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
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
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
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
Angraecum sesquipedale,also known as Darwin’s orchid,possesses an exceptionally long nectar spur.Charles Darwin predicted the orchid to be pollinated by a hawkmoth with a correspondingly long proboscis,later identifi...Angraecum sesquipedale,also known as Darwin’s orchid,possesses an exceptionally long nectar spur.Charles Darwin predicted the orchid to be pollinated by a hawkmoth with a correspondingly long proboscis,later identified as Xanthopan praedicta.In this plant-pollinator interaction,the A.sesquipedale flower emits a complex blend of scent compounds dominated by diurnally regulated oximes(R_(1)R_(2)C=N-OH)to attract crepuscular and nocturnal pollinators.The molecular mechanism of oxime biosynthesis remains unclear in orchids.Here,we present the chromosome-level genome of A.sesquipedale.The haploid genome size is 2.10 Gb and represents 19 pseudochromosomes.Cytochrome P450 encoding genes of the CYP79 family known to be involved in oxime biosynthesis in seed plants are not present in the A.sesquipedale genome nor the genomes of other members of the orchid family.Metabolomic analysis of the A.sesquipedale flower revealed a substantial release of oximes at dusk during the blooming stage.By integrating metabolomic and transcriptomic correlation approaches,flavin-containing monooxygenases(FMOs)encoded by six tandem-repeat genes in the A.sesquipedale genome are identified as catalyzing the formation of oximes present.Further in vitro and in vivo assays confirm the function of FMOs in the oxime biosynthesis.We designate these FMOs as orchid oxime synthases 1-6.The evolutionary aspects related to the CYP79 gene losses and neofunctionalization of FMO-catalyzed biosynthesis of oximes in Darwin’s orchid provide new insights into the convergent evolution of biosynthetic pathways.展开更多
Animal body coverings provide protection and allow for adaptation to environmental pressures such as heat,ultraviolet radiation,water loss,and mechanical forces.Here,using a comparative genomics analysis of 39 mammal ...Animal body coverings provide protection and allow for adaptation to environmental pressures such as heat,ultraviolet radiation,water loss,and mechanical forces.Here,using a comparative genomics analysis of 39 mammal species spanning three skin covering types(hairless,scaly and spiny),we found some genes(e.g.,UVRAG,POLH,and XPC)involved in skin inflammation,skin innate immunity,and ultraviolet radiation damage repair were under selection in hairless ocean mammals(e.g.,whales and manatees).These signatures might be associated with a high risk of skin diseases from pathogens and ultraviolet radiation.Moreover,the genomes from three spiny mammal species shared convergent genomic regions(EPHB2,EPHA4,and NIN)and unique positively selected genes(FZD6,INVS,and CDC42)involved in skin cell polarity,which might be related to the development of spines.In scaly mammals,the shared convergent genomic regions(e.g.,FREM2)were associated with the integrity of the skin epithelium and epidermal adhesion.This study identifies potential convergent genomic features among distantly related mammals with the same skin covering type.展开更多
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 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.
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supported by grants from the Shanghai Landscaping and City Appearance Administrative Bureau(G222406,G232408)Sino-Africa Joint Research Center,CAS(SAJC201607)+4 种基金the Science and Technology Commission of Shanghai Municipality(19390743600)the National Wild Plant Germplasm Resource Centre for Shanghai Chenshan Botanical Garden(ZWGX2102)to W.C.H.and K.J.,and by a Distinguished Investigator grant(NNF190CO05456)from the Novo Nordisk Foundation to B.L.M.E.H.J.N.acknowledges funding from the Novo Nordisk Foundation(0054890)the Independent Research Fund Denmark(1131-00002B and 1051-00083 B).
文摘Angraecum sesquipedale,also known as Darwin’s orchid,possesses an exceptionally long nectar spur.Charles Darwin predicted the orchid to be pollinated by a hawkmoth with a correspondingly long proboscis,later identified as Xanthopan praedicta.In this plant-pollinator interaction,the A.sesquipedale flower emits a complex blend of scent compounds dominated by diurnally regulated oximes(R_(1)R_(2)C=N-OH)to attract crepuscular and nocturnal pollinators.The molecular mechanism of oxime biosynthesis remains unclear in orchids.Here,we present the chromosome-level genome of A.sesquipedale.The haploid genome size is 2.10 Gb and represents 19 pseudochromosomes.Cytochrome P450 encoding genes of the CYP79 family known to be involved in oxime biosynthesis in seed plants are not present in the A.sesquipedale genome nor the genomes of other members of the orchid family.Metabolomic analysis of the A.sesquipedale flower revealed a substantial release of oximes at dusk during the blooming stage.By integrating metabolomic and transcriptomic correlation approaches,flavin-containing monooxygenases(FMOs)encoded by six tandem-repeat genes in the A.sesquipedale genome are identified as catalyzing the formation of oximes present.Further in vitro and in vivo assays confirm the function of FMOs in the oxime biosynthesis.We designate these FMOs as orchid oxime synthases 1-6.The evolutionary aspects related to the CYP79 gene losses and neofunctionalization of FMO-catalyzed biosynthesis of oximes in Darwin’s orchid provide new insights into the convergent evolution of biosynthetic pathways.
基金supported by the National Natural Science Fund for Outstanding Youth Fund(31222009,31272295,31570489,81622048 and 81473377)the Project of Quality Guarantee System of Chinese Herbal Medicines(201507002)+1 种基金Science Foundation for Distinguished Young Scholars of Jiangsu Province(BK20140049)the Priority Academic Program Development of Jiangsu Higher Education Institutions(PAPD).
文摘Animal body coverings provide protection and allow for adaptation to environmental pressures such as heat,ultraviolet radiation,water loss,and mechanical forces.Here,using a comparative genomics analysis of 39 mammal species spanning three skin covering types(hairless,scaly and spiny),we found some genes(e.g.,UVRAG,POLH,and XPC)involved in skin inflammation,skin innate immunity,and ultraviolet radiation damage repair were under selection in hairless ocean mammals(e.g.,whales and manatees).These signatures might be associated with a high risk of skin diseases from pathogens and ultraviolet radiation.Moreover,the genomes from three spiny mammal species shared convergent genomic regions(EPHB2,EPHA4,and NIN)and unique positively selected genes(FZD6,INVS,and CDC42)involved in skin cell polarity,which might be related to the development of spines.In scaly mammals,the shared convergent genomic regions(e.g.,FREM2)were associated with the integrity of the skin epithelium and epidermal adhesion.This study identifies potential convergent genomic features among distantly related mammals with the same skin covering type.
