Dear Editor,Lotus(Nelumbo nucifera Gaertn.),which has been domesticated and cultivated for several thousands of years and endowed with religious and cultural symbolism[1],belongs to the Nelumbo genus Nelumbonaceae fam...Dear Editor,Lotus(Nelumbo nucifera Gaertn.),which has been domesticated and cultivated for several thousands of years and endowed with religious and cultural symbolism[1],belongs to the Nelumbo genus Nelumbonaceae family.As an early eudicot,it is not only essential for plant phylogeny but also widely used as a vegetable,a medic-inal herb,and for ornamental use.It contains abundant func-tional compounds,such as f lavonoids and benzylisoquinoline alkaloids(BIAs),which are used to treat diverse diseases.展开更多
Heterosis and polyploidy have an overwhelming influence on plant evolution.Recently,polyploid rice hybrids have been used to breed new rice varieties because they combine the advantages of both heterosis and polyploid...Heterosis and polyploidy have an overwhelming influence on plant evolution.Recently,polyploid rice hybrids have been used to breed new rice varieties because they combine the advantages of both heterosis and polyploidy.In this study,we generated six rice lines:autotetraploid rice hybrids and their autotetraploid parents,diploid donors,and hybrids of the diploid donors.To investigate the molecular mechanism controlling the effects of both hybridization and polyploidization,we performed bisulfite and RNA sequencing on young panicles at the pollen meiosis stage to compare the DNA metabolomes and transcriptomes among the six rice lines.The hybrids lines were hypermethylated compared to their corresponding parents and the autotetraploid lines showed globally increased DNA methylation of their transposable elements compared to the diploid donors.The alteration in DNA methylation level corresponded to the differential gene expressions among the rice genotypes,suggesting that methylation changes induced by polyploidization and hybridization may affect gene expression.Groups of gene candidates were identified that may be associated with heterosis and polyploidy.Our results provide DNA information that can be used to investigate epigenetic modification during heterosis and polyploidy in rice.展开更多
Common buckwheat(Fagopyrum esculentum),a specialty crop in southwest China,is not only used as a supplement to primary grain crops but also to produce beverages,such as tea and wine.To fully exploit the products made ...Common buckwheat(Fagopyrum esculentum),a specialty crop in southwest China,is not only used as a supplement to primary grain crops but also to produce beverages,such as tea and wine.To fully exploit the products made from common buckwheat flower,ultra-performance liquid chromatography–electrospray ionization–tandem mass spectrometry(UPLC–ESI–MS/MS)was conducted to analyze the metabolites in red-(‘Guihong 2’)and white-flowered(‘Fengtian 1’)buckwheat cultivars.A total of 784 metabolites were identified of which flavonoids were the largest group with 191 components,followed by organic acids and derivatives(126),and amino acids and derivatives(95).Besides,dozens of phenylpropanoids,nucleotides and derivates,lipids,alkaloids as well as several kinds of indole derivatives and sterides were detected.Among these rich varieties of metabolites,24 metabolites were only detected in the red flower that mainly included 8 anthocyanins and 6 flavones,while 22 metabolites were only detected in the white flower,which mainly contained 5 lipids,5 flavonoids,and 5 organic acids and derivatives.Our results enrich the metabolites’information of buckwheat and may be helpful for the exploitation of products from common buckwheat flowers.展开更多
Sacred lotus(Nelumbo nucifera)is a typical aquatic plant,belonging to basal eudicot plant,which is ideal for genome and genetic evolutionary study.Understanding lotus gene diversity is important for the study of molec...Sacred lotus(Nelumbo nucifera)is a typical aquatic plant,belonging to basal eudicot plant,which is ideal for genome and genetic evolutionary study.Understanding lotus gene diversity is important for the study of molecular genetics and breeding.In this research,public RNA-seq data and the annotated reference genome were used to identify the genes in lotus.A total of 26,819 consensus and 1,081 novel genes were identified.Meanwhile,a comprehensive analysis of gene alternative splicing events was conducted,and a total of 19,983“internal”alternative splicing(AS)events and 14,070“complete”AS events were detected in 5,878 and 5,881 multi-exon expression genes,respectively.Observations made from the AS events show the predominance of intron retention(IR)subtype of AS events representing 33%.IR is followed by alternative acceptor(AltA),alternative donor(AltD)and exon skipping(ES),highlighting the universality of the intron definition model in plants.In addition,functional annotations of the gene with AS indicated its relationship to a number of biological processes such as cellular process and metabolic process,showing the key role for alternative splicing in influencing the growth and development of lotus.The results contribute to a better understanding of the current gene diversity in lotus,and provide an abundant resource for future functional genome analysis in lotus.展开更多
Plant peptides play crucial roles in various biological processes, including stress responses. This study investigatesthe functions of plant peptides in response to different adversity stresses, focusing on drought, s...Plant peptides play crucial roles in various biological processes, including stress responses. This study investigatesthe functions of plant peptides in response to different adversity stresses, focusing on drought, salt, high temperature,and other environmental challenges. In drought conditions, specific peptides such as CLE25 and CLE9 were foundto regulate stomatal closure and root architecture to enhance the efficiency of water utilization. Salt stress inducesthe expression of CAPE1 and CEP3, which are involved in ion homeostasis and osmoregulation, thereby contributingto salt tolerance in plants. Heat stress triggers the expression of peptides such as CEL45, which contributes to the heattolerance of cells. Besides, we have also verified a new class of non-conventional peptides, and a large numberof non-conventional peptides have been identified in rice seedlings. Understanding the origin and functions of thesepeptides presents both challenges and opportunities for developing stress-resistant crops. Future research shouldfocus on elucidating the precise molecular mechanisms of peptide-mediated stress responses and exploring theirpotential applications in agriculture and biotechnology.展开更多
Sacred lotus(Nelumbo nucifera or lotus) is an important aquatic plant in horticulture and ecosystems. As a foundation for exploring genomic variation and evolution among different germplasms, we re-sequenced 19 indivi...Sacred lotus(Nelumbo nucifera or lotus) is an important aquatic plant in horticulture and ecosystems. As a foundation for exploring genomic variation and evolution among different germplasms, we re-sequenced 19 individuals from three cultivated temperate lotus subgroups(rhizome,seed and flower lotus), one wild temperate lotus subgroup(wild lotus), one tropical lotus group(Thai lotus) and an outgroup(Nelumbo lutea). Through genetic diversity and polymorphism analysis by non-missing SNP sites widely distributed in the whole genome, we confirmed that wild and Thai lotus exhibited greater differentiation with a higher genomic diversity compared to cultivated lotus. Rhizome lotus had the lowest genomic diversity and a closer relationship to wild lotus, whereas the genomes of seed and flower lotus were admixed. Genes in energy metabolism process and plant immunity evolved rapidly in lotus, reflecting local adaptation.We established that candidate genes in genomic regions with significant differentiation associated with temperate and tropical lotus divergence always exhibited highly divergent expression pattern. Together, this study comprehensive and credible interpretates important patterns of genetic diversity and relationships, gene evolution, and genomic signature from ecotypic differentiation of sacred lotus.展开更多
Water absorption is a prerequisite for seed germination. During imbibition, water influx causes the resumption of many physiological and metabolic processes in growing seed. In order to obtain more complete knowledge ...Water absorption is a prerequisite for seed germination. During imbibition, water influx causes the resumption of many physiological and metabolic processes in growing seed. In order to obtain more complete knowledge about the mechanism of seed germination, two-dimensional gel electrophoresis was applied to investigate the protein profile changes of rice seed during the first 48 h of imbibition. Thirty- nine differentially expressed proteins were identified, including 19 down-regulated and 20 up-regulated proteins. Storage proteins and some seed development- and desiccation-associated proteins were down regulated. The changed patterns of these proteins indicated extensive mobilization of seed reserves. By contrast, catabolism-associated proteins were up regulated upon imbibition. Semi-quantitative real time polymerase chain reaction analysis showed that most of the genes encoding the down- or up- regulated proteins were also down or up regulated at mRNA level. The expression of these genes was largely consistent at mRNA and protein levels. In providing additional information concerning gene regulation in early plant life, this study will facilitate understanding of the molecular mechanisms of seed germination.展开更多
Liangyoupeijiu is a two-parental-line, and Shanyou63 is a three-parental-line hybrid rice （Oryza sativa L.）. Although both belong to the indica subspecies, they have obvious differences with respect to morphology, p...Liangyoupeijiu is a two-parental-line, and Shanyou63 is a three-parental-line hybrid rice （Oryza sativa L.）. Although both belong to the indica subspecies, they have obvious differences with respect to morphology, physiology and grain quality. Variations in endosperm protein compositions were studied by comparing the 2-D electrophoresis （2-DE） maps for these two cultivars of hybrid rice. After matrix-assisted laser desorption/ionization time of flight mass spectrometry （MALDI-TOF/MS） analysis, a 21-kDa precursor of 19- kDa globulin was identified as the major storage protein for both cultivars. Some isoforms of peroxiredoxin and seed maturation protein were found to only exist in Shanyou63, whereas aldose reductase and starch granule-bound starch synthase were only detected in Liangyoupeijiu. These data might provide a foundation for further comparative studies of these two cultivars of hybrid rice.展开更多
Transcriptome analysis based on high-throughput sequencing of a cDNA library has been widely applied to functional genomic studies.However,the cDNA dependence of most RNA sequencing techniques constrains their ability...Transcriptome analysis based on high-throughput sequencing of a cDNA library has been widely applied to functional genomic studies.However,the cDNA dependence of most RNA sequencing techniques constrains their ability to detect base modifications on RNA,which is an important element for the post-transcriptional regulation of gene expression.To comprehensively profile the N^(6)-methyladenosine(m^(6)A)and N^(5)-methylcytosine(m5 C)modifications on RNA,direct RNA sequencing(DRS)using the latest Oxford Nanopore Technology was applied to analyze the transcriptome of six tissues in rice.Approximately 94 million reads were generated,with an average length ranging from 619 nt to 1013 nt,and a total of 45,707 transcripts across 34,763 genes were detected.Expression profiles of transcripts at the isoform level were quantified among tissues.Transcriptome-wide mapping of m^(6)A and m5 C demonstrated that both modifications exhibited tissue-specific characteristics.The transcripts with m^(6)A modifications tended to be modified by m5 C,and the transcripts with modifications presented higher expression levels along with shorter poly(A)tails than transcripts without modifications,suggesting the complexity of gene expression regulation.Gene Ontology analysis demonstrated that m^(6)A-and m5 C-modified transcripts were involved in central metabolic pathways related to the life cycle,with modifications on the target genes selected in a tissue-specific manner.Furthermore,most modified sites were located within quantitative trait loci that control important agronomic traits,highlighting the value of cloning functional loci.The results provide new insights into the expression regulation complexity and data resource of the transcriptome and epitranscriptome,improving our understanding of the rice genome.展开更多
Consumption of arsenic contaminated water and cereals is a serious threat to humans all over the world. Rice （Oryza sativa ＂Nipponbare＂）, as a main cereal crop, can accumulate arsenic more than 10-fold that of in ...Consumption of arsenic contaminated water and cereals is a serious threat to humans all over the world. Rice （Oryza sativa ＂Nipponbare＂）, as a main cereal crop, can accumulate arsenic more than 10-fold that of in other cereals. To gain a comprehensive understanding of the response of rice subjected to 100 μM arsenate stress, a comparative proteomic analysis of rice shoots in combination with morphological and biochemical investigations have been performed in this study. The results demonstrated that arsenate suppressed the growth of rice seedlings, destroyed the cellular ultra-structure and changed the homeostasis of reactive oxygen species. Moreover, a total of 38 differentially displayed proteins, which were mainly involved in metabolism, redox and protein-metabolism, were identified. The data suggest the arsenic can inhibit rice growth through negatively affecting chloroplast structure and photosynthesis. In addition, upregulation of the proteins involved in redox and protein metabolism might help the rice to be resistant or tolerant to arsenic toxicity. In general, this study improves our understanding about the rice arsenic responsive mechanism.展开更多
基金This work was supported by the National Natural Science Foundation of China(NSFC no.32102422).
文摘Dear Editor,Lotus(Nelumbo nucifera Gaertn.),which has been domesticated and cultivated for several thousands of years and endowed with religious and cultural symbolism[1],belongs to the Nelumbo genus Nelumbonaceae family.As an early eudicot,it is not only essential for plant phylogeny but also widely used as a vegetable,a medic-inal herb,and for ornamental use.It contains abundant func-tional compounds,such as f lavonoids and benzylisoquinoline alkaloids(BIAs),which are used to treat diverse diseases.
基金supported by the Key Research and Development Program of Hubei Province(2020BBA032)the Wuhan Science and Technology Major Project “Development and application of polyploid rice”,the Open Research Fund of State Key Laboratory of Hybrid Rice(Hunan Hybrid Rice Research Center)(19KF06)the Youth Grant of Hubei University.
文摘Heterosis and polyploidy have an overwhelming influence on plant evolution.Recently,polyploid rice hybrids have been used to breed new rice varieties because they combine the advantages of both heterosis and polyploidy.In this study,we generated six rice lines:autotetraploid rice hybrids and their autotetraploid parents,diploid donors,and hybrids of the diploid donors.To investigate the molecular mechanism controlling the effects of both hybridization and polyploidization,we performed bisulfite and RNA sequencing on young panicles at the pollen meiosis stage to compare the DNA metabolomes and transcriptomes among the six rice lines.The hybrids lines were hypermethylated compared to their corresponding parents and the autotetraploid lines showed globally increased DNA methylation of their transposable elements compared to the diploid donors.The alteration in DNA methylation level corresponded to the differential gene expressions among the rice genotypes,suggesting that methylation changes induced by polyploidization and hybridization may affect gene expression.Groups of gene candidates were identified that may be associated with heterosis and polyploidy.Our results provide DNA information that can be used to investigate epigenetic modification during heterosis and polyploidy in rice.
基金This work was funded by the National Natural Science Foundation of China-Project of Karst Science Research Center of Guizhou Provincial People’s Government(U1812401)the Science and Technology Foundation of Guizhou Province(QianKeHeJiChu[2020]1Y095)+3 种基金Guizhou provincial department of education youth science and technology talent growth project(Qianjiaohe KY Zi[2018]128)the National Natural Science Foundation of China(31701494,31760419)the Initial Fund for Doctor Research in Guizhou Normal University(11904/0516026)the Earmarked Fund for construction of the Key Laboratory for Conservation and Innovation of Buckwheat Germplasm in Guizhou(QianJiaoHe KY Zi[2017]002).
文摘Common buckwheat(Fagopyrum esculentum),a specialty crop in southwest China,is not only used as a supplement to primary grain crops but also to produce beverages,such as tea and wine.To fully exploit the products made from common buckwheat flower,ultra-performance liquid chromatography–electrospray ionization–tandem mass spectrometry(UPLC–ESI–MS/MS)was conducted to analyze the metabolites in red-(‘Guihong 2’)and white-flowered(‘Fengtian 1’)buckwheat cultivars.A total of 784 metabolites were identified of which flavonoids were the largest group with 191 components,followed by organic acids and derivatives(126),and amino acids and derivatives(95).Besides,dozens of phenylpropanoids,nucleotides and derivates,lipids,alkaloids as well as several kinds of indole derivatives and sterides were detected.Among these rich varieties of metabolites,24 metabolites were only detected in the red flower that mainly included 8 anthocyanins and 6 flavones,while 22 metabolites were only detected in the white flower,which mainly contained 5 lipids,5 flavonoids,and 5 organic acids and derivatives.Our results enrich the metabolites’information of buckwheat and may be helpful for the exploitation of products from common buckwheat flowers.
文摘Sacred lotus(Nelumbo nucifera)is a typical aquatic plant,belonging to basal eudicot plant,which is ideal for genome and genetic evolutionary study.Understanding lotus gene diversity is important for the study of molecular genetics and breeding.In this research,public RNA-seq data and the annotated reference genome were used to identify the genes in lotus.A total of 26,819 consensus and 1,081 novel genes were identified.Meanwhile,a comprehensive analysis of gene alternative splicing events was conducted,and a total of 19,983“internal”alternative splicing(AS)events and 14,070“complete”AS events were detected in 5,878 and 5,881 multi-exon expression genes,respectively.Observations made from the AS events show the predominance of intron retention(IR)subtype of AS events representing 33%.IR is followed by alternative acceptor(AltA),alternative donor(AltD)and exon skipping(ES),highlighting the universality of the intron definition model in plants.In addition,functional annotations of the gene with AS indicated its relationship to a number of biological processes such as cellular process and metabolic process,showing the key role for alternative splicing in influencing the growth and development of lotus.The results contribute to a better understanding of the current gene diversity in lotus,and provide an abundant resource for future functional genome analysis in lotus.
基金supported by Hubei Provincial Natural Science Foundation of China(202310701201614).
文摘Plant peptides play crucial roles in various biological processes, including stress responses. This study investigatesthe functions of plant peptides in response to different adversity stresses, focusing on drought, salt, high temperature,and other environmental challenges. In drought conditions, specific peptides such as CLE25 and CLE9 were foundto regulate stomatal closure and root architecture to enhance the efficiency of water utilization. Salt stress inducesthe expression of CAPE1 and CEP3, which are involved in ion homeostasis and osmoregulation, thereby contributingto salt tolerance in plants. Heat stress triggers the expression of peptides such as CEL45, which contributes to the heattolerance of cells. Besides, we have also verified a new class of non-conventional peptides, and a large numberof non-conventional peptides have been identified in rice seedlings. Understanding the origin and functions of thesepeptides presents both challenges and opportunities for developing stress-resistant crops. Future research shouldfocus on elucidating the precise molecular mechanisms of peptide-mediated stress responses and exploring theirpotential applications in agriculture and biotechnology.
基金financially supported by National Natural Science Foundation of China (No. 31471899)the Knowledge Innovation Project of the Chinese Academy of Sciences (No. Y455421Z02)
文摘Sacred lotus(Nelumbo nucifera or lotus) is an important aquatic plant in horticulture and ecosystems. As a foundation for exploring genomic variation and evolution among different germplasms, we re-sequenced 19 individuals from three cultivated temperate lotus subgroups(rhizome,seed and flower lotus), one wild temperate lotus subgroup(wild lotus), one tropical lotus group(Thai lotus) and an outgroup(Nelumbo lutea). Through genetic diversity and polymorphism analysis by non-missing SNP sites widely distributed in the whole genome, we confirmed that wild and Thai lotus exhibited greater differentiation with a higher genomic diversity compared to cultivated lotus. Rhizome lotus had the lowest genomic diversity and a closer relationship to wild lotus, whereas the genomes of seed and flower lotus were admixed. Genes in energy metabolism process and plant immunity evolved rapidly in lotus, reflecting local adaptation.We established that candidate genes in genomic regions with significant differentiation associated with temperate and tropical lotus divergence always exhibited highly divergent expression pattern. Together, this study comprehensive and credible interpretates important patterns of genetic diversity and relationships, gene evolution, and genomic signature from ecotypic differentiation of sacred lotus.
基金supported by the 100 Talents Program of the Chinese Academy of Sciences
文摘Water absorption is a prerequisite for seed germination. During imbibition, water influx causes the resumption of many physiological and metabolic processes in growing seed. In order to obtain more complete knowledge about the mechanism of seed germination, two-dimensional gel electrophoresis was applied to investigate the protein profile changes of rice seed during the first 48 h of imbibition. Thirty- nine differentially expressed proteins were identified, including 19 down-regulated and 20 up-regulated proteins. Storage proteins and some seed development- and desiccation-associated proteins were down regulated. The changed patterns of these proteins indicated extensive mobilization of seed reserves. By contrast, catabolism-associated proteins were up regulated upon imbibition. Semi-quantitative real time polymerase chain reaction analysis showed that most of the genes encoding the down- or up- regulated proteins were also down or up regulated at mRNA level. The expression of these genes was largely consistent at mRNA and protein levels. In providing additional information concerning gene regulation in early plant life, this study will facilitate understanding of the molecular mechanisms of seed germination.
文摘Liangyoupeijiu is a two-parental-line, and Shanyou63 is a three-parental-line hybrid rice （Oryza sativa L.）. Although both belong to the indica subspecies, they have obvious differences with respect to morphology, physiology and grain quality. Variations in endosperm protein compositions were studied by comparing the 2-D electrophoresis （2-DE） maps for these two cultivars of hybrid rice. After matrix-assisted laser desorption/ionization time of flight mass spectrometry （MALDI-TOF/MS） analysis, a 21-kDa precursor of 19- kDa globulin was identified as the major storage protein for both cultivars. Some isoforms of peroxiredoxin and seed maturation protein were found to only exist in Shanyou63, whereas aldose reductase and starch granule-bound starch synthase were only detected in Liangyoupeijiu. These data might provide a foundation for further comparative studies of these two cultivars of hybrid rice.
基金supported by the National Natural Science Foundation of China(Grant No.31671775).
文摘Transcriptome analysis based on high-throughput sequencing of a cDNA library has been widely applied to functional genomic studies.However,the cDNA dependence of most RNA sequencing techniques constrains their ability to detect base modifications on RNA,which is an important element for the post-transcriptional regulation of gene expression.To comprehensively profile the N^(6)-methyladenosine(m^(6)A)and N^(5)-methylcytosine(m5 C)modifications on RNA,direct RNA sequencing(DRS)using the latest Oxford Nanopore Technology was applied to analyze the transcriptome of six tissues in rice.Approximately 94 million reads were generated,with an average length ranging from 619 nt to 1013 nt,and a total of 45,707 transcripts across 34,763 genes were detected.Expression profiles of transcripts at the isoform level were quantified among tissues.Transcriptome-wide mapping of m^(6)A and m5 C demonstrated that both modifications exhibited tissue-specific characteristics.The transcripts with m^(6)A modifications tended to be modified by m5 C,and the transcripts with modifications presented higher expression levels along with shorter poly(A)tails than transcripts without modifications,suggesting the complexity of gene expression regulation.Gene Ontology analysis demonstrated that m^(6)A-and m5 C-modified transcripts were involved in central metabolic pathways related to the life cycle,with modifications on the target genes selected in a tissue-specific manner.Furthermore,most modified sites were located within quantitative trait loci that control important agronomic traits,highlighting the value of cloning functional loci.The results provide new insights into the expression regulation complexity and data resource of the transcriptome and epitranscriptome,improving our understanding of the rice genome.
基金supported by the 100 Talents Program of the Chinese Academy of Sciences
文摘Consumption of arsenic contaminated water and cereals is a serious threat to humans all over the world. Rice （Oryza sativa ＂Nipponbare＂）, as a main cereal crop, can accumulate arsenic more than 10-fold that of in other cereals. To gain a comprehensive understanding of the response of rice subjected to 100 μM arsenate stress, a comparative proteomic analysis of rice shoots in combination with morphological and biochemical investigations have been performed in this study. The results demonstrated that arsenate suppressed the growth of rice seedlings, destroyed the cellular ultra-structure and changed the homeostasis of reactive oxygen species. Moreover, a total of 38 differentially displayed proteins, which were mainly involved in metabolism, redox and protein-metabolism, were identified. The data suggest the arsenic can inhibit rice growth through negatively affecting chloroplast structure and photosynthesis. In addition, upregulation of the proteins involved in redox and protein metabolism might help the rice to be resistant or tolerant to arsenic toxicity. In general, this study improves our understanding about the rice arsenic responsive mechanism.
