Medicago polymorpha is a nutritious and palatable forage and vegetable plant that also fixes nitrogen.Here,we reveal the chromosome-scale genome sequence of M.polymorpha using an integrated approach including Illumina...Medicago polymorpha is a nutritious and palatable forage and vegetable plant that also fixes nitrogen.Here,we reveal the chromosome-scale genome sequence of M.polymorpha using an integrated approach including Illumina,PacBio and Hi-C technologies.We combined PacBio full-length RNA-seq,metabolomic analysis,structural anatomy analysis and related physiological indexes to elucidate the important agronomic traits of M.polymorpha for forage and vegetable usage.The assembled M.polymorpha genome consisted of 457.53Mb with a long scaffold N50 of 57.72Mb,and 92.92%(441.83Mb)of the assembly was assigned to seven pseudochromosomes.Comparative genomic analysis revealed that expansion and contraction of the photosynthesis and lignin biosynthetic gene families,respectively,led to enhancement of nutritious compounds and reduced lignin biosynthesis in M.polymorpha.In addition,we found that several positively selected nitrogen metabolism-related genes were responsible for crude protein biosynthesis.Notably,the metabolomic results revealed that a large number of flavonoids,vitamins,alkaloids,and terpenoids were enriched in M.polymorpha.These results imply that the decreased lignin content but relatively high nutrient content of M.polymorpha enhance its edibility and nutritional value as a forage and vegetable.Our genomic data provide a genetic basis that will accelerate functional genomic and breeding research on M.polymorpha as well as other Medicago and legume plants.展开更多
Autumn leaf senescence and coloration is a complex process and a striking natural phenomenon.Here,through biology approach integrating transcriptomic analyses in Ginkgo biloba,we determined that the content of chlorop...Autumn leaf senescence and coloration is a complex process and a striking natural phenomenon.Here,through biology approach integrating transcriptomic analyses in Ginkgo biloba,we determined that the content of chlorophyll decreased during leaf senescence,while carotenoid components increased until late October in the turning stage(TS)and then decreased in the yellow leaf stage(YS).Simultaneously,chlorophyll biosynthesis genes exhibited significantly lower expression levels while chlorophyll degradation genes showed increased expression from the green leaf stage(GS)to YS.However,carotenoid biosynthesis-related genes showed enhanced expression,especially in TS.An analysis of the expression of genes related to senescence demonstrated that the expression levels of most abscisic acid-and jasmonic acid-related genes,autophagy,WRKY,and NAC genes increased,whereas cytoskeleton-,photosynthesis-,and antioxidation-related genes decreased from GS to YS.Furthermore,G.biloba seedlings exogenously treated with abscisic acid,jasmonic acid,or ultraviolet-B radiation all showed obvious color variation and senescence symptoms.We used these exogenously seedlings to further validate the function of several genes involved in chlorophyll biosynthesis and senescence.Taken together,these results contribute to the elucidation of the molecular mechanisms of leaf coloration and senescence in G.biloba as well as in the identification of candidate genes involved in this process.展开更多
Jasminum sambac(jasmine flower),a world-renowned plant appreciated for its exceptional flower fragrance,is of cultural and economic importance.However,the genetic basis of its fragrance is largely unknown.Here,we pres...Jasminum sambac(jasmine flower),a world-renowned plant appreciated for its exceptional flower fragrance,is of cultural and economic importance.However,the genetic basis of its fragrance is largely unknown.Here,we present the first de novo genome assembly of J.sambac with 550.12 Mb(scaffold N50=40.10 Mb)assembled into 13 pseudochromosomes.Terpene synthase(TPS)genes associated with flower fragrance are considerably amplified in the form of gene clusters through tandem duplications in the genome.Gene clusters within the salicylic acid/benzoic acid/theobromine(SABATH)and benzylalcohol O-acetyltransferase/anthocyanin O-hydroxycinnamoyltransferases/anthranilate N-hydroxycinnamoyl/benzoyltransferase/deacetylvindoline 4-O-acetyltransferase(BAHD)superfamilies were identified to be related to the biosynthesis of phenylpropanoid/benzenoid compounds.Several key genes involved in jasmonate biosynthesis were duplicated,causing an increase in copy numbers.In addition,multi-omics analyses identified various aromatic compounds and many genes involved in fragrance biosynthesis pathways.Furthermore,the roles of JsTPS3 in b-ocimene biosynthesis,as well as JsAOC1 and JsAOS in jasmonic acid biosynthesis,were functionally validated.The genome assembled in this study for J.sambac offers a basic genetic resource for studying floral scent and jasmonate biosynthesis,and provides a foundation for functional genomic research and variety improvements in Jasminum.展开更多
基金the Graduate Student Innovation Foundation of Jiangsu Province(No.KYCX20_2992).
文摘Medicago polymorpha is a nutritious and palatable forage and vegetable plant that also fixes nitrogen.Here,we reveal the chromosome-scale genome sequence of M.polymorpha using an integrated approach including Illumina,PacBio and Hi-C technologies.We combined PacBio full-length RNA-seq,metabolomic analysis,structural anatomy analysis and related physiological indexes to elucidate the important agronomic traits of M.polymorpha for forage and vegetable usage.The assembled M.polymorpha genome consisted of 457.53Mb with a long scaffold N50 of 57.72Mb,and 92.92%(441.83Mb)of the assembly was assigned to seven pseudochromosomes.Comparative genomic analysis revealed that expansion and contraction of the photosynthesis and lignin biosynthetic gene families,respectively,led to enhancement of nutritious compounds and reduced lignin biosynthesis in M.polymorpha.In addition,we found that several positively selected nitrogen metabolism-related genes were responsible for crude protein biosynthesis.Notably,the metabolomic results revealed that a large number of flavonoids,vitamins,alkaloids,and terpenoids were enriched in M.polymorpha.These results imply that the decreased lignin content but relatively high nutrient content of M.polymorpha enhance its edibility and nutritional value as a forage and vegetable.Our genomic data provide a genetic basis that will accelerate functional genomic and breeding research on M.polymorpha as well as other Medicago and legume plants.
基金This work was supported financially by National Key R&D Program of China(Grant No.2017YFD0600701)Natural Science Foundation of China(Grant No.31670181)+1 种基金Six talent peaks project in Jiangsu Province(Grant No.NY-090)Qing Lan Project of Jiangsu Province。
文摘Autumn leaf senescence and coloration is a complex process and a striking natural phenomenon.Here,through biology approach integrating transcriptomic analyses in Ginkgo biloba,we determined that the content of chlorophyll decreased during leaf senescence,while carotenoid components increased until late October in the turning stage(TS)and then decreased in the yellow leaf stage(YS).Simultaneously,chlorophyll biosynthesis genes exhibited significantly lower expression levels while chlorophyll degradation genes showed increased expression from the green leaf stage(GS)to YS.However,carotenoid biosynthesis-related genes showed enhanced expression,especially in TS.An analysis of the expression of genes related to senescence demonstrated that the expression levels of most abscisic acid-and jasmonic acid-related genes,autophagy,WRKY,and NAC genes increased,whereas cytoskeleton-,photosynthesis-,and antioxidation-related genes decreased from GS to YS.Furthermore,G.biloba seedlings exogenously treated with abscisic acid,jasmonic acid,or ultraviolet-B radiation all showed obvious color variation and senescence symptoms.We used these exogenously seedlings to further validate the function of several genes involved in chlorophyll biosynthesis and senescence.Taken together,these results contribute to the elucidation of the molecular mechanisms of leaf coloration and senescence in G.biloba as well as in the identification of candidate genes involved in this process.
基金We thank Novogene for genome sequencing and assembly.We thank Dr.Feng Cheng for his comments on our manuscript.This work was supported by the Elite Young Scientists Program of Chinese Academy of Agricultural Sciences(CAAS),the Agricultural Science and Technology Innovation Program in China and self-raised funds.
文摘Jasminum sambac(jasmine flower),a world-renowned plant appreciated for its exceptional flower fragrance,is of cultural and economic importance.However,the genetic basis of its fragrance is largely unknown.Here,we present the first de novo genome assembly of J.sambac with 550.12 Mb(scaffold N50=40.10 Mb)assembled into 13 pseudochromosomes.Terpene synthase(TPS)genes associated with flower fragrance are considerably amplified in the form of gene clusters through tandem duplications in the genome.Gene clusters within the salicylic acid/benzoic acid/theobromine(SABATH)and benzylalcohol O-acetyltransferase/anthocyanin O-hydroxycinnamoyltransferases/anthranilate N-hydroxycinnamoyl/benzoyltransferase/deacetylvindoline 4-O-acetyltransferase(BAHD)superfamilies were identified to be related to the biosynthesis of phenylpropanoid/benzenoid compounds.Several key genes involved in jasmonate biosynthesis were duplicated,causing an increase in copy numbers.In addition,multi-omics analyses identified various aromatic compounds and many genes involved in fragrance biosynthesis pathways.Furthermore,the roles of JsTPS3 in b-ocimene biosynthesis,as well as JsAOC1 and JsAOS in jasmonic acid biosynthesis,were functionally validated.The genome assembled in this study for J.sambac offers a basic genetic resource for studying floral scent and jasmonate biosynthesis,and provides a foundation for functional genomic research and variety improvements in Jasminum.
