Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.; Department of Wood Science, University of British Columbia, Vancouver, BC, Canada.; Department of Botany, University of British Columbia, Vancouver, BC, Canada.; DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, Madison, WI 53726, USA.; School of Agriculture, Food and Wine & Waite Research Institute, University of Adelaide, Glen Osmond, SA, Australia.; Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA.
Modification of lignin in feedstocks via genetic engineering aims to reduce biomass recalcitrance to facilitate efficient conversion processes. These improvements can be achieved by expressing exogenous enzymes that interfere with native biosynthetic pathways responsible for the production of the lignin precursors. In planta expression of a bacterial 3-dehydroshikimate dehydratase in poplar trees reduced lignin content and altered the monomer composition, which enabled higher yields of sugars after cell wall polysaccharide hydrolysis. Understanding how plants respond to such genetic modifications at the transcriptional and metabolic levels is needed to facilitate further improvement and field deployment. In this work, we acquired fundamental knowledge on lignin-modified poplar expressing 3-dehydroshikimate dehydratase using RNA-seq and metabolomics. The data clearly demonstrate that changes in gene expression and metabolite abundance can occur in a strict spatiotemporal fashion, revealing tissue-specific responses in the xylem, phloem, or periderm. In the poplar line that exhibited the strongest reduction in lignin, we found that 3% of the transcripts had altered expression levels and ~19% of the detected metabolites had differential abundance in the xylem from older stems. The changes affected predominantly the shikimate and phenylpropanoid pathways as well as secondary cell wall metabolism, and resulted in significant accumulation of hydroxybenzoates derived from protocatechuate and salicylate.
PMID: 38809816
Front Plant Sci , IF:5.753 , 2024 , V15 : P1451403 doi: 10.3389/fpls.2024.1451403
Comparing time-series transcriptomes between chilling-resistant and -susceptible rice reveals potential transcription factors responding to chilling stress.
State Key Laboratory of Plant Environmental Resilience, College of Life Sciences, Zhejiang University, Hangzhou, China.; Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Zhejiang Province, Zhejiang University, Hangzhou, China.
Low temperature is one of the most important environmental factors that inhibits rice growth and grain yield. Transcription factors (TFs) play crucial roles in chilling acclimation by regulating gene expression. However, transcriptional dynamics and key regulators responding to low temperature remain largely unclear in rice. In this study, a transcriptome-based comparative analysis was performed to explore genome-wide gene expression profiles between a chilling-resistant cultivar DC90 and a chilling-susceptible cultivar 9311 at a series of time points under low temperature treatment and recovery condition. A total of 3,590 differentially expressed genes (DEGs) between two cultivars were determined and divided into 12 co-expression modules. Meanwhile, several biological processes participating in the chilling response such as abscisic acid (ABA) responses, water deprivation, protein metabolic processes, and transcription regulator activities were revealed. Through weighted gene co-expression network analysis (WGCNA), 15 hub TFs involved in chilling conditions were identified. Further, we used the gene regulatory network (GRN) to evaluate the top 50 TFs, which might have potential roles responding to chilling stress. Finally, five TFs, including a C-repeat binding factor (OsCBF3), a zinc finger-homeodomain protein (OsZHD8), a tandem zinc finger protein (OsTZF1), carbon starved anther (CSA), and indeterminate gametophyte1 (OsIG1) were identified as crucial candidates responsible for chilling resistance in rice. This study deepens our understanding in the gene regulation networks of chilling stress in rice and offers potential gene resources for breeding climate-resilient crops.
PMID: 39166246
Mol Plant Pathol , IF:5.663 , 2024 Aug , V25 (8) : Pe13467 doi: 10.1111/mpp.13467
N-acyl homoserine lactone cell-cell diffusible signalling in the Ralstonia solanacearum species complex.
Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, China.; International Centre for Genetic Engineering and Biotechnology, Trieste, Italy.; Interdisciplinary Research Center for Agriculture Green Development in Yangtze River Basin, Southwest University, Chongqing, China.; School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yatsen University, Shenzhen, China.; African Genome Center, University Mohammed VI Polytechnic (UM6P), Ben Guerir, Morocco.
Ralstonia solanacearum species complex (RSSC) includes soilborne bacterial plant pathogens with worldwide distribution and wide host ranges. Virulence factors are regulated via four hierarchically organized cell-cell contact independent quorum-sensing (QS) signalling systems: the Phc, which uses as signals (R)-methyl 3-hydroxypalmitate [(R)-3-OH PAME] or (R)-methyl 3-hydroxymyristate [(R)-3-OH MAME], the N-acyl homoserine lactone (AHL)-dependent RasI/R and SolI/R systems, and the recently identified anthranilic acid-dependent system. The unique Phc QS system has been extensively studied; however, the role of the two AHL QS systems has only recently been addressed. In this microreview, we present and discuss current data of the SolI/R and RasI/R QS systems in the RSSC. We also present the distribution and frequency of these AHL QS systems in the RSSC, discuss possible ecological roles and evolutive implications. The complex QS hierarchical networks emphasizes the crucial role of cell-cell signalling in the virulence of the RSSC.
PMID: 39099210
J Agric Food Chem , IF:5.279 , 2024 Aug , V72 (33) : P18573-18584 doi: 10.1021/acs.jafc.4c03012
Joint GWAS and WGCNA Identify Genes Regulating the Isoflavone Content in Soybean Seeds.
Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin 150030, China.; Daqing Branch, Heilongjiang Academy of Agricultural Science, Daqing 163711, China.; Qiqihar Branch, Heilongjiang Academy of Agricultural Science, Qiqihar 161006, China.
Isoflavone is a secondary metabolite of the soybean phenylpropyl biosynthesis pathway with physiological activity and is beneficial to human health. In this study, the isoflavone content of 205 soybean germplasm resources from 3 locations in 2020 showed wide phenotypic variation. A joint genome-wide association study (GWAS) and weighted gene coexpression network analysis (WGCNA) identified 33 single-nucleotide polymorphisms and 11 key genes associated with soybean isoflavone content. Gene ontology enrichment analysis, gene coexpression, and haplotype analysis revealed natural variations in the Glyma.12G109800 (GmOMT7) gene and promoter region, with Hap1 being the elite haplotype. Transient overexpression and knockout of GmOMT7 increased and decreased the isoflavone content, respectively, in hairy roots. The combination of GWAS and WGCNA effectively revealed the genetic basis of soybean isoflavone and identified potential genes affecting isoflavone synthesis and accumulation in soybean, providing a valuable basis for the functional study of soybean isoflavone.
PMID: 39105709
J Proteome Res , IF:4.466 , 2024 Aug , V23 (8) : P2857-2869 doi: 10.1021/acs.jproteome.3c00485
Longitudinal Transcriptomic, Proteomic, and Metabolomic Response of Citrus sinensis to Diaphorina citri Inoculation of Candidatus Liberibacter asiaticus.
Department of Food Science and Technology, University of California Davis, Davis, California 95616, United States.; Agricultural Research Service, Emerging Pests and Pathogens Research Unit, Ithaca, New York 14853, United States.; Boyce Thompson Institute for Plant Research, Ithaca, New York 14853, United States.; Department of Genome Sciences, University of Washington, Seattle, Washington 98195, United States.; Plant Pathology and Plant Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853, United States.; Department of Nutrition, University of California Davis, Davis, California 95616, United States.
Huanglongbing (HLB) is a fatal citrus disease that is currently threatening citrus varieties worldwide. One putative causative agent, Candidatus Liberibacter asiaticus (CLas), is vectored by Diaphorina citri, known as the Asian citrus psyllid (ACP). Understanding the details of CLas infection in HLB disease has been hindered by its Candidatus nature and the inability to confidently detect it in diseased trees during the asymptomatic stage. To identify early changes in citrus metabolism in response to inoculation of CLas using its natural psyllid vector, leaves from Madam Vinous sweet orange (Citrus sinensis (L.) Osbeck) trees were exposed to CLas-positive ACP or CLas-negative ACP and longitudinally analyzed using transcriptomics (RNA sequencing), proteomics (liquid chromatography-tandem mass spectrometry; data available in Dryad: 10.25338/B83H1Z), and metabolomics (proton nuclear magnetic resonance). At 4 weeks postexposure (wpe) to psyllids, the initial HLB plant response was primarily to the ACP and, to a lesser extent, the presence or absence of CLas. Additionally, analysis of 4, 8, 12, and 16 wpe identified 17 genes and one protein as consistently differentially expressed between leaves exposed to CLas-positive ACP versus CLas-negative ACP. This study informs identification of early detection molecular targets and contributes to a broader understanding of vector-transmitted plant pathogen interactions.
PMID: 38373055
BMC Plant Biol , IF:4.215 , 2024 Aug , V24 (1) : P801 doi: 10.1186/s12870-024-05446-1
Improved pokeweed genome assembly and early gene expression changes in response to jasmonic acid.
Department of Biology, York University, 4700 Keele St, Toronto, ON, M3J 1P3, Canada.; Department of Biology, York University, 4700 Keele St, Toronto, ON, M3J 1P3, Canada. hudak@yorku.ca.
BACKGROUND: Jasmonic acid (JA) is a phytohormone involved in regulating responses to biotic and abiotic stress. Although the JA pathway is well characterized in model plants such as Arabidopsis thaliana, less is known about many non-model plants. Phytolacca americana (pokeweed) is native to eastern North Americana and is resilient to environmental stress. The goal of this study was to produce a publicly available pokeweed genome assembly and annotations and use this resource to determine how early response to JA changes gene expression, with particular focus on genes involved in defense. RESULTS: We assembled the pokeweed genome de novo from approximately 30 Gb of PacBio Hifi long reads and achieved an NG50 of ~ 13.2 Mb and a minimum 93.9% complete BUSCO score for gene annotations. With this reference, we investigated the early changes in pokeweed gene expression following JA treatment. Approximately 5,100 genes were differentially expressed during the 0-6 h time course with almost equal number of genes with increased and decreased transcript levels. Cluster and gene ontology analyses indicated the downregulation of genes associated with photosynthesis and upregulation of genes involved in hormone signaling and defense. We identified orthologues of key transcription factors and constructed the first JA gene response network integrated with our transcriptomic data from orthologues of Arabidopsis genes. We discovered that pokeweed did not use leaf senescence as a means of reallocating resources during stress; rather, most secondary metabolite synthesis genes were constitutively expressed, suggesting that pokeweed directs its resources for survival over the long term. In addition, pokeweed synthesizes several RNA N-glycosylases hypothesized to function in defense, each with unique expression profiles in response to JA. CONCLUSIONS: Our investigation of the early response of pokeweed to JA illustrates patterns of gene expression involved in defence and stress tolerance. Pokeweed provides insight into the defense mechanisms of plants beyond those observed in research models and crops, and further study may yield novel approaches to improving the resilience of plants to environmental changes. Our assembled pokeweed genome is the first within the taxonomic family Phytolaccaceae to be publicly available for continued research.
PMID: 39179987
Plant Mol Biol , IF:4.076 , 2024 Aug , V114 (5) : P93 doi: 10.1007/s11103-024-01493-2
Decoding the plant clock: a review of mathematical models for the circadian regulatory network.
Department of Biological Sciences and Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar, Gujarat, India.; Department of Biological Sciences and Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar, Gujarat, India. ashutosh.s@iitgn.ac.in.
Most organisms have evolved specific mechanisms to respond to changes in environmental conditions such as light and temperature over the course of day. These periodic changes in the physiology and behaviour of organisms, referred to as circadian rhythms, are a consequence of intricate molecular mechanisms in the form of transcription and translational feedback loops. The plant circadian regulatory network is a complex web of interconnected feedback loops involving various transcription factors such as CCA1, LHY, PRRs, TOC1, LUX, ELF3, ELF4, RVE8, and more. This network enables plants to adapt and thrive in diverse environmental conditions. It responds to entrainment signals, including light, temperature, and nutrient concentrations and interacts with most of the physiological functions such as flowering, growth and stress response. Mathematical modelling of these gene regulatory networks enables a deeper understanding of not only the function but also the perturbations that may affect the plant growth and function with changing climate. Over the years, numerous mathematical models have been developed to understand the diverse aspects of plant circadian regulation. In this review, we have delved into the systematic development of these models, outlining the model components and refinements over time. We have also highlighted strengths and limitations of each of the models developed so far. Finally, we conclude the review by describing the prospects for investigation and advancement of these models for better understanding of plant circadian regulation.
PMID: 39207587
Phytopathology , IF:4.025 , 2024 Aug , V114 (8) : P1742-1752 doi: 10.1094/PHYTO-02-24-0054-KC
From Microbes to Microbiomes: Applications for Plant Health and Sustainable Agriculture.
International Alliance for Phytobiomes Research, Eau Claire, WI 54701, U.S.A.; Department of Plant Pathology, Entomology and Microbiology, Iowa State University, Ames, IA 50014, U.S.A.; Food Futures Institute, Murdoch University, Murdoch, Western Australia 6150, Australia.; Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN 37830, U.S.A.; Mosaic Biosciences, Plant City, FL 33567, U.S.A.; Bioresources Unit, AIT Austrian Institute of Technology, 3430 Tulln, Austria.; Trace Genomics, Ames, IA 50010, U.S.A.; Eversole Associates, Arlington, MA 02476, U.S.A.
Plant-microbe interaction research has had a transformative trajectory, from individual microbial isolate studies to comprehensive analyses of plant microbiomes within the broader phytobiome framework. Acknowledging the indispensable role of plant microbiomes in shaping plant health, agriculture, and ecosystem resilience, we underscore the urgent need for sustainable crop production strategies in the face of contemporary challenges. We discuss how the synergies between advancements in 'omics technologies and artificial intelligence can help advance the profound potential of plant microbiomes. Furthermore, we propose a multifaceted approach encompassing translational considerations, transdisciplinary research initiatives, public-private partnerships, regulatory policy development, and pragmatic expectations for the practical application of plant microbiome knowledge across diverse agricultural landscapes. We advocate for strategic collaboration and intentional transdisciplinary efforts to unlock the benefits offered by plant microbiomes and address pressing global issues in food security. By emphasizing a nuanced understanding of plant microbiome complexities and fostering realistic expectations, we encourage the scientific community to navigate the transformative journey from discoveries in the laboratory to field applications. As companies specializing in agricultural microbes and microbiomes undergo shifts, we highlight the necessity of understanding how to approach sustainable agriculture with site-specific management solutions. While cautioning against overpromising, we underscore the excitement of exploring the many impacts of microbiome-plant interactions. We emphasize the importance of collaborative endeavors with societal partners to accelerate our collective capacity to harness the diverse and yet-to-be-discovered beneficial activities of plant microbiomes.
PMID: 38776137
Am J Bot , IF:3.844 , 2024 Aug : Pe16381 doi: 10.1002/ajb2.16381
Phylogenetic systematics of Vigna sensu stricto in the context of Physostigma and allies.
Department of Biology, Utah Valley University, Orem, 84058, UT, USA.; Department of Plant Sciences, Section of Crop and Ecosystem Sciences, University of California, Davis, CA, USA.; DIADE, IRD, Univ Montpellier, Montpellier, France.; Institute of Decision Science for a Sustainable Society, Kyushu University, Fukuoka, Japan.; Kyushu University Museum, Kyushu University, Fukuoka, Japan.; Departamento de Botanica, Instituto de Biologia, Universidad Nacional Autonoma de Mexico, Apartado postal 70-233, CDMX, 04510, Mexico.; Systematic Biology, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Norbyvagen 18D, Uppsala, SE-75236, Sweden.; Liggins Institute, University of Auckland, New Zealand.
PREMISE: Vigna includes economically vital crops and wild species. Molecular systematic studies of Vigna species resulted in generic segregates of many New World (NW) species. However, limited Old World (OW) sampling left questions regarding inter- and intraspecific relationships in Vigna s.s. METHODS: African species, including the putative sister genus Physostigma, were comprehensively sampled within the context of NW relatives. Maximum likelihood and Bayesian inference analyses of the chloroplast matK-trnK and nuclear ribosomal ITS/5.8 S (ITS) DNA regions were undertaken to resolve OW Vigna taxonomic questions. Divergence dates were estimated using BEAST to date key nodes in the phylogeny. RESULTS: Analyses of matK and ITS data supported five clades of Vigna s.s.: subg. Lasiospron, a reduced subg. Vigna, subg. Haydonia, subg. Ceratotropis, an enlarged subg. Plectrotropis, and a clade including V. kirkii and V. stenophylla. Genome size estimates of 601 Mb for V. kirkii are near the overall mean of the genus, whereas V. stenophylla had a larger genome (810 Mb), similar to some Vigna subg. Ceratotropis or Plectrotropis species. CONCLUSIONS: Former subg. Vigna is reduced to yellow- and blue-flowered species and subg. Plectrotropis is enlarged to mostly all white-, pink-, and purple-flowered species. The age of the split between NW and OW Vigna lineages is ~6-7 Myr. Genome size estimates cannot rule out a polyploid or hybrid origin for V. stenophylla, potentially involving extinct lineage ancestors of Vigna subg. Ceratotropis or Plectrotropis, as indicated by network and phylogenetic analyses. Taxonomic revisions are suggested based on these results.
PMID: 39107933
Insect Mol Biol , IF:3.585 , 2024 Aug , V33 (4) : P387-404 doi: 10.1111/imb.12908
Polygenic adaptation of a cosmopolitan pest to a novel thermal environment.
State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China.; Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, China.; Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China.; Institute of Plant Protection Fujian Academy of Agricultural Sciences, Fuzhou, China.; BGI Research, Sanya, China.; Department of Biological Sciences, Brock University, St. Catharines, Ontario, Canada.
The fluctuation in temperature poses a significant challenge for poikilothermic organisms, notably insects, particularly in the context of changing climatic conditions. In insects, temperature adaptation has been driven by polygenes. In addition to genes that directly affect traits (core genes), other genes (peripheral genes) may also play a role in insect temperature adaptation. This study focuses on two peripheral genes, the GRIP and coiled-coil domain containing 2 (GCC2) and karyopherin subunit beta 1 (KPNB1). These genes are differentially expressed at different temperatures in the cosmopolitan pest, Plutella xylostella. GCC2 and KPNB1 in P. xylostella were cloned, and their relative expression patterns were identified. Reduced capacity for thermal adaptation (development, reproduction and response to temperature extremes) in the GCC2-deficient and KPNB1-deficient P. xylostella strains, which were constructed by CRISPR/Cas9 technique. Deletion of the PxGCC2 or PxKPNB1 genes in P. xylostella also had a differential effect on gene expression for many traits including stress resistance, resistance to pesticides, involved in immunity, trehalose metabolism, fatty acid metabolism and so forth. The ability of the moth to adapt to temperature via different pathways is likely to be key to its ability to remain an important pest species under predicted climate change conditions.
PMID: 38488345
Photosynth Res , IF:3.573 , 2024 Sep , V161 (3) : P213-232 doi: 10.1007/s11120-024-01103-8
Chlamydomonas cells transition through distinct Fe nutrition stages within 48 h of transfer to Fe-free medium.
Department of Plant and Microbial Biology, University of California, Berkeley, CA, 99354, USA.; Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA.; Competence Network IBD, Hopfenstrasse 60, 24103, Kiel, Germany.; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, 94720, USA.; Plant Research Laboratory, Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA.; Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.; Department of Plant and Microbial Biology, University of California, Berkeley, CA, 99354, USA. sabeeha@berkeley.edu.; Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA. sabeeha@berkeley.edu.; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, 94720, USA. sabeeha@berkeley.edu.; Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA. sabeeha@berkeley.edu.; Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. sabeeha@berkeley.edu.
Low iron (Fe) bioavailability can limit the biosynthesis of Fe-containing proteins, which are especially abundant in photosynthetic organisms, thus negatively affecting global primary productivity. Understanding cellular coping mechanisms under Fe limitation is therefore of great interest. We surveyed the temporal responses of Chlamydomonas (Chlamydomonas reinhardtii) cells transitioning from an Fe-rich to an Fe-free medium to document their short and long-term adjustments. While slower growth, chlorosis and lower photosynthetic parameters are evident only after one or more days in Fe-free medium, the abundance of some transcripts, such as those for genes encoding transporters and enzymes involved in Fe assimilation, change within minutes, before changes in intracellular Fe content are noticeable, suggestive of a sensitive mechanism for sensing Fe. Promoter reporter constructs indicate a transcriptional component to this immediate primary response. With acetate provided as a source of reduced carbon, transcripts encoding respiratory components are maintained relative to transcripts encoding components of photosynthesis and tetrapyrrole biosynthesis, indicating metabolic prioritization of respiration over photosynthesis. In contrast to the loss of chlorophyll, carotenoid content is maintained under Fe limitation despite a decrease in the transcripts for carotenoid biosynthesis genes, indicating carotenoid stability. These changes occur more slowly, only after the intracellular Fe quota responds, indicating a phased response in Chlamydomonas, involving both primary and secondary responses during acclimation to poor Fe nutrition.
PMID: 39017982
Plant Commun , 2024 Aug , V5 (8) : P100978 doi: 10.1016/j.xplc.2024.100978
Single-cell network analysis reveals gene expression programs for Arabidopsis root development and metabolism.
MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Innovation Academy for Seed Design, Chinese Academy of Sciences, Hefei 230027, China.; MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Innovation Academy for Seed Design, Chinese Academy of Sciences, Hefei 230027, China; School of Data Science, University of Science and Technology of China, Hefei 230027, China. Electronic address: sma@ustc.edu.cn.
Single-cell RNA-sequencing datasets of Arabidopsis roots have been generated, but related comprehensive gene co-expression network analyses are lacking. We conducted a single-cell gene co-expression network analysis with publicly available scRNA-seq datasets of Arabidopsis roots using a SingleCellGGM algorithm. The analysis identified 149 gene co-expression modules, which we considered to be gene expression programs (GEPs). By examining their spatiotemporal expression, we identified GEPs specifically expressed in major root cell types along their developmental trajectories. These GEPs define gene programs regulating root cell development at different stages and are enriched with relevant developmental regulators. As examples, a GEP specific for the quiescent center (QC) contains 20 genes regulating QC and stem cell niche homeostasis, and four GEPs are expressed in sieve elements (SEs) from early to late developmental stages, with the early-stage GEP containing 17 known SE developmental regulators. We also identified GEPs for metabolic pathways with cell-type-specific expression, suggesting the existence of cell-type-specific metabolism in roots. Using the GEPs, we discovered and verified a columella-specific gene, NRL27, as a regulator of the auxin-related root gravitropism response. Our analysis thus systematically reveals GEPs that regulate Arabidopsis root development and metabolism and provides ample resources for root biology studies.
PMID: 38783601