The rubber tree,Hevea brasiliensis,produces natural rubber that serves as an essential industrial raw material.Here,we present a high-quality reference genome for a rubber tree cultivar GT1 using single-molecule real-...The rubber tree,Hevea brasiliensis,produces natural rubber that serves as an essential industrial raw material.Here,we present a high-quality reference genome for a rubber tree cultivar GT1 using single-molecule real-time sequencing(SMRT)and Hi-C technologies to anchor the~1.47-Gb genome assembly into 18 pseudochromosomes.The chromosome-based genome analysis enabled us to establish a model of spurge chromosome evolution,since the common paleopolyploid event occurred before the split of Hevea and Manihot.We show recent and rapid bursts of the three Hevea-specific LTR-retrotransposon families during the last 10 million years,leading to the massive expansion by~65.88%(~970 Mbp)of the whole rubber tree genome since the divergence from Manihot.We identify large-scale expansion of genes associated with whole rubber biosynthesis processes,such as basal metabolic processes,ethylene biosynthesis,and the activation of polysaccharide and glycoprotein lectin,which are important properties for latex production.A map of genomic variation between the cultivated and wild rubber trees was obtained,which contains~15.7 million high-quality single-nucleotide polymorphisms.We identified hundreds of candidate domestication genes with drastically lowered genomic diversity in the cultivated but not wild rubber trees despite a relatively short domestication history of rubber tree,some of which are involved in rubber biosynthesis.This genome assembly represents key resources for future rubber tree research and breeding,providing novel targets for improving plant biotic and abiotic tolerance and rubber production.展开更多
Dear Editor,The tea tree Camellia sinensis,a member of the genus Camellia in the Theaceae family,includes two major cultivated varieties,C.sinensis var.assamica(CSA\Assam type)and C.sinensis var.sinensis(CSS;Chinese t...Dear Editor,The tea tree Camellia sinensis,a member of the genus Camellia in the Theaceae family,includes two major cultivated varieties,C.sinensis var.assamica(CSA\Assam type)and C.sinensis var.sinensis(CSS;Chinese type)(Ming and Bartholomew,2007).Due to the high economic importance of the tea tree,considerable efforts have been made to explore genetic basis of the biosynthesis of natural metabolites that determine health benefits and diverse tea flavors(Shi et al.,2011;Li et al.,2011;Li et al.,2015;Xia et aL,2017;Liu et al.,2019).展开更多
Complex structural variants(CSVs) are genomic alterations that have more than two breakpoints and are considered as the simultaneous occurrence of simple structural variants.However,detecting the compounded mutational...Complex structural variants(CSVs) are genomic alterations that have more than two breakpoints and are considered as the simultaneous occurrence of simple structural variants.However,detecting the compounded mutational signals of CSVs is challenging through a commonly used model-match strategy.As a result,there has been limited progress for CSV discovery compared with simple structural variants.Here,we systematically analyzed the multi-breakpoint connection feature of CSVs,and proposed Mako,utilizing a bottom-up guided model-free strategy,to detect CSVs from paired-end short-read sequencing.Specifically,we implemented a graph-based pattern growth approach,where the graph depicts potential breakpoint connections,and pattern growth enables CSV detection without pre-defined models.Comprehensive evaluations on both simulated and real datasets revealed that Mako outperformed other algorithms.Notably,validation rates of CSVs on real data based on experimental and computational validations as well as manual inspections are around 70%,where the medians of experimental and computational breakpoint shift are 13 bp and 26 bp,respectively.Moreover,the Mako CSV subgraph effectively characterized the breakpoint connections of a CSV event and uncovered a total of 15 CSV types,including two novel types of adjacent segment swap and tandem dispersed duplication.Further analysis of these CSVs also revealed the impact of sequence homology on the formation of CSVs.Mako is publicly available at https://github.com/xjtu-omics/Mako.展开更多
基金supported by Yunnan Innovation Team Project and the start-up grant from South China Agricultural University(to L.G.).
文摘The rubber tree,Hevea brasiliensis,produces natural rubber that serves as an essential industrial raw material.Here,we present a high-quality reference genome for a rubber tree cultivar GT1 using single-molecule real-time sequencing(SMRT)and Hi-C technologies to anchor the~1.47-Gb genome assembly into 18 pseudochromosomes.The chromosome-based genome analysis enabled us to establish a model of spurge chromosome evolution,since the common paleopolyploid event occurred before the split of Hevea and Manihot.We show recent and rapid bursts of the three Hevea-specific LTR-retrotransposon families during the last 10 million years,leading to the massive expansion by~65.88%(~970 Mbp)of the whole rubber tree genome since the divergence from Manihot.We identify large-scale expansion of genes associated with whole rubber biosynthesis processes,such as basal metabolic processes,ethylene biosynthesis,and the activation of polysaccharide and glycoprotein lectin,which are important properties for latex production.A map of genomic variation between the cultivated and wild rubber trees was obtained,which contains~15.7 million high-quality single-nucleotide polymorphisms.We identified hundreds of candidate domestication genes with drastically lowered genomic diversity in the cultivated but not wild rubber trees despite a relatively short domestication history of rubber tree,some of which are involved in rubber biosynthesis.This genome assembly represents key resources for future rubber tree research and breeding,providing novel targets for improving plant biotic and abiotic tolerance and rubber production.
基金This study was supported by a startup grant from the South China Agricultural University and Yunnan Innovation Team Project(to L.-Z.G.).E.E.E.is an investigator of the Howard Hughes Medical Institute.
文摘Dear Editor,The tea tree Camellia sinensis,a member of the genus Camellia in the Theaceae family,includes two major cultivated varieties,C.sinensis var.assamica(CSA\Assam type)and C.sinensis var.sinensis(CSS;Chinese type)(Ming and Bartholomew,2007).Due to the high economic importance of the tea tree,considerable efforts have been made to explore genetic basis of the biosynthesis of natural metabolites that determine health benefits and diverse tea flavors(Shi et al.,2011;Li et al.,2011;Li et al.,2015;Xia et aL,2017;Liu et al.,2019).
基金supported by the National Key R&D Program of China(Grant Nos.2018YFC0910400 and 2017YFC0907500)the National Science Foundation of China(Grant Nos.31671372,61702406,and 31701739)+3 种基金the Fundamental Research Funds for the Central Universitiesthe World-Class Universities(Disciplines)the Characteristic Development Guidance Funds for the Central Universitiesthe Shanghai Municipal Science and Technology Major Project(Grant No.2017SHZDZX01)。
文摘Complex structural variants(CSVs) are genomic alterations that have more than two breakpoints and are considered as the simultaneous occurrence of simple structural variants.However,detecting the compounded mutational signals of CSVs is challenging through a commonly used model-match strategy.As a result,there has been limited progress for CSV discovery compared with simple structural variants.Here,we systematically analyzed the multi-breakpoint connection feature of CSVs,and proposed Mako,utilizing a bottom-up guided model-free strategy,to detect CSVs from paired-end short-read sequencing.Specifically,we implemented a graph-based pattern growth approach,where the graph depicts potential breakpoint connections,and pattern growth enables CSV detection without pre-defined models.Comprehensive evaluations on both simulated and real datasets revealed that Mako outperformed other algorithms.Notably,validation rates of CSVs on real data based on experimental and computational validations as well as manual inspections are around 70%,where the medians of experimental and computational breakpoint shift are 13 bp and 26 bp,respectively.Moreover,the Mako CSV subgraph effectively characterized the breakpoint connections of a CSV event and uncovered a total of 15 CSV types,including two novel types of adjacent segment swap and tandem dispersed duplication.Further analysis of these CSVs also revealed the impact of sequence homology on the formation of CSVs.Mako is publicly available at https://github.com/xjtu-omics/Mako.