Plants are capable of regulating their shoot architecture in response to diverse internal and external environments.The circadian clock is an adaptive mechanism that integrates information from internal and ambient co...Plants are capable of regulating their shoot architecture in response to diverse internal and external environments.The circadian clock is an adaptive mechanism that integrates information from internal and ambient conditions to help plants cope with recurring environmental fluctuations.Despite the current understanding of plant circadian clock and genetic framework underlying plant shoot architecture,the intricate connection between these two adaptive mechanisms remains largely unclear.In this study,we elucidated how the core clock gene LUX ARRHYTHMO(LUX)regulates shoot architecture in the model legume plant Medicago truncatula.We show that mtlux mutant displays increased main stem height,reduced lateral shoot length,and decreased the number of lateral branches and biomass yield.Gene expression analysis revealed that Mt LUX regulated shoot architecture by repressing the expression of strigolactone receptor MtD14 and MtTB1/MtTCP1A,a TCP gene that functions centrally in modulating shoot architecture.In vivo and in vitro experiments showed that Mt LUX directly binds to a cis-element in the promoter of MtTB1/MtTCP1A,suggesting that Mt LUX regulates branching by rhythmically suppressing MtTB1/MtTCP1A.This work demonstrates the regulatory effect of the circadian clock on shoot architecture,offering a new understanding underlying the genetic basis towards the flexibility of plant shoot architecture.展开更多
The R2R3-MYB genes make up one of the largest transcription factor families in plants, and play regulatory roles in various biological processes such as development, metabolism and defense response. Although genome-wi...The R2R3-MYB genes make up one of the largest transcription factor families in plants, and play regulatory roles in various biological processes such as development, metabolism and defense response. Although genome-wide analyses of this gene family have been conducted in several species, R2R3-MYB genes have not been systematically analyzed in Medicago truncatula, a sequenced model legume plant. Here, we performed a comprehensive, genome-wide computational analysis of the structural characteristics, phylogeny, functions and expression patterns of M. truncatula R2R3-MYB genes. DNA binding domains are highly conserved among the 155 putative MtR2R3-MYB proteins that we identified. Chromosomal location analysis revealed that these genes were distributed across all eight chromosomes. Results showed that the expansion of the MtR2R3-MYB family was mainly attributable to segmental duplication and tandem duplication. A comprehensive classification was performed based on phylogenetic analysis of the R2R3-MYB gene families in M. truncatula, Arabidopsis thaliana and other plant species. Evolutionary relationships within clades were supported by clade-specific conserved motifs outside the MYB domain. Species-specific clades have been gained or lost during evolution, resulting in functional divergence. Also, tissue-specific expression patterns were investigated. The functions of stress response-related clades were further verified by the changes in transcript levels of representative R2R3-MYB genes upon treatment with abiotic and biotic stresses. This study is the first report on identification and characterization of R2R3-MYB gene family based on the genome of M. truncatula, and will facilitate functional analysis of this gene family in the future.展开更多
Synonymous codon usage pattern presumably reflects gene expression optimization as a result of molecular evolution. Though much attention has been paid to various model organisms ranging from prokaryotes to eukaryotes...Synonymous codon usage pattern presumably reflects gene expression optimization as a result of molecular evolution. Though much attention has been paid to various model organisms ranging from prokaryotes to eukaryotes, codon usage has yet been extensively investigated for model legume Medicago truncatula. In present study, 39 531 available coding sequences （CDSs） from M. truncatula were examined for codon usage bias （CUB）. Based on analyses including neutrality plots, effective number of codons plots, and correlations between optimal codons frequency and codon adaptation index, we conclude that natural selection is a major driving force in M. truncatula CUB. We have identified 30 optimal codons encoding 18 amino acids based on relative synonymous codon usage. These optimal codons characteristically end with A or T, except for AGG and TTG encoding arginine and leucine respectively. Optimal codon usage is positively correlated with the GC content at three nucleotide positions of codons and the GC content of CDSs. The abundance of expressed sequence tag is a proxy for gene expression intensity in the legume, but has no relatedness with either CDS length or GC content. Collectively, we unravel the synonymous codon usage pattern in M. truncatula, which may serve as the valuable information on genetic engineering of the model legume and forage crop.展开更多
Phytosulfokine-α(PSK-α),a sulfated pentapeptide with the sequence YIYTQ,is encoded by a small precursor gene family in Arabidopsis.PSK-αregulates multiple growth and developmental processes as a novel peptide hormo...Phytosulfokine-α(PSK-α),a sulfated pentapeptide with the sequence YIYTQ,is encoded by a small precursor gene family in Arabidopsis.PSK-αregulates multiple growth and developmental processes as a novel peptide hormone.Despite its importance,functions of PSK-αin M.truncatula growth remains unknown.In this study,we identified five genes to encode PSK-αprecursors in M.truncatula.All of these precursors possess conserved PSK-αsignature motif.Expression pattern analysis of these MtPSK genes revealed that each gene was expressed in a tissue-specific or ubiquitous pattern and three of them were remarkably expressed in root.Treatment of M.truncatula seedlings with synthetic PSK-αpeptide significantly promoted root elongation.In addition,expression analysis of downstream genes by RNA-seq and qRT-PCR assays suggested that PSK-αsignaling might regulate cell wall structure via PMEI-PME module to promote root cell growth.Taken together,our results shed light on the mechanism by which PSK-αpromotes root growth in M.truncatula,providing a new resource for improvement of root growth in agriculture.展开更多
Root nodule symbiosis(RNs)between legumes and rhizobia is a major source of nitrogen in agricultural systems.Effective symbiosis requires precise regulation of plant defense responses.The role of the defense hormone j...Root nodule symbiosis(RNs)between legumes and rhizobia is a major source of nitrogen in agricultural systems.Effective symbiosis requires precise regulation of plant defense responses.The role of the defense hormone jasmonic acid(JA)in the immune response has been extensively studied.Current research shows that JA can play either a positive or negative regulatory role in RNS depending on its concentration,but the molecular mechanisms remain to be elucidated.In this study,we found that inoculation with the rhizobia Sm1021 induces the JA pathway in Medicago truncatula,and blocking the JA pathway significantly reduces the number of infection threads.Mutations in the MtMYc2 gene,which encodes a JA signaling master transcription factor,significantly inhibited rhizobia infection,terminal differentiation,and symbiotic cell formation.Combining RNA sequencing and chromatin immunoprecipitation sequencing,we discovered that MtMYc2 regulates the expression of nodule-specific MtDNF2,MtNAD1,and MtSymCRK to suppress host defense,while it activates MtDNF1 expression to regulate the maturation of MtNCRs,which in turn promotes bacteroid formation.More importantly,MtMYC2 participates in symbiotic signal transduction by promoting the expression of MtiPD3.Notably,the MtMYC2-MtiPD3 transcriptional regulatory module is specifically present in legumes,and the Mtmyc2 mutants are susceptible to the infection by the pathogen Rhizoctonia solani.Collectively,these findings reveal the molecular mechanisms of how the JA pathway regulates RNS,broadening our understanding of the roles of JA in plant-microbe interactions.展开更多
MicroRNAs(miRNAs)是一类内源性非编码小分子RNA,参与调控植物的生长发育、代谢和逆境响应等过程。本研究通过构建蒺藜苜蓿miR167c的海绵载体,探究miR167c及其靶基因对拟南芥生长发育的影响。靶基因预测结果显示,生长素响应因子6/8(Auxi...MicroRNAs(miRNAs)是一类内源性非编码小分子RNA,参与调控植物的生长发育、代谢和逆境响应等过程。本研究通过构建蒺藜苜蓿miR167c的海绵载体,探究miR167c及其靶基因对拟南芥生长发育的影响。靶基因预测结果显示,生长素响应因子6/8(Auxin response factor 6/8,ARF6/8)、类受体蛋白激酶家族蛋白(Receptor-like protein kinase-related family protein,RPK)和IAA-氨基酸水解酶(IAA-Alanine resistant 3,IAR3)基因为拟南芥miR167c的靶基因。实时荧光定量分析表明,转基因拟南芥植株中At-miR167c表达量较野生型显著降低,而上述4个靶基因的表达量显著上调。转基因拟南芥的花期提前,花序紧凑,花苞数量增多;莲座叶数量和鲜重显著增加;株高、分枝数和果荚数明显增加。研究结果为进一步解析miR167调控植物生长和花器官发育的分子机制提供了参考依据。展开更多
Medicago truncatula is a chosen model for legumes towards deciphering fundamental legume biology,especially symbiotic nitrogen fixation.Current genomic resources for M.truncatula include a completed whole genome seque...Medicago truncatula is a chosen model for legumes towards deciphering fundamental legume biology,especially symbiotic nitrogen fixation.Current genomic resources for M.truncatula include a completed whole genome sequence information for R108 and Jemalong A17 accessions along with the sparse draft genome sequences for other 226 M.truncatula accessions.These genomic resources are complemented by the availability of mutant resources such as retrotransposon(Tnt1)insertion mutants in R108 and fast neutron bombardment(FNB)mutants in A17.In addition,several M.truncatula databases such as small secreted peptides(SSPs)database,transporter protein database,gene expression atlas,proteomic atlas,and metabolite atlas are available to the research community.This review describes these resources and provide information regarding how to access these resources.展开更多
基金supported by Laboratory of Lingnan Modern Agriculture Project(NZ2021001)State Key Laboratory for Conservation and Utilization of Subtropical Agrobioresources(SKICUSA-a202007)Natural Science Foundation of Guangdong Province(2022A1515011027,2019A1515012009)。
文摘Plants are capable of regulating their shoot architecture in response to diverse internal and external environments.The circadian clock is an adaptive mechanism that integrates information from internal and ambient conditions to help plants cope with recurring environmental fluctuations.Despite the current understanding of plant circadian clock and genetic framework underlying plant shoot architecture,the intricate connection between these two adaptive mechanisms remains largely unclear.In this study,we elucidated how the core clock gene LUX ARRHYTHMO(LUX)regulates shoot architecture in the model legume plant Medicago truncatula.We show that mtlux mutant displays increased main stem height,reduced lateral shoot length,and decreased the number of lateral branches and biomass yield.Gene expression analysis revealed that Mt LUX regulated shoot architecture by repressing the expression of strigolactone receptor MtD14 and MtTB1/MtTCP1A,a TCP gene that functions centrally in modulating shoot architecture.In vivo and in vitro experiments showed that Mt LUX directly binds to a cis-element in the promoter of MtTB1/MtTCP1A,suggesting that Mt LUX regulates branching by rhythmically suppressing MtTB1/MtTCP1A.This work demonstrates the regulatory effect of the circadian clock on shoot architecture,offering a new understanding underlying the genetic basis towards the flexibility of plant shoot architecture.
基金supported by the National Natural Science Foundation of China(31372362)
文摘The R2R3-MYB genes make up one of the largest transcription factor families in plants, and play regulatory roles in various biological processes such as development, metabolism and defense response. Although genome-wide analyses of this gene family have been conducted in several species, R2R3-MYB genes have not been systematically analyzed in Medicago truncatula, a sequenced model legume plant. Here, we performed a comprehensive, genome-wide computational analysis of the structural characteristics, phylogeny, functions and expression patterns of M. truncatula R2R3-MYB genes. DNA binding domains are highly conserved among the 155 putative MtR2R3-MYB proteins that we identified. Chromosomal location analysis revealed that these genes were distributed across all eight chromosomes. Results showed that the expansion of the MtR2R3-MYB family was mainly attributable to segmental duplication and tandem duplication. A comprehensive classification was performed based on phylogenetic analysis of the R2R3-MYB gene families in M. truncatula, Arabidopsis thaliana and other plant species. Evolutionary relationships within clades were supported by clade-specific conserved motifs outside the MYB domain. Species-specific clades have been gained or lost during evolution, resulting in functional divergence. Also, tissue-specific expression patterns were investigated. The functions of stress response-related clades were further verified by the changes in transcript levels of representative R2R3-MYB genes upon treatment with abiotic and biotic stresses. This study is the first report on identification and characterization of R2R3-MYB gene family based on the genome of M. truncatula, and will facilitate functional analysis of this gene family in the future.
基金supported by the National Basic Research Program of China (2014CB138702)the National Natural Science Foundation of China (31502001)
文摘Synonymous codon usage pattern presumably reflects gene expression optimization as a result of molecular evolution. Though much attention has been paid to various model organisms ranging from prokaryotes to eukaryotes, codon usage has yet been extensively investigated for model legume Medicago truncatula. In present study, 39 531 available coding sequences （CDSs） from M. truncatula were examined for codon usage bias （CUB）. Based on analyses including neutrality plots, effective number of codons plots, and correlations between optimal codons frequency and codon adaptation index, we conclude that natural selection is a major driving force in M. truncatula CUB. We have identified 30 optimal codons encoding 18 amino acids based on relative synonymous codon usage. These optimal codons characteristically end with A or T, except for AGG and TTG encoding arginine and leucine respectively. Optimal codon usage is positively correlated with the GC content at three nucleotide positions of codons and the GC content of CDSs. The abundance of expressed sequence tag is a proxy for gene expression intensity in the legume, but has no relatedness with either CDS length or GC content. Collectively, we unravel the synonymous codon usage pattern in M. truncatula, which may serve as the valuable information on genetic engineering of the model legume and forage crop.
基金This work is supported by the National Natural Science Foundation of China(31500197).
文摘Phytosulfokine-α(PSK-α),a sulfated pentapeptide with the sequence YIYTQ,is encoded by a small precursor gene family in Arabidopsis.PSK-αregulates multiple growth and developmental processes as a novel peptide hormone.Despite its importance,functions of PSK-αin M.truncatula growth remains unknown.In this study,we identified five genes to encode PSK-αprecursors in M.truncatula.All of these precursors possess conserved PSK-αsignature motif.Expression pattern analysis of these MtPSK genes revealed that each gene was expressed in a tissue-specific or ubiquitous pattern and three of them were remarkably expressed in root.Treatment of M.truncatula seedlings with synthetic PSK-αpeptide significantly promoted root elongation.In addition,expression analysis of downstream genes by RNA-seq and qRT-PCR assays suggested that PSK-αsignaling might regulate cell wall structure via PMEI-PME module to promote root cell growth.Taken together,our results shed light on the mechanism by which PSK-αpromotes root growth in M.truncatula,providing a new resource for improvement of root growth in agriculture.
基金National Natural Science Foundation of China(32370253,and 32070272)the National Key Research Development Program of China(2022YFA0912100,and 2023YFF1001400).
文摘Root nodule symbiosis(RNs)between legumes and rhizobia is a major source of nitrogen in agricultural systems.Effective symbiosis requires precise regulation of plant defense responses.The role of the defense hormone jasmonic acid(JA)in the immune response has been extensively studied.Current research shows that JA can play either a positive or negative regulatory role in RNS depending on its concentration,but the molecular mechanisms remain to be elucidated.In this study,we found that inoculation with the rhizobia Sm1021 induces the JA pathway in Medicago truncatula,and blocking the JA pathway significantly reduces the number of infection threads.Mutations in the MtMYc2 gene,which encodes a JA signaling master transcription factor,significantly inhibited rhizobia infection,terminal differentiation,and symbiotic cell formation.Combining RNA sequencing and chromatin immunoprecipitation sequencing,we discovered that MtMYc2 regulates the expression of nodule-specific MtDNF2,MtNAD1,and MtSymCRK to suppress host defense,while it activates MtDNF1 expression to regulate the maturation of MtNCRs,which in turn promotes bacteroid formation.More importantly,MtMYC2 participates in symbiotic signal transduction by promoting the expression of MtiPD3.Notably,the MtMYC2-MtiPD3 transcriptional regulatory module is specifically present in legumes,and the Mtmyc2 mutants are susceptible to the infection by the pathogen Rhizoctonia solani.Collectively,these findings reveal the molecular mechanisms of how the JA pathway regulates RNS,broadening our understanding of the roles of JA in plant-microbe interactions.
文摘MicroRNAs(miRNAs)是一类内源性非编码小分子RNA,参与调控植物的生长发育、代谢和逆境响应等过程。本研究通过构建蒺藜苜蓿miR167c的海绵载体,探究miR167c及其靶基因对拟南芥生长发育的影响。靶基因预测结果显示,生长素响应因子6/8(Auxin response factor 6/8,ARF6/8)、类受体蛋白激酶家族蛋白(Receptor-like protein kinase-related family protein,RPK)和IAA-氨基酸水解酶(IAA-Alanine resistant 3,IAR3)基因为拟南芥miR167c的靶基因。实时荧光定量分析表明,转基因拟南芥植株中At-miR167c表达量较野生型显著降低,而上述4个靶基因的表达量显著上调。转基因拟南芥的花期提前,花序紧凑,花苞数量增多;莲座叶数量和鲜重显著增加;株高、分枝数和果荚数明显增加。研究结果为进一步解析miR167调控植物生长和花器官发育的分子机制提供了参考依据。
基金supported by the National Science Foundation USA,Plant Genome Program grants (DBI 0703285,IOS-1127155,and IOS-1733470)in part by Noble Research Institute,LLC.
文摘Medicago truncatula is a chosen model for legumes towards deciphering fundamental legume biology,especially symbiotic nitrogen fixation.Current genomic resources for M.truncatula include a completed whole genome sequence information for R108 and Jemalong A17 accessions along with the sparse draft genome sequences for other 226 M.truncatula accessions.These genomic resources are complemented by the availability of mutant resources such as retrotransposon(Tnt1)insertion mutants in R108 and fast neutron bombardment(FNB)mutants in A17.In addition,several M.truncatula databases such as small secreted peptides(SSPs)database,transporter protein database,gene expression atlas,proteomic atlas,and metabolite atlas are available to the research community.This review describes these resources and provide information regarding how to access these resources.
