Flavonoids,which are a diverse class of phytonutrients,are used by organisms to respond to nearly all abiotic stresses and are beneficial for human health.Glycosyltransferase,used during the last step of flavonoid bio...Flavonoids,which are a diverse class of phytonutrients,are used by organisms to respond to nearly all abiotic stresses and are beneficial for human health.Glycosyltransferase,used during the last step of flavonoid biosynthesis,is important in flavonoid enrichment.However,little is known about glycosyltransferase in the orchid Dendrobium catenatum(D.officinale).In this study,we isolated a novel C-glycosyltransferase(designated DcaCGT)from the orchid D.catenatum by identifying and analyzing 82 putative genes in the GT1 family.DcaCGT could specifically catalyze not only di-C-glycosylation but also O-glycosylation.Apart from the normal function of catalyzing 2-hydroxynaringenin and phloretin to the respective di-C-glycosides,DcaCGT also catalyzes apigenin to cosmosiin.Targeted metabolic profiling of the substrates(2-hydroxynaringenin,phloretin,and apigenin)and products(vitexin,isovitexin,vicenin-2,nothofagin,3’,5’-di-C-glucosylphloretin,and cosmosiin)in different tissues showed that vicenin-2 was the most abundant product of this novel enzyme.Cosmosiin was detected in flowers and flower buds.We also established that DcaCGT functions expanded throughout the evolution of D.catenatum.Residual OGT activity may help D.catenatum resist drought stress.Our study illustrates the function,origin,and differentiation of DcaCGT and provides insights into glycosylation and molecular propagation processes,which can be used to improve the production of flavonoids by the cultivated medicinal plant D.catenatum.展开更多
As one of the largest families of angiosperms,the Orchidaceae family is diverse.Dendrobium represents the second largest genus of the Orchidaceae.However,an assembled high-quality genome of species in this genus is la...As one of the largest families of angiosperms,the Orchidaceae family is diverse.Dendrobium represents the second largest genus of the Orchidaceae.However,an assembled high-quality genome of species in this genus is lacking.Here,we report a chromosome-scale reference genome of Dendrobium chrysotoxum,an important ornamental and medicinal orchid species.The assembled genome size of D.chrysotoxum was 1.37 Gb,with a contig N50 value of 1.54 Mb.Of the sequences,95.75%were anchored to 19 pseudochromosomes.There were 30,044 genes predicted in the D.chrysotoxum genome.Two whole-genome polyploidization events occurred in D.chrysotoxum.In terms of the second event,whole-genome duplication(WGD)was also found to have occurred in other Orchidaceae members,which diverged mainly via gene loss immediately after the WGD event occurred;the first duplication was found to have occurred in most monocots(tau event).We identified sugar transporter(SWEET)gene family expansion,which might be related to the abundant medicinal compounds and fleshy stems of D.chrysotoxum.MADS-box genes were identified in D.chrysotoxum,as well as members of TPS and Hsp90 gene families,which are associated with resistance,which may contribute to the adaptive evolution of orchids.We also investigated the interplay among carotenoid,ABA,and ethylene biosynthesis in D.chrysotoxum to elucidate the regulatory mechanisms of the short flowering period of orchids with yellow flowers.The reference D.chrysotoxum genome will provide important insights for further research on medicinal active ingredients and breeding and enhances the understanding of orchid evolution.展开更多
Lauraceae includes the genus Phoebe,and the family is linked to the evolution of magnoliids.We sequenced the genome of Phoebe bournei Nanmu.The assembled genome size was 989.19 Mb,with a contig N50 value of 2.05 Mb.A ...Lauraceae includes the genus Phoebe,and the family is linked to the evolution of magnoliids.We sequenced the genome of Phoebe bournei Nanmu.The assembled genome size was 989.19 Mb,with a contig N50 value of 2.05 Mb.A total of 28,198 protein-coding genes were annotated in P.bournei.Whole-genome duplication(WGD)analysis showed that Lauraceae has experienced two WGD events;the older WGD event occurred just before the divergence of Lauraceae and Magnoliales,and the more recent WGD was shared by all lineages of Lauraceae.The phylogenetic tree showed that magnoliids form a sister clade to monocots and eudicots.We also identified 63 MADS-box genes,including AGL12-like genes that may be related to the regulation of P.bournei roots and FIN219-like genes encoding GH3 proteins,which are involved in photomorphogenesis.SAUR50-like genes involved in light signal-mediated pedicel or stem development were also identified.Four ATMYB46-and three PtrEPSP-homologous genes related to lignin biosynthesis were identified.These genes may be associated with the formation of straight trunks in P.bournei.Overall,the P.bournei reference genome provides insight into the origin,evolution,and diversification of Phoebe and other magnoliids.展开更多
Singchia Z. J. Liu ＆ L. J. Chen, a new orchid genus, is established based on the new species S. malipoensis Z. J. Liu ＆ L. J. Chen found in southeast Yunnan, China. The new genus is related to Pteroceras, from which...Singchia Z. J. Liu ＆ L. J. Chen, a new orchid genus, is established based on the new species S. malipoensis Z. J. Liu ＆ L. J. Chen found in southeast Yunnan, China. The new genus is related to Pteroceras, from which it differs by having a lip with its basal margins immovably adnate to the lower part of the pendent column foot, a thin-walled spur, and very unequally and deeply split pollinia, each with a distinct caudicle. In addition to a discussion on Ascocentrum pusillum, a species of questionable placement, another new genus, namely Gunnaria S. C. Chen ex Z. J. Liu ＆ L. J. Chen, is set up and a new combination, namely G. pusilla （Aver.） Z. J. Liu ＆ L. J. Chen, is made. The new genus Gunnaria differs from its allyAscocentrum by having a cross-shaped pollinarium, sulcate or split pollinia, each with a distinct caudicle attached to a common linear stipe much longer than either pollinia or viscidium, and strongly incurved side lobes of the lip.展开更多
Cymbidium,which includes approximately 80 species,is one of the most ornamental and cultivated orchid genera.However,a lack of markers and sparse sampling have posed great challenges to resolving the phylogenetic rela...Cymbidium,which includes approximately 80 species,is one of the most ornamental and cultivated orchid genera.However,a lack of markers and sparse sampling have posed great challenges to resolving the phylogenetic relationships within the genus.In the present study,we reconstructed the phylogenetic relationships by utilizing one nuclear DNA(nrITS)and seven plastid genes(rbcL,trnS,trnG,matK,trnL,psbA,and atpI)from 70 species(varieties)in Cymbidium.We also examined the occurrence of phylogenetic conflict between nuclear(nrITS)and plastid loci and investigated how phylogenetic conflict bears on taxonomic classification within the genus.We found that phylogenetic conflict and low support values may be explained by hybridization and a lack of informative characteristics.Our results do not support previous classification of the subgenera and sections within Cymbidium.Discordance between gene trees and network analysis indicate that reticulate evolution occurred in the genus Cymbidium.Overall,our study indicates that Cymbidium has undergone a complex evolution.展开更多
The mangrove Kandelia obovata(Rhizophoraceae)is an important coastal shelterbelt and landscape tree distributed in tropical and subtropical areas across East Asia and Southeast Asia.Herein,a chromosome-level reference...The mangrove Kandelia obovata(Rhizophoraceae)is an important coastal shelterbelt and landscape tree distributed in tropical and subtropical areas across East Asia and Southeast Asia.Herein,a chromosome-level reference genome of K.obovata based on PacBio,Illumina,and Hi-C data is reported.The high-quality assembled genome size is 177.99 Mb,with a contig N50 value of 5.74 Mb.A large number of contracted gene families and a small number of expanded gene families,as well as a small number of repeated sequences,may account for the small K.obovata genome.We found that K.obovata experienced two whole-genome polyploidization events:one whole-genome duplication shared with other Rhizophoreae and one shared with most eudicots(γevent).We confidently annotated 19,138 protein-coding genes in K.obovata and identified the MADS-box gene class and the RPW8 gene class,which might be related to flowering and resistance to powdery mildew in K.obovata and Rhizophora apiculata,respectively.The reference K.obovata genome described here will be very useful for further molecular elucidation of various traits,the breeding of this coastal shelterbelt species,and evolutionary studies with related taxa.展开更多
After online publication of the article 1 the author noticed minor typo in Fig.4c.CeSEP1/2/3/4 should be read as CeSEP1/3/4.Revised figure supplied during the proof correction was inadvertently not reproduced in the f...After online publication of the article 1 the author noticed minor typo in Fig.4c.CeSEP1/2/3/4 should be read as CeSEP1/3/4.Revised figure supplied during the proof correction was inadvertently not reproduced in the final version.In addition,the affiliation numbers of the authors revised in the original article during proof correction,but not reflected in the title page in Supplementary Information.展开更多
Magnoliids represent the third largest branch of the most diverse and species-rich angiosperms,and their phylogenetic position relative to monocots and eudicots remains uncertain(Dong et al.,2021).Here,we describe the...Magnoliids represent the third largest branch of the most diverse and species-rich angiosperms,and their phylogenetic position relative to monocots and eudicots remains uncertain(Dong et al.,2021).Here,we describe the assembly of a high-quality chromosome-level genome sequence for Cinnamomum camphora(camphor),an evergreen tree belonging to Lauraceae.Genomebased phylogenetic analysis indicated possible incomplete lineage sorting(ILS)during the rapid diversification of the early diverging branches of angiosperms,which may have led to the unstable phylogenetic position of magnoliids.展开更多
The marvelously diverse Orchidaceae constitutes the largest family of angiosperms.The genus Cymbidium in Orchidaceae is well known for its unique vegetation,floral morphology,and flower scent traits.Here,a chromosomes...The marvelously diverse Orchidaceae constitutes the largest family of angiosperms.The genus Cymbidium in Orchidaceae is well known for its unique vegetation,floral morphology,and flower scent traits.Here,a chromosomescale assembly of the genome of Cymbidium ensifolium(Jianlan)is presented.Comparative genomic analysis showed that C.ensifolium has experienced two whole-genome duplication(WGD)events,the most recent of which was shared by all orchids,while the older event was the t event shared by most monocots.The results of MADS-box genes analysis provided support for establishing a unique gene model of orchid flower development regulation,and flower shape mutations in C.ensifolium were shown to be associated with the abnormal expression of MADS-box genes.The most abundant floral scent components identi fied included methyl jasmonate,acacia alcohol and linalool,and the genes involved in the floral scent component network of C.ensifolium were determined.Furthermore,the decreased expression of photosynthesis-antennae and photosynthesis metabolic pathway genes in leaves was shown to result in colorful striped leaves,while the increased expression of MADS-box genes in leaves led to perianth-like leaves.Our results provide fundamental insights into orchid evolution and diversi fication.展开更多
The genetic diversity of germplasm is critical for exploring genetic and phenotypic resources and has important implications for crop-breeding sustainability and improvement.However,little is known about the factors t...The genetic diversity of germplasm is critical for exploring genetic and phenotypic resources and has important implications for crop-breeding sustainability and improvement.However,little is known about the factors that shape and maintain genetic diversity.Here,we assembled a high-quality chromosome-level reference of the Chinese common apricot‘Yinxiangbai’,and we resequenced 180 apricot accessions that cover four major ecogeographical groups in China and other accessions from occidental countries.We concluded that Chinese-cultivated common apricot germplasms possessed much higher genetic diversity than those cultivated in Western countries.We also detected seven migration events among different apricot groups,where 27%of the genome was identified as being introgressed.Remarkably,we demonstrated that these introgressed regions drove the current high level of germplasm diversity in Chinese-cultivated common apricots by introducing different genes related to distinct phenotypes from different cultivated groups.Our results highlight the consideration that introgressed regions may provide an important reservoir of genetic resources that can be used to sustain modern breeding programs.展开更多
Oxalidaceae is one of the most important plant families in horticulture,and its key commercially relevant genus,Averrhoa,has diverse growth habits and fruit types.Here,we describe the assembly of a high-quality chromo...Oxalidaceae is one of the most important plant families in horticulture,and its key commercially relevant genus,Averrhoa,has diverse growth habits and fruit types.Here,we describe the assembly of a high-quality chromosomescale genome sequence for Averrhoa carambola(star fruit).Ks distribution analysis showed that A.carambola underwent a whole-genome triplication event,i.e.,the gamma event shared by most eudicots.Comparisons between A.carambola and other angiosperms also permitted the generation of Oxalidaceae gene annotations.We identified unique gene families and analyzed gene family expansion and contraction.This analysis revealed significant changes in MADS-box gene family content,which might be related to the cauliflory of A.carambola.In addition,we identified and analyzed a total of 204 nucleotide-binding site,leucine-rich repeat receptor(NLR)genes and 58 WRKY genes in the genome,which may be related to the defense response.Our results provide insights into the origin,evolution and diversification of star fruit.展开更多
Melastomataceae has abundant morphological diversity with high economic and ornamental merit in Myrtales. The phylogenetic position of Myrtales is still contested. Here, we report the chromosome-level genome assembly ...Melastomataceae has abundant morphological diversity with high economic and ornamental merit in Myrtales. The phylogenetic position of Myrtales is still contested. Here, we report the chromosome-level genome assembly of Melastoma dodecandrum in Melastomataceae. The assembled genome size is299.81 Mb with a contig N50 value of 3.00 Mb. Genome evolution analysis indicated that M. dodecandrum,Eucalyptus grandis, and Punica granatum were clustered into a clade of Myrtales and formed a sister group with the ancestor of fabids and malvids. We found that M. dodecandrum experienced four whole-genome polyploidization events: the ancient event was shared with most eudicots, one event was shared with Myrtales, and the other two events were unique to M. dodecandrum. Moreover, we identified MADS-box genes and found that the AP1-like genes expanded, and AP3-like genes might have undergone subfunctionalization. The SUAR63-like genes and AG-like genes showed different expression patterns in stamens, which may be associated with heteranthery. In addition, we found that LAZY1-like genes were involved in the negative regulation of stem branching development, which may be related to its creeping features. Our study sheds new light on the evolution of Melastomataceae and Myrtales, which provides a comprehensive genetic resource for future research.展开更多
Cymbidium goeringii is one of the important ornamental orchids,but its high-quality genome has not been previously published.Here,we report a chromosome-level genome of C.goeringii and report the gene family expansion...Cymbidium goeringii is one of the important ornamental orchids,but its high-quality genome has not been previously published.Here,we report a chromosome-level genome of C.goeringii and report the gene family expansion,and contraction of the C.goeringii genome and the regulation mechanism of MADS-box genes in floral organ development.We constructed the pathways of carotenoids and anthocyanins that contribute to the different flower colors of C.goeringii and the metabolic pathways of the main components of flower fragrance.Moreover,we found the genes that regulate colourful leaves and analyzed the resistance genes involved in the adaptive evolution of C.goeringii.Our results provide valuable genomic resources for the improvement of orchids and other ornamental plants.展开更多
基金supported by the 2018 Shaoguan City Science and Technology Plan Project:Special Project of Industry-University-Research Cooperation(no.2018CS11919)2019 Guangdong Province Special Fund for Science and Technology(‘Big project+task list’)Project:Ecological Cultivation and Sustainable Utilization of Danxia Dendrobium officinale,a rare Southern Medicine in Guangdong Province(no.2019gdskjzxzj-zt3-2)+2 种基金Fundamental Research Project of Shenzhen,China(JCYJ20170817105300166)National Key Research and Development Program of China(no.2018YFD1000401)Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization Construction Funds(nos.115/118990050,115/KJG18016A)awarded to Z.-J.L.
文摘Flavonoids,which are a diverse class of phytonutrients,are used by organisms to respond to nearly all abiotic stresses and are beneficial for human health.Glycosyltransferase,used during the last step of flavonoid biosynthesis,is important in flavonoid enrichment.However,little is known about glycosyltransferase in the orchid Dendrobium catenatum(D.officinale).In this study,we isolated a novel C-glycosyltransferase(designated DcaCGT)from the orchid D.catenatum by identifying and analyzing 82 putative genes in the GT1 family.DcaCGT could specifically catalyze not only di-C-glycosylation but also O-glycosylation.Apart from the normal function of catalyzing 2-hydroxynaringenin and phloretin to the respective di-C-glycosides,DcaCGT also catalyzes apigenin to cosmosiin.Targeted metabolic profiling of the substrates(2-hydroxynaringenin,phloretin,and apigenin)and products(vitexin,isovitexin,vicenin-2,nothofagin,3’,5’-di-C-glucosylphloretin,and cosmosiin)in different tissues showed that vicenin-2 was the most abundant product of this novel enzyme.Cosmosiin was detected in flowers and flower buds.We also established that DcaCGT functions expanded throughout the evolution of D.catenatum.Residual OGT activity may help D.catenatum resist drought stress.Our study illustrates the function,origin,and differentiation of DcaCGT and provides insights into glycosylation and molecular propagation processes,which can be used to improve the production of flavonoids by the cultivated medicinal plant D.catenatum.
基金This project was supported by the Guangdong Innovation Research Team Fund(2014ZT05S078)National Natural Science Foundation of China(grants 31571252 and 31772322)+7 种基金Guangdong Special Support Program for Young Talents in Innovation Research of Science and Technology(2019TQ05N940)Shenzhen Peacock Grant(827/000189)Science and Technology Program of Guangdong Province,China(2019B121202006)Program of Forestry Administration of Guangdong Province(E036011002)Department for Wildlife and Forest Plant Protection of the National Forest and Grassland Administration(2019073010)National Key Research and Development Program of China(No.2018YFD1000400)Special Research Foundation of Hebei Agricultural University(YJ201848)Natural Science Foundation of Hebei Province(C2019204295).
文摘As one of the largest families of angiosperms,the Orchidaceae family is diverse.Dendrobium represents the second largest genus of the Orchidaceae.However,an assembled high-quality genome of species in this genus is lacking.Here,we report a chromosome-scale reference genome of Dendrobium chrysotoxum,an important ornamental and medicinal orchid species.The assembled genome size of D.chrysotoxum was 1.37 Gb,with a contig N50 value of 1.54 Mb.Of the sequences,95.75%were anchored to 19 pseudochromosomes.There were 30,044 genes predicted in the D.chrysotoxum genome.Two whole-genome polyploidization events occurred in D.chrysotoxum.In terms of the second event,whole-genome duplication(WGD)was also found to have occurred in other Orchidaceae members,which diverged mainly via gene loss immediately after the WGD event occurred;the first duplication was found to have occurred in most monocots(tau event).We identified sugar transporter(SWEET)gene family expansion,which might be related to the abundant medicinal compounds and fleshy stems of D.chrysotoxum.MADS-box genes were identified in D.chrysotoxum,as well as members of TPS and Hsp90 gene families,which are associated with resistance,which may contribute to the adaptive evolution of orchids.We also investigated the interplay among carotenoid,ABA,and ethylene biosynthesis in D.chrysotoxum to elucidate the regulatory mechanisms of the short flowering period of orchids with yellow flowers.The reference D.chrysotoxum genome will provide important insights for further research on medicinal active ingredients and breeding and enhances the understanding of orchid evolution.
基金funded by the Project of Forestry Peak Discipline at Fujian Agriculture and Forestry University,China(118/712018007)the Science and Technology Innovation Special Fund at Fujian Agriculture and Forestry University(118/KF2015088)the 6th Project of Forest Seeding Breaking in Fujian Province([2–19]357).
文摘Lauraceae includes the genus Phoebe,and the family is linked to the evolution of magnoliids.We sequenced the genome of Phoebe bournei Nanmu.The assembled genome size was 989.19 Mb,with a contig N50 value of 2.05 Mb.A total of 28,198 protein-coding genes were annotated in P.bournei.Whole-genome duplication(WGD)analysis showed that Lauraceae has experienced two WGD events;the older WGD event occurred just before the divergence of Lauraceae and Magnoliales,and the more recent WGD was shared by all lineages of Lauraceae.The phylogenetic tree showed that magnoliids form a sister clade to monocots and eudicots.We also identified 63 MADS-box genes,including AGL12-like genes that may be related to the regulation of P.bournei roots and FIN219-like genes encoding GH3 proteins,which are involved in photomorphogenesis.SAUR50-like genes involved in light signal-mediated pedicel or stem development were also identified.Four ATMYB46-and three PtrEPSP-homologous genes related to lignin biosynthesis were identified.These genes may be associated with the formation of straight trunks in P.bournei.Overall,the P.bournei reference genome provides insight into the origin,evolution,and diversification of Phoebe and other magnoliids.
基金supported financially by the National Program for Wild Life Conservation and Nature Reserve Construction,China,and by the Science & Technology Plan of Shenzhen,China (SYF 200646408).
文摘Singchia Z. J. Liu ＆ L. J. Chen, a new orchid genus, is established based on the new species S. malipoensis Z. J. Liu ＆ L. J. Chen found in southeast Yunnan, China. The new genus is related to Pteroceras, from which it differs by having a lip with its basal margins immovably adnate to the lower part of the pendent column foot, a thin-walled spur, and very unequally and deeply split pollinia, each with a distinct caudicle. In addition to a discussion on Ascocentrum pusillum, a species of questionable placement, another new genus, namely Gunnaria S. C. Chen ex Z. J. Liu ＆ L. J. Chen, is set up and a new combination, namely G. pusilla （Aver.） Z. J. Liu ＆ L. J. Chen, is made. The new genus Gunnaria differs from its allyAscocentrum by having a cross-shaped pollinarium, sulcate or split pollinia, each with a distinct caudicle attached to a common linear stipe much longer than either pollinia or viscidium, and strongly incurved side lobes of the lip.
基金funded by The National Key Research and Development Program of China(Nos.2018YFD1000401 and 2018YFD1000400)the Natural Science Foundation of Guangdong Province(No.2017A030312004)the Science and Technology Plan Project of Shenzhen(No.JCYJ20170817151501595).
文摘Cymbidium,which includes approximately 80 species,is one of the most ornamental and cultivated orchid genera.However,a lack of markers and sparse sampling have posed great challenges to resolving the phylogenetic relationships within the genus.In the present study,we reconstructed the phylogenetic relationships by utilizing one nuclear DNA(nrITS)and seven plastid genes(rbcL,trnS,trnG,matK,trnL,psbA,and atpI)from 70 species(varieties)in Cymbidium.We also examined the occurrence of phylogenetic conflict between nuclear(nrITS)and plastid loci and investigated how phylogenetic conflict bears on taxonomic classification within the genus.We found that phylogenetic conflict and low support values may be explained by hybridization and a lack of informative characteristics.Our results do not support previous classification of the subgenera and sections within Cymbidium.Discordance between gene trees and network analysis indicate that reticulate evolution occurred in the genus Cymbidium.Overall,our study indicates that Cymbidium has undergone a complex evolution.
基金funded by the National Science Foundation of China(41801062)the Special Project for the Cultivation of Major Achievements in the Peak Discipline of Forestry Science(118/71201800709)+1 种基金the Special Subsidy for Leading Talents of Scientific and Technological Innovation in Fujian Province(118/KRC16006A)the Fujian Forestry Science and Technology Research Project(Min[2019]6).
文摘The mangrove Kandelia obovata(Rhizophoraceae)is an important coastal shelterbelt and landscape tree distributed in tropical and subtropical areas across East Asia and Southeast Asia.Herein,a chromosome-level reference genome of K.obovata based on PacBio,Illumina,and Hi-C data is reported.The high-quality assembled genome size is 177.99 Mb,with a contig N50 value of 5.74 Mb.A large number of contracted gene families and a small number of expanded gene families,as well as a small number of repeated sequences,may account for the small K.obovata genome.We found that K.obovata experienced two whole-genome polyploidization events:one whole-genome duplication shared with other Rhizophoreae and one shared with most eudicots(γevent).We confidently annotated 19,138 protein-coding genes in K.obovata and identified the MADS-box gene class and the RPW8 gene class,which might be related to flowering and resistance to powdery mildew in K.obovata and Rhizophora apiculata,respectively.The reference K.obovata genome described here will be very useful for further molecular elucidation of various traits,the breeding of this coastal shelterbelt species,and evolutionary studies with related taxa.
文摘After online publication of the article 1 the author noticed minor typo in Fig.4c.CeSEP1/2/3/4 should be read as CeSEP1/3/4.Revised figure supplied during the proof correction was inadvertently not reproduced in the final version.In addition,the affiliation numbers of the authors revised in the original article during proof correction,but not reflected in the title page in Supplementary Information.
基金support received through the Special Funds for Leading Scientific and Technological Innovation Talents of Fujian Province,China(KRC16006A)awarded to S.-Q.Z.Fujian Forestry Science and Technology Project—Genome Sequencing and Application of High-quality Resources Screening of Camphor tree,China(2021FKJ19)awarded to G.-R.C.Fujian Forestry Science and Technology Extension Project—Cultivation Demonstration of a New Camphor Variety Nan’an No.1,China(2021TG10)awarded to X.-H.W.
文摘Magnoliids represent the third largest branch of the most diverse and species-rich angiosperms,and their phylogenetic position relative to monocots and eudicots remains uncertain(Dong et al.,2021).Here,we describe the assembly of a high-quality chromosome-level genome sequence for Cinnamomum camphora(camphor),an evergreen tree belonging to Lauraceae.Genomebased phylogenetic analysis indicated possible incomplete lineage sorting(ILS)during the rapid diversification of the early diverging branches of angiosperms,which may have led to the unstable phylogenetic position of magnoliids.
基金The authors acknowledge support from the National Key Research and Development Program of China(no.2019YFD1000400)the National Natural Science Foundation of China(no.31700618)+2 种基金the Outstanding Young Scientific Research Talent Project of Fujian Agriculture and Forestry University(no.xjq201910)the Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilizati on Construction Funds(nos.115/118990050,115/KJG18016A)the Furopean Research Council(ERC)under the Furopean Union's Horizon 2020 research and innovation program(grant agreement No 833522).
文摘The marvelously diverse Orchidaceae constitutes the largest family of angiosperms.The genus Cymbidium in Orchidaceae is well known for its unique vegetation,floral morphology,and flower scent traits.Here,a chromosomescale assembly of the genome of Cymbidium ensifolium(Jianlan)is presented.Comparative genomic analysis showed that C.ensifolium has experienced two whole-genome duplication(WGD)events,the most recent of which was shared by all orchids,while the older event was the t event shared by most monocots.The results of MADS-box genes analysis provided support for establishing a unique gene model of orchid flower development regulation,and flower shape mutations in C.ensifolium were shown to be associated with the abnormal expression of MADS-box genes.The most abundant floral scent components identi fied included methyl jasmonate,acacia alcohol and linalool,and the genes involved in the floral scent component network of C.ensifolium were determined.Furthermore,the decreased expression of photosynthesis-antennae and photosynthesis metabolic pathway genes in leaves was shown to result in colorful striped leaves,while the increased expression of MADS-box genes in leaves led to perianth-like leaves.Our results provide fundamental insights into orchid evolution and diversi fication.
基金This work was funded by the National Key Research and Development Program of China(2019YFD1000600)the National Natural Science Foundation of China(No.3197236)+2 种基金the National Natural Science Foundation of China(No.31870199)the Scientific Research Fund for Public Welfare in Liaoning(20180025)the Program of Conservation and Utilization of Crop Germplasm Resources and National Crop Germplasm Resources Platform of China,and the National Key R&D Program of China(Grant No.2019YFD1000400).
文摘The genetic diversity of germplasm is critical for exploring genetic and phenotypic resources and has important implications for crop-breeding sustainability and improvement.However,little is known about the factors that shape and maintain genetic diversity.Here,we assembled a high-quality chromosome-level reference of the Chinese common apricot‘Yinxiangbai’,and we resequenced 180 apricot accessions that cover four major ecogeographical groups in China and other accessions from occidental countries.We concluded that Chinese-cultivated common apricot germplasms possessed much higher genetic diversity than those cultivated in Western countries.We also detected seven migration events among different apricot groups,where 27%of the genome was identified as being introgressed.Remarkably,we demonstrated that these introgressed regions drove the current high level of germplasm diversity in Chinese-cultivated common apricots by introducing different genes related to distinct phenotypes from different cultivated groups.Our results highlight the consideration that introgressed regions may provide an important reservoir of genetic resources that can be used to sustain modern breeding programs.
基金supported by The National Key Research and Development Program of China(ref.2019YFC1711103)the Fujian Agriculture and Forestry University Science and Technology Innovation Special Fund Project(ref.KFA17331A)+1 种基金the Natural Science Foundation of Fujian(ref.2019J01410)the Fujian Agriculture and Forestry University 2015 Outstanding Youth Fund Project(ref.xjq201620).
文摘Oxalidaceae is one of the most important plant families in horticulture,and its key commercially relevant genus,Averrhoa,has diverse growth habits and fruit types.Here,we describe the assembly of a high-quality chromosomescale genome sequence for Averrhoa carambola(star fruit).Ks distribution analysis showed that A.carambola underwent a whole-genome triplication event,i.e.,the gamma event shared by most eudicots.Comparisons between A.carambola and other angiosperms also permitted the generation of Oxalidaceae gene annotations.We identified unique gene families and analyzed gene family expansion and contraction.This analysis revealed significant changes in MADS-box gene family content,which might be related to the cauliflory of A.carambola.In addition,we identified and analyzed a total of 204 nucleotide-binding site,leucine-rich repeat receptor(NLR)genes and 58 WRKY genes in the genome,which may be related to the defense response.Our results provide insights into the origin,evolution and diversification of star fruit.
基金supports from The Innovation and Application Engineering Technology Research Center of Ornamental Plant Germplasm Resources in Fujian Province (115-PTJH16005)The Plateau Discipline Construction Program of Fujian Province (115712018010)Special Fund for Forest Scientific Research in the Public Welfare (201204604)。
文摘Melastomataceae has abundant morphological diversity with high economic and ornamental merit in Myrtales. The phylogenetic position of Myrtales is still contested. Here, we report the chromosome-level genome assembly of Melastoma dodecandrum in Melastomataceae. The assembled genome size is299.81 Mb with a contig N50 value of 3.00 Mb. Genome evolution analysis indicated that M. dodecandrum,Eucalyptus grandis, and Punica granatum were clustered into a clade of Myrtales and formed a sister group with the ancestor of fabids and malvids. We found that M. dodecandrum experienced four whole-genome polyploidization events: the ancient event was shared with most eudicots, one event was shared with Myrtales, and the other two events were unique to M. dodecandrum. Moreover, we identified MADS-box genes and found that the AP1-like genes expanded, and AP3-like genes might have undergone subfunctionalization. The SUAR63-like genes and AG-like genes showed different expression patterns in stamens, which may be associated with heteranthery. In addition, we found that LAZY1-like genes were involved in the negative regulation of stem branching development, which may be related to its creeping features. Our study sheds new light on the evolution of Melastomataceae and Myrtales, which provides a comprehensive genetic resource for future research.
基金funded by the project of Jiangsu agricultural science and technology innovation fund:'Research on the breeding technique of new varieties with red flowers of spring orchids'(No.CX(19)3118)Research Fund of Agricultural Science Institute in Lixiahe area of Jiangsu Province(No.SJ(21)302)Platform for the protection and utilization of agricultural germplasm resources in Jiangsu Province:'The germplasm resources nursery of Chinese orchids'(No.JSGB2018-01).
文摘Cymbidium goeringii is one of the important ornamental orchids,but its high-quality genome has not been previously published.Here,we report a chromosome-level genome of C.goeringii and report the gene family expansion,and contraction of the C.goeringii genome and the regulation mechanism of MADS-box genes in floral organ development.We constructed the pathways of carotenoids and anthocyanins that contribute to the different flower colors of C.goeringii and the metabolic pathways of the main components of flower fragrance.Moreover,we found the genes that regulate colourful leaves and analyzed the resistance genes involved in the adaptive evolution of C.goeringii.Our results provide valuable genomic resources for the improvement of orchids and other ornamental plants.
