Sweet osmanthus(Osmanthus fragrans)is a very popular ornamental tree species throughout Southeast Asia and USA particularly for its extremely fragrant aroma.We constructed a chromosome-level reference genome of O.frag...Sweet osmanthus(Osmanthus fragrans)is a very popular ornamental tree species throughout Southeast Asia and USA particularly for its extremely fragrant aroma.We constructed a chromosome-level reference genome of O.fragrans to assist in studies of the evolution,genetic diversity,and molecular mechanism of aroma development.A total of over 118 Gb of polished reads was produced from HiSeq(45.1 Gb)and PacBio Sequel(73.35 Gb),giving 100×depth coverage for long reads.The combination of Illumina-short reads,PacBio-long reads,and Hi-C data produced the final chromosome quality genome of O.fragrans with a genome size of 727 Mb and a heterozygosity of 1.45%.The genome was annotated using de novo and homology comparison and further refined with transcriptome data.The genome of O.fragrans was predicted to have 45,542 genes,of which 95.68%were functionally annotated.Genome annotation found 49.35%as the repetitive sequences,with long terminal repeats(LTR)being the richest(28.94%).Genome evolution analysis indicated the evidence of whole-genome duplication 15 million years ago,which contributed to the current content of 45,242 genes.Metabolic analysis revealed that linalool,a monoterpene is the main aroma compound.Based on the genome and transcriptome,we further demonstrated the direct connection between terpene synthases(TPSs)and the rich aromatic molecules in O.fragrans.We identified three new flower-specific TPS genes,of which the expression coincided with the production of linalool.Our results suggest that the high number of TPS genes and the flower tissue-and stage-specific TPS genes expressions might drive the strong unique aroma production of O.fragrans.展开更多
Terpenoids,including aromatic volatile monoterpenoids and sesquiterpenoids,function in defense against pathogens and herbivores.Phoebe trees are remarkable for their scented wood and decay resistance.Unlike other Laur...Terpenoids,including aromatic volatile monoterpenoids and sesquiterpenoids,function in defense against pathogens and herbivores.Phoebe trees are remarkable for their scented wood and decay resistance.Unlike other Lauraceae species investigated to date,Phoebe species predominantly accumulate sesquiterpenoids instead of monoterpenoids.Limited genomic data restrict the elucidation of terpenoid variation and functions.Here,we present a chromosome-scale genome assembly of a Lauraceae tree,Phoebe bournei,and identify 72 full-length terpene synthase(TPS)genes.Genome-level comparison shows pervasive lineage-specific duplication and contraction of TPS subfamilies,which have contributed to the extreme terpenoid variation within Lauraceae species.Although the TPS-a and TPS-b subfamilies were both expanded via tandem duplication in P.bournei,more TPS-a copies were retained and constitutively expressed,whereas more TPS-b copies were lost.The TPS-a genes on chromosome 8 functionally diverged to synthesize eight highly accumulated sesquiterpenes in P.bournei.The essential oil of P.bournei and its main component,b-caryophyllene,exhibited antifungal activities against the three most widespread canker pathogens of trees.The TPS-a and TPS-b subfamilies have experienced contrasting fates over the evolution of P.bournei.The abundant sesquiterpenoids produced by TPS-a proteins contribute to the excellent pathogen resistance of P.bournei trees.Overall,this study sheds light on the evolution and adaptation of terpenoids in Lauraceae and provides valuable resources for boosting plant immunity against pathogens in various trees and crops.展开更多
Gelsemium elegans(G.elegans)(2 n=2 x=16)is genus of flowering plants belonging to the Gelsemicaeae family.Here,a high-quality genome assembly using the Oxford Nanopore Technologies(ONT)platform and high-throughput chr...Gelsemium elegans(G.elegans)(2 n=2 x=16)is genus of flowering plants belonging to the Gelsemicaeae family.Here,a high-quality genome assembly using the Oxford Nanopore Technologies(ONT)platform and high-throughput chromosome conformation capture techniques(Hi-C)were used.A total of 56.11 Gb of raw GridION X5 platform ONT reads(6.23 Gb per cell)were generated.After filtering,53.45 Gb of clean reads were obtained,giving 160 x coverage depth.The de novo genome assemblies 335.13 Mb,close to the 338 Mb estimated by k-mer analysis,was generated with contig N50 of 10.23 Mb.The vast majority(99.2%)of the G.elegans assembled sequence was anchored onto 8 pseudo-chromosomes.The genome completeness was then evaluated and 1338 of the 1440 conserved genes(92.9%)could be found in the assembly.Genome annotation revealed that 43.16%of the G.elegans genome is composed of repetitive elements and 23.9%is composed of long terminal repeat elements.We predicted 26,768 protein-coding genes,of which 84.56%were functionally annotated.The genomic sequences of G.elegans could be a valuable source for comparative genomic analysis in the Gelsemicaeae family and will be useful for understanding the phylogenetic relationships of the indole alkaloid metabolism.展开更多
Eucommia ulmoides, also called hardy rubber tree, is an economically important tree; however, the lack of its genome sequence restricts the fundamental biological research and applied studies of this plant species. He...Eucommia ulmoides, also called hardy rubber tree, is an economically important tree; however, the lack of its genome sequence restricts the fundamental biological research and applied studies of this plant species. Here, we present a high-quality assembly of its ~l.2-Gb genome (scaffold N50 = 1.88 Mb) with at least 26 723 predicted genes for E. ulmoides, the first sequenced genome of the order Garryales, which was obtained using an integrated strategy combining Illumina sequencing, PacBio sequencing, and BioNano mapping. As a sister taxon to lamiids and campanulids, E. ulmoides underwent an ancient genome triplication shared by core eudicots but no further whole-genome duplication in the last ~125 million years. E. ulmoides exhibits high expression levels and/or gene number expansion for multiple genes involved in stress responses and the biosynthesis of secondary metabolites, which may account for its considerable environmental adaptability. In contrast to the rubber tree (Hevea brasiliensis), which produces cis-polyisoprene, E. ulmoides has evolved to synthe- size long-chain trans-polyisoprene via farnesyl diphosphate synthases (FPSs). Moreover, FPS and rub- ber elongation factor/small rubber particle protein gene families were expanded independently from the H. brasiliensis lineage. These results provide new insights into the biology of E. ulmoides and the origin of polyisoprene biosynthesis.展开更多
Tung tree(Vernicia fordii) is an economically important woody oil plant that produces tung oil rich in eleostearic acid. Here, we report a high-quality chromosome-scale genome sequence of tung tree. The genome sequenc...Tung tree(Vernicia fordii) is an economically important woody oil plant that produces tung oil rich in eleostearic acid. Here, we report a high-quality chromosome-scale genome sequence of tung tree. The genome sequence was assembled by combining Illumina short reads, Pacific Biosciences single-molecule real-time long reads, and Hi-C sequencing data. The size of tung tree genome is 1.12 Gb, with 28,422 predicted genes and over 73% repeat sequences. The V. fordii underwent an ancient genome triplication event shared by core eudicots but no further wholegenome duplication in the subsequent ca. 34.55 million years of evolutionary history of the tung tree lineage. Insertion time analysis revealed that repeat-driven genome expansion might have arisen as a result of long-standing long terminal repeat retrotransposon bursts and lack of efficient DNA deletion mechanisms. The genome harbors 88 resistance genes encoding nucleotide-binding sites;17 of these genes may be involved in early-infection stage of Fusarium wilt resistance. Further, 651 oil-related genes were identified, 88 of which are predicted to be directly involved in tung oil biosynthesis. Relatively few phosphoenolpyruvate carboxykinase genes, and synergistic effects between transcription factors and oil biosynthesis-related genes might contribute to the high oil content of tung seed. The tung tree genome constitutes a valuable resource for understanding genome evolution, as well as for molecular breeding and genetic improvements for oil production.展开更多
Here,through single-molecule real-time sequencing,we present a high-quality genome sequence of the Japanese larch(Larix kaempferi),a conifer species with great value for wood production and ecological afforestation.Th...Here,through single-molecule real-time sequencing,we present a high-quality genome sequence of the Japanese larch(Larix kaempferi),a conifer species with great value for wood production and ecological afforestation.The assembled genome is 10.97 Gb in size,harboring 45,828 protein-coding genes.Of the genome,66.8%consists of repeat sequences,of which long terminal repeat retrotransposons are dominant and make up 69.86%.We find that tandem duplications have been responsible for the expansion of genes involved in transcriptional regulation and stress responses,unveiling their crucial roles in adaptive evolution.Population transcriptome analysis reveals that lignin content in L.kaempferi is mainly determined by the process of monolignol polymerization.The expression values of six genes(LkC OMT7,LkC OMT8,LkL AC23,LkL AC102,LkP RX148,and LkP RX166)have significantly positive correlations with lignin content.These results indicated that the increased expression of these six genes might be responsible for the high lignin content of the larches’wood.Overall,this study provides new genome resources for investigating the evolution and biological function of conifer trees,and also offers new insights into wood properties of larches.展开更多
Dear Editor,African swine fever(ASF)is one of the most pathogenic viral diseases in pigs caused by African swine fever virus(ASFV).The fatality rate is almost 100%,which brings huge economic losses to the hog industry...Dear Editor,African swine fever(ASF)is one of the most pathogenic viral diseases in pigs caused by African swine fever virus(ASFV).The fatality rate is almost 100%,which brings huge economic losses to the hog industry in countries with epiepidemics(Galindo and Alonso,2017).China was the first Asian country to have an ASF epidemic,and it spread quickly across the country after the first epidemic was re・ported in August 2018(Ge et al.,2018).After that,Mongolia,Vietnam,Cambodia and North Korea also reported on the ASF epidemic in succession(OIE,2019).展开更多
基金This work was supported by research grants provided by the National Natural Science Foundation(31870695 and 31601785)the Project of Key Research and Development Plan(Modern Agriculture)in Jiangsu(BE2017375)+1 种基金the Selection and Breeding of Excellent Tree Species and Effective Cultivation Techniques(CX(16)1005)the Project of Osmanthus National Germplasm Bank,and the Top-notch Academic Programs Project of Jiangsu Higher Education Institutions.
文摘Sweet osmanthus(Osmanthus fragrans)is a very popular ornamental tree species throughout Southeast Asia and USA particularly for its extremely fragrant aroma.We constructed a chromosome-level reference genome of O.fragrans to assist in studies of the evolution,genetic diversity,and molecular mechanism of aroma development.A total of over 118 Gb of polished reads was produced from HiSeq(45.1 Gb)and PacBio Sequel(73.35 Gb),giving 100×depth coverage for long reads.The combination of Illumina-short reads,PacBio-long reads,and Hi-C data produced the final chromosome quality genome of O.fragrans with a genome size of 727 Mb and a heterozygosity of 1.45%.The genome was annotated using de novo and homology comparison and further refined with transcriptome data.The genome of O.fragrans was predicted to have 45,542 genes,of which 95.68%were functionally annotated.Genome annotation found 49.35%as the repetitive sequences,with long terminal repeats(LTR)being the richest(28.94%).Genome evolution analysis indicated the evidence of whole-genome duplication 15 million years ago,which contributed to the current content of 45,242 genes.Metabolic analysis revealed that linalool,a monoterpene is the main aroma compound.Based on the genome and transcriptome,we further demonstrated the direct connection between terpene synthases(TPSs)and the rich aromatic molecules in O.fragrans.We identified three new flower-specific TPS genes,of which the expression coincided with the production of linalool.Our results suggest that the high number of TPS genes and the flower tissue-and stage-specific TPS genes expressions might drive the strong unique aroma production of O.fragrans.
基金supported by the National Key Research and Development Program of China(2018YFD1000300)National Crop Germplasm Resources Protection of Ministry of Agriculture of China(NB2018-2130135-07).
文摘Since the publication of this article,the authors have noticed that the NCBI accession number is missing from article.
基金supported by the Zhejiang Science and Technology Major Program on Agricultural New Variety Breeding(grant 2021C02070-10)the National Natural Science Foundation of China(grants 32171828 and 32101545)the State Key Laboratory of Subtropical Silviculture(grant ZY20180204).
文摘Terpenoids,including aromatic volatile monoterpenoids and sesquiterpenoids,function in defense against pathogens and herbivores.Phoebe trees are remarkable for their scented wood and decay resistance.Unlike other Lauraceae species investigated to date,Phoebe species predominantly accumulate sesquiterpenoids instead of monoterpenoids.Limited genomic data restrict the elucidation of terpenoid variation and functions.Here,we present a chromosome-scale genome assembly of a Lauraceae tree,Phoebe bournei,and identify 72 full-length terpene synthase(TPS)genes.Genome-level comparison shows pervasive lineage-specific duplication and contraction of TPS subfamilies,which have contributed to the extreme terpenoid variation within Lauraceae species.Although the TPS-a and TPS-b subfamilies were both expanded via tandem duplication in P.bournei,more TPS-a copies were retained and constitutively expressed,whereas more TPS-b copies were lost.The TPS-a genes on chromosome 8 functionally diverged to synthesize eight highly accumulated sesquiterpenes in P.bournei.The essential oil of P.bournei and its main component,b-caryophyllene,exhibited antifungal activities against the three most widespread canker pathogens of trees.The TPS-a and TPS-b subfamilies have experienced contrasting fates over the evolution of P.bournei.The abundant sesquiterpenoids produced by TPS-a proteins contribute to the excellent pathogen resistance of P.bournei trees.Overall,this study sheds light on the evolution and adaptation of terpenoids in Lauraceae and provides valuable resources for boosting plant immunity against pathogens in various trees and crops.
基金financially supported by Hunan Provincial Natural Science Foundation of China(grant 2017JJ1017)National Key R&D Program of China(grant 2017YFD0501403)+1 种基金National Natural Science Foundation of China(grant 31400275)Hunan Provincial Natural Science Foundation of China(2018JJ2172).
文摘Gelsemium elegans(G.elegans)(2 n=2 x=16)is genus of flowering plants belonging to the Gelsemicaeae family.Here,a high-quality genome assembly using the Oxford Nanopore Technologies(ONT)platform and high-throughput chromosome conformation capture techniques(Hi-C)were used.A total of 56.11 Gb of raw GridION X5 platform ONT reads(6.23 Gb per cell)were generated.After filtering,53.45 Gb of clean reads were obtained,giving 160 x coverage depth.The de novo genome assemblies 335.13 Mb,close to the 338 Mb estimated by k-mer analysis,was generated with contig N50 of 10.23 Mb.The vast majority(99.2%)of the G.elegans assembled sequence was anchored onto 8 pseudo-chromosomes.The genome completeness was then evaluated and 1338 of the 1440 conserved genes(92.9%)could be found in the assembly.Genome annotation revealed that 43.16%of the G.elegans genome is composed of repetitive elements and 23.9%is composed of long terminal repeat elements.We predicted 26,768 protein-coding genes,of which 84.56%were functionally annotated.The genomic sequences of G.elegans could be a valuable source for comparative genomic analysis in the Gelsemicaeae family and will be useful for understanding the phylogenetic relationships of the indole alkaloid metabolism.
文摘Eucommia ulmoides, also called hardy rubber tree, is an economically important tree; however, the lack of its genome sequence restricts the fundamental biological research and applied studies of this plant species. Here, we present a high-quality assembly of its ~l.2-Gb genome (scaffold N50 = 1.88 Mb) with at least 26 723 predicted genes for E. ulmoides, the first sequenced genome of the order Garryales, which was obtained using an integrated strategy combining Illumina sequencing, PacBio sequencing, and BioNano mapping. As a sister taxon to lamiids and campanulids, E. ulmoides underwent an ancient genome triplication shared by core eudicots but no further whole-genome duplication in the last ~125 million years. E. ulmoides exhibits high expression levels and/or gene number expansion for multiple genes involved in stress responses and the biosynthesis of secondary metabolites, which may account for its considerable environmental adaptability. In contrast to the rubber tree (Hevea brasiliensis), which produces cis-polyisoprene, E. ulmoides has evolved to synthe- size long-chain trans-polyisoprene via farnesyl diphosphate synthases (FPSs). Moreover, FPS and rub- ber elongation factor/small rubber particle protein gene families were expanded independently from the H. brasiliensis lineage. These results provide new insights into the biology of E. ulmoides and the origin of polyisoprene biosynthesis.
基金supported by the National Key R&D Program of China(Grant No.2017YFD0600703)the National Forestry Public Welfare Industry Research Project of China(Grant No.201204403)+2 种基金the Outstanding Youth Project of the Education Department of Hunan Province,China(Grant No.17B279)the US Department of AgricultureAgricultural Research Service(USDA-ARS)National Program for Quality and Utilization of Agricultural Products(NP 306Grant No.CRIS 6054-41000-103-00-D).
文摘Tung tree(Vernicia fordii) is an economically important woody oil plant that produces tung oil rich in eleostearic acid. Here, we report a high-quality chromosome-scale genome sequence of tung tree. The genome sequence was assembled by combining Illumina short reads, Pacific Biosciences single-molecule real-time long reads, and Hi-C sequencing data. The size of tung tree genome is 1.12 Gb, with 28,422 predicted genes and over 73% repeat sequences. The V. fordii underwent an ancient genome triplication event shared by core eudicots but no further wholegenome duplication in the subsequent ca. 34.55 million years of evolutionary history of the tung tree lineage. Insertion time analysis revealed that repeat-driven genome expansion might have arisen as a result of long-standing long terminal repeat retrotransposon bursts and lack of efficient DNA deletion mechanisms. The genome harbors 88 resistance genes encoding nucleotide-binding sites;17 of these genes may be involved in early-infection stage of Fusarium wilt resistance. Further, 651 oil-related genes were identified, 88 of which are predicted to be directly involved in tung oil biosynthesis. Relatively few phosphoenolpyruvate carboxykinase genes, and synergistic effects between transcription factors and oil biosynthesis-related genes might contribute to the high oil content of tung seed. The tung tree genome constitutes a valuable resource for understanding genome evolution, as well as for molecular breeding and genetic improvements for oil production.
基金funded by the Forestry Industry Research Special Funds for Public Welfare Projects(201504104)National Natural Science Foundation of China(31901335)+2 种基金Fundamental Research Funds for the Central Non-profit Research Institution of CAF(CAFYBB2017QA001,CAFYBB 2018ZY001-4,LYSZX202002)National Transgenic Major Program(2018ZX08020-003)funded by a postdoctoral fellowship from the Special Research Fund of Ghent University(BOFPDO2018001701)。
文摘Here,through single-molecule real-time sequencing,we present a high-quality genome sequence of the Japanese larch(Larix kaempferi),a conifer species with great value for wood production and ecological afforestation.The assembled genome is 10.97 Gb in size,harboring 45,828 protein-coding genes.Of the genome,66.8%consists of repeat sequences,of which long terminal repeat retrotransposons are dominant and make up 69.86%.We find that tandem duplications have been responsible for the expansion of genes involved in transcriptional regulation and stress responses,unveiling their crucial roles in adaptive evolution.Population transcriptome analysis reveals that lignin content in L.kaempferi is mainly determined by the process of monolignol polymerization.The expression values of six genes(LkC OMT7,LkC OMT8,LkL AC23,LkL AC102,LkP RX148,and LkP RX166)have significantly positive correlations with lignin content.These results indicated that the increased expression of these six genes might be responsible for the high lignin content of the larches’wood.Overall,this study provides new genome resources for investigating the evolution and biological function of conifer trees,and also offers new insights into wood properties of larches.
基金supported by the National Key R&D Program of China (2016YFC1200800 & 2018YFC0840402)Research Project of African Swine Fever of Chinese Academy of Sciences (KJZD-SWL06)+2 种基金China Mega-Project for Infectious Disease (2017ZX10103005-005)the State Key Laboratory of Veterinary Biotechnology Research Fund (SKLVBF201902)supported by Youth Innovation Promotion Association of CAS (2019091)
文摘Dear Editor,African swine fever(ASF)is one of the most pathogenic viral diseases in pigs caused by African swine fever virus(ASFV).The fatality rate is almost 100%,which brings huge economic losses to the hog industry in countries with epiepidemics(Galindo and Alonso,2017).China was the first Asian country to have an ASF epidemic,and it spread quickly across the country after the first epidemic was re・ported in August 2018(Ge et al.,2018).After that,Mongolia,Vietnam,Cambodia and North Korea also reported on the ASF epidemic in succession(OIE,2019).