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
Weeping forsythia (Forsythia suspensa,Oleaceae) is a deciduous broad-leaved tree species distributed in the warm temperate zone of China.However,the species still lacks a chromosome-level genome.In this study,the form...Weeping forsythia (Forsythia suspensa,Oleaceae) is a deciduous broad-leaved tree species distributed in the warm temperate zone of China.However,the species still lacks a chromosome-level genome.In this study,the former draft genome (Accession No.WIPI00000000) of weeping forsythia was assembled into 14 chromosomes with a 712.9 Mb genome size.Weeping forsythia underwent a and b whole-genome duplication events.After the divergence between weeping forsythia and Olea europaea,1 453 gene families had a significant expansion,and 1 146 gene families had a significant contraction.The enrichment pathways and ontologies of expanded genes suggested that the tillering,photosynthesis and growth capacity of weeping forsythia were enhanced after the divergence of weeping forsythia and O.europaea.The contracted genes suggested that the resistance of weeping forsythia to cold and drought was weakened.The last glacial period led to a significant decline in the effective population size of weeping forsythia.Forty-six candidate genes were identified for the synthesis of the forsythin and forsythoside A by genomic and transcriptomic data.In this study,we improved the previous draft genome of weeping forsythia.Our genome will provide genomic resources for the subsequent evolution and breeding research of weeping forsythia.展开更多
The Fagaceae,a plant family with a wide distribution and diverse adaptability,has garnered significant interest as a subject of study in plant speciation and adaptation.Meanwhile,certain Fagaceae species are regarded ...The Fagaceae,a plant family with a wide distribution and diverse adaptability,has garnered significant interest as a subject of study in plant speciation and adaptation.Meanwhile,certain Fagaceae species are regarded as highly valuable wood resources due to the exceptional quality of their wood.In this study,we present two high-quality,chromosome-scale genome sequences for Quercus sichourensis(848.75 Mb)and Quercus rex(883.46 Mb).Comparative genomics analysis reveals that the difference in the number of plant disease resistance genes and the nonsynonymous and synonymous substitution ratio(Ka/Ks)of protein-coding genes among Fagaceae species are related to different environmental adaptations.Interestingly,most genes related to starch synthesis in the investigated Quercoideae species are located on a single chromosome,as compared to the outgroup species,Fagus sylvatica.Furthermore,resequencing and population analysis of Q.sichourensis and Q.rex reveal that Q.sichourensis has lower genetic diversity and higher deleterious mutations compared to Q.rex.The high-quality,chromosome-level genomes and the population genomic analysis of the critically endangered Q.sichourensis and Q.rex will provide an invaluable resource as well as insights for future study in these two species,even the genus Quercus,to facilitate their conservation.展开更多
目的探讨胎儿先天性心脏痫基因型与临床表型之间的关联性，旨在为先天性心脏病遗传学咨询发病机制研究提供信息。方法选取2012年9月至2015年6月间首都医科大学北京安贞医院胎儿心脏病母胎医学会诊中心胎儿心脏畸形数据库心肌等组织标本6...目的探讨胎儿先天性心脏痫基因型与临床表型之间的关联性，旨在为先天性心脏病遗传学咨询发病机制研究提供信息。方法选取2012年9月至2015年6月间首都医科大学北京安贞医院胎儿心脏病母胎医学会诊中心胎儿心脏畸形数据库心肌等组织标本62例，按区段月不胎学分类法进行分型，并送深圳华大基因研究院利用全基因组低覆盖度测序检测染色体缺失／重复，目标区域捕获测序检测先天性心脏病相关基因的单核苷酸变异及小的捅入缺失片段。结果（1）本研究中胎儿先天性心脏病以圆锥动脉干畸形（conotruncal defects，CTD）最常见（69．4％，43／62）。（2）共30例胎儿检出〉100kb的拷贝数变异（copy number variations，CNVs）（48．4％，30／62），其中11例检出〉1Mb的CNVs，11例中7例为致病意义明确，7例中有6例心脏临床表刊累及CTD。（3）5例胎儿检出已知及疑似致病基因，其中4例胎儿存在心室流出道梗阻。结论本研究中胎儿的心脏临床表型以CTD常见，检出致病意义明确的胎儿心脏表型亦以CTD常见；检出疑似致病突变基因的胎儿，其临床表型以心事流出道梗阻多见。展开更多
先天性心脏病、多指(趾)、唇裂、先天性脑积水及马蹄内翻足在出生缺陷患儿疾病中位居前5位,有报告指出上述疾病的发生与染色体的微缺失、微重复异常有关。产前诊断是预防出生缺陷的主要手段,是在胎儿出生前利用先进技术对胎儿的先天性...先天性心脏病、多指(趾)、唇裂、先天性脑积水及马蹄内翻足在出生缺陷患儿疾病中位居前5位,有报告指出上述疾病的发生与染色体的微缺失、微重复异常有关。产前诊断是预防出生缺陷的主要手段,是在胎儿出生前利用先进技术对胎儿的先天性疾病进行诊断。研究表明低深度全基因组测序技术(copy number variation sequencing,CNV-seq)可对产前染色体微缺失、微重复异常进行诊断,将染色体异常的检出率增加至2.8%。CNV-seq技术是在高通量测序基础上发展的全基因组测序技术,其检测范围广、分辨率高,可检测全基因组水平的微缺失、微重复异常,已逐步应用于胎儿先天性疾病及流产组织遗传学病因的检测,还可用于明确未知来源的染色体畸变。综述CNV-seq技术在产前诊断中的研究进展。展开更多
It has been shown that duplicate genes on the X chromosome evolve much faster than duplicate genes on autosomes in Drosophila melanogaster. However, whether this phenomenon is general and can be applied to other speci...It has been shown that duplicate genes on the X chromosome evolve much faster than duplicate genes on autosomes in Drosophila melanogaster. However, whether this phenomenon is general and can be applied to other species is not known. Here we examined this issue in chicken that have heterogametic females （females have ZW sex chromosome）. We compared sequence divergence of duplicate genes on the Z chromosome with those on autosomes. We found that duplications on the Z chromosome indeed evolved faster than those on autosomes and show distinct patterns of molecular evolution from autosomal duplications. Examination of the expression of duplicate genes revealed an enrichment of duplications on the Z chromosome having male-biased expression and an enrichment of duplications on the autosomes having female-biased expression. These results suggest an evolutionary trend of the recruitment of duplicate genes towards reproduction-specific function. The faster evolution of duplications on Z than on the autosomes is most likely contributed by the selective forces driving the fixation of adaptive mutations on Z. Therefore, the common phenomena observed in both flies and chicken suggest that duplicate genes on sex chromosomes have distinct dynamics and are more influenced by natural selection than autosomal duplications, regardless of the kind of sex determination systems.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supported by the Open Fund of State Key Laboratory of Tree Genetics and Breeding (Chinese Academy of Forestry)(Grant No.TGB2021004)National Natural Science Foundation of China (Grant Nos.31770225,31570594)Program of Guangzhou Municipal Science and Technology Bureau(Grant No.202102021257)。
文摘Weeping forsythia (Forsythia suspensa,Oleaceae) is a deciduous broad-leaved tree species distributed in the warm temperate zone of China.However,the species still lacks a chromosome-level genome.In this study,the former draft genome (Accession No.WIPI00000000) of weeping forsythia was assembled into 14 chromosomes with a 712.9 Mb genome size.Weeping forsythia underwent a and b whole-genome duplication events.After the divergence between weeping forsythia and Olea europaea,1 453 gene families had a significant expansion,and 1 146 gene families had a significant contraction.The enrichment pathways and ontologies of expanded genes suggested that the tillering,photosynthesis and growth capacity of weeping forsythia were enhanced after the divergence of weeping forsythia and O.europaea.The contracted genes suggested that the resistance of weeping forsythia to cold and drought was weakened.The last glacial period led to a significant decline in the effective population size of weeping forsythia.Forty-six candidate genes were identified for the synthesis of the forsythin and forsythoside A by genomic and transcriptomic data.In this study,we improved the previous draft genome of weeping forsythia.Our genome will provide genomic resources for the subsequent evolution and breeding research of weeping forsythia.
基金“the Thousand Talents Plan”(5113190037 to J.C.)Fundamental Research Funds for the Central Universities(3102019JC007)+1 种基金Science and Technology Basic Resources Investigation Program of China(2017FY100100)NSFC(National Natural Science Foundation of China)-Yunnan Joint Fund(U1302262).
文摘The Fagaceae,a plant family with a wide distribution and diverse adaptability,has garnered significant interest as a subject of study in plant speciation and adaptation.Meanwhile,certain Fagaceae species are regarded as highly valuable wood resources due to the exceptional quality of their wood.In this study,we present two high-quality,chromosome-scale genome sequences for Quercus sichourensis(848.75 Mb)and Quercus rex(883.46 Mb).Comparative genomics analysis reveals that the difference in the number of plant disease resistance genes and the nonsynonymous and synonymous substitution ratio(Ka/Ks)of protein-coding genes among Fagaceae species are related to different environmental adaptations.Interestingly,most genes related to starch synthesis in the investigated Quercoideae species are located on a single chromosome,as compared to the outgroup species,Fagus sylvatica.Furthermore,resequencing and population analysis of Q.sichourensis and Q.rex reveal that Q.sichourensis has lower genetic diversity and higher deleterious mutations compared to Q.rex.The high-quality,chromosome-level genomes and the population genomic analysis of the critically endangered Q.sichourensis and Q.rex will provide an invaluable resource as well as insights for future study in these two species,even the genus Quercus,to facilitate their conservation.
文摘目的探讨胎儿先天性心脏痫基因型与临床表型之间的关联性，旨在为先天性心脏病遗传学咨询发病机制研究提供信息。方法选取2012年9月至2015年6月间首都医科大学北京安贞医院胎儿心脏病母胎医学会诊中心胎儿心脏畸形数据库心肌等组织标本62例，按区段月不胎学分类法进行分型，并送深圳华大基因研究院利用全基因组低覆盖度测序检测染色体缺失／重复，目标区域捕获测序检测先天性心脏病相关基因的单核苷酸变异及小的捅入缺失片段。结果（1）本研究中胎儿先天性心脏病以圆锥动脉干畸形（conotruncal defects，CTD）最常见（69．4％，43／62）。（2）共30例胎儿检出〉100kb的拷贝数变异（copy number variations，CNVs）（48．4％，30／62），其中11例检出〉1Mb的CNVs，11例中7例为致病意义明确，7例中有6例心脏临床表刊累及CTD。（3）5例胎儿检出已知及疑似致病基因，其中4例胎儿存在心室流出道梗阻。结论本研究中胎儿的心脏临床表型以CTD常见，检出致病意义明确的胎儿心脏表型亦以CTD常见；检出疑似致病突变基因的胎儿，其临床表型以心事流出道梗阻多见。
文摘先天性心脏病、多指(趾)、唇裂、先天性脑积水及马蹄内翻足在出生缺陷患儿疾病中位居前5位,有报告指出上述疾病的发生与染色体的微缺失、微重复异常有关。产前诊断是预防出生缺陷的主要手段,是在胎儿出生前利用先进技术对胎儿的先天性疾病进行诊断。研究表明低深度全基因组测序技术(copy number variation sequencing,CNV-seq)可对产前染色体微缺失、微重复异常进行诊断,将染色体异常的检出率增加至2.8%。CNV-seq技术是在高通量测序基础上发展的全基因组测序技术,其检测范围广、分辨率高,可检测全基因组水平的微缺失、微重复异常,已逐步应用于胎儿先天性疾病及流产组织遗传学病因的检测,还可用于明确未知来源的染色体畸变。综述CNV-seq技术在产前诊断中的研究进展。
基金supported by the National Science Foundation of China (No. 30600064)the National Basic Research Program of China (973 Program) (No. 2007CB815702) to X.Lu
文摘It has been shown that duplicate genes on the X chromosome evolve much faster than duplicate genes on autosomes in Drosophila melanogaster. However, whether this phenomenon is general and can be applied to other species is not known. Here we examined this issue in chicken that have heterogametic females （females have ZW sex chromosome）. We compared sequence divergence of duplicate genes on the Z chromosome with those on autosomes. We found that duplications on the Z chromosome indeed evolved faster than those on autosomes and show distinct patterns of molecular evolution from autosomal duplications. Examination of the expression of duplicate genes revealed an enrichment of duplications on the Z chromosome having male-biased expression and an enrichment of duplications on the autosomes having female-biased expression. These results suggest an evolutionary trend of the recruitment of duplicate genes towards reproduction-specific function. The faster evolution of duplications on Z than on the autosomes is most likely contributed by the selective forces driving the fixation of adaptive mutations on Z. Therefore, the common phenomena observed in both flies and chicken suggest that duplicate genes on sex chromosomes have distinct dynamics and are more influenced by natural selection than autosomal duplications, regardless of the kind of sex determination systems.
