The rapid expansion of next-generation sequencing （NGS） has generated a powerful array of approaches to address fundamental questions in biology. Several genome-partitioning strategies to sequence selected subsets o...The rapid expansion of next-generation sequencing （NGS） has generated a powerful array of approaches to address fundamental questions in biology. Several genome-partitioning strategies to sequence selected subsets of the genome have emerged in the fields of phylogenomics and evolutionary genomics. In this review, we summarize the applications, advantages and limitations of four NGS-based genome- partitioning approaches in plant phylogenomics： genome skimming, transcriptome sequencing （RNA- seq）, restriction site associated DNA sequencing （RAD-Seq）, and targeted capture （Hyb-seq）. Of these four genome-partitioning approaches, targeted capture （especially Hyb-seq） shows the greatest promise for plant phy^ogenetics over the next fex~ years. This reviex~ wi~ aid ~esea^chers in their selection of appropriate genome-partitioning approaches to address questions of evolutionary scale, where we anticipate continued development and expansion ofwhole-genome sequencing strategies in the fields of plant phylogenomics and evolutionary biology research.展开更多
As one of the most powerful tools in biomedical research,DNA sequencing not only has been improving its productivity at an exponential growth rate but has also been evolving into a new layout of technological territor...As one of the most powerful tools in biomedical research,DNA sequencing not only has been improving its productivity at an exponential growth rate but has also been evolving into a new layout of technological territories toward engineering and physical disciplines over the past three decades.In this technical review,we look into technical characteristics of the next-generation sequencers and provide insights into their future development and applications.We envisage that some of the emerging platforms are capable of supporting the USD1000 genome and USD100 genome goals if given a few years for technical maturation.We also suggest that scientists from China should play an active role in this campaign that will have a profound impact on both scientific research and societal healthcare systems.展开更多
With the rapid development of medicine,the studies of genes have become increasingly concerned by more people and being the contend of a great of researches.The next generation sequencing with its own advantages has b...With the rapid development of medicine,the studies of genes have become increasingly concerned by more people and being the contend of a great of researches.The next generation sequencing with its own advantages has been widely used in gene research nowadays.It has almost replaced the traditional sequencing methods(such as Sanger sequencing method),and played an important role in a variety of complex disease researches,including breast cancer.The next generation sequencing technology has the advantages of high speed,high throughput and high accuracy.It has been widely used in various cancers(such as prostate cancer,lung cancer,pancreatic cancer,liver cancer,etc.),especially in breast cancer.Moreover,the use of the next generation sequencing technology to make DNA sequence analysis and risk prediction has made a great contribution to the research of breast cancer.We will focus on the application of whole genome sequencing,exon sequencing and targeted gene sequencing in breast cancer gene research.展开更多
Background： Congenital cataract （CC） is the leading cause of visual impairment or blindness in children worldwide. Because of highly genetic and clinical heterogeneity, a molecular diagnosis of the lens disease rem...Background： Congenital cataract （CC） is the leading cause of visual impairment or blindness in children worldwide. Because of highly genetic and clinical heterogeneity, a molecular diagnosis of the lens disease remains a challenge. Methods： In this study, we tested a three-generation Chinese family with autosomal dominant CCs by targeted sequencing of 45 CC genes on next generation sequencing and evaluated the pathogenicity of the detected mutation by protein structure, pedigree validation, and molecular dynamics （MD） simulation. Results： A novel 15 bp deletion on GJA8 （c.426_440delGCTGGAGGGGACCCT or p. 143147delLEGTL） was detected in the family. The deletion, concerned with an in-frame deletion of 5 amino acid residues in a highly evolutionarily conserved region within the cytoplasmic loop domain of the gap junction channel protein connexin 50 （CxS0）, was in full cosegregation with the cataract phenotypes in the family but not found in 1100 control exomes. MD simulation revealed that the introduction of the deletion destabilized the Cx50 gap junction channel, indicating the deletion as a dominant-negative mutation, Conclusions： The above results support the pathogenic role of the 15 bp deletion on GJA8 in the Chinese family and demonstrate targeted genes sequencing as a resolution to molecular diagnosis of CCs.展开更多
Family Cortinariaceae currently includes only one genus,Cortinarius,which is the largest Agaricales genus,with thousands of species worldwide.The species are important ectomycorrhizal fungi and form associations with ...Family Cortinariaceae currently includes only one genus,Cortinarius,which is the largest Agaricales genus,with thousands of species worldwide.The species are important ectomycorrhizal fungi and form associations with many vascular plant gen-era from tropicals to arctic regions.Genus Cortinarius contains a lot of morphological variation,and its complexity has led many taxonomists to specialize in particular on infrageneric groups.The previous attempts to divide Cortinarius have been shown to be unnatural and the phylogenetic studies done to date have not been able to resolve the higher-level classification of the group above section level.Genomic approaches have revolutionized our view on fungal relationships and provide a way to tackle difficult groups.We used both targeted capture sequencing and shallow whole genome sequencing to produce data and to perform phylogenomic analyses of 75 single-copy genes from 19 species.In addition,a wider 5-locus analysis of 245 species,from the Northern and Southern Hemispheres,was also done.Based on our results,a classification of the family Cortinariaceae into ten genera-Cortinarius,Phlegmacium,Thaxterogaster,Calonarius,Aureonarius,Cystinarius,Volvanarius,Hygronarius,Mystinarius,and Austrocortinarius-is proposed.Seven genera,10 subgenera,and four sec-tions are described as new to science and five subgenera are introduced as new combinations in a new rank.In addition,41 section names and 514 species names are combined in new genera and four lecto-and epitypes designated.The position of Stephanopus in suborder Agaricineae remains to be studied.Targeted capture sequencing is used for the first time in fungal taxonomy in Basidiomycetes.It provides a cost-efficient way to produce-omics data in species-rich groups.The-omics data was produced from fungarium specimens up to 21 years old,demonstrating the value of museum specimens in the study of the fungal tree of life.This study is the first family revision in Agaricales based on genomics data and hopefully many others will soon follow.展开更多
基金supported by the Large-scale Scientific Facilities of the Chinese Academy of Sciences (Grant No: 2017-LSFGBOWS-01)the Strategic Priority Research Program of the Chinese Academy of Sciences (XDB31000000)the Program of Science and Technology Talents Training of Yunnan Province (2017HA014)
文摘The rapid expansion of next-generation sequencing （NGS） has generated a powerful array of approaches to address fundamental questions in biology. Several genome-partitioning strategies to sequence selected subsets of the genome have emerged in the fields of phylogenomics and evolutionary genomics. In this review, we summarize the applications, advantages and limitations of four NGS-based genome- partitioning approaches in plant phylogenomics： genome skimming, transcriptome sequencing （RNA- seq）, restriction site associated DNA sequencing （RAD-Seq）, and targeted capture （Hyb-seq）. Of these four genome-partitioning approaches, targeted capture （especially Hyb-seq） shows the greatest promise for plant phy^ogenetics over the next fex~ years. This reviex~ wi~ aid ~esea^chers in their selection of appropriate genome-partitioning approaches to address questions of evolutionary scale, where we anticipate continued development and expansion ofwhole-genome sequencing strategies in the fields of plant phylogenomics and evolutionary biology research.
文摘为建立一种高同源区段的单核苷酸多态性(SNP)基因分型技术,通过构建本地Blast对SNP所在的200和400 bp区段进行同源性评估,并筛选出高同源区段的SNP。利用第一轮多重长PCR(polymerase chain reaction)捕获329个样本的9个高同源区段SNP所在的长片段,使用纯化后的第一轮PCR产物作为模板进行扩增子建库测序,检测样本共得2 928个SNP位点信息,测序成功率高达98.885 6%。利用Hardy-Weinberg(HWE)法则计算试验研究的9个高同源区段SNP位点的基因频率(p值均大于0.05,符合HWE法则),并与NCBI(national center for biotechnology information)中千人基因组数据库中获取的基因频率相比对,发现二者单碱基基因频率一致(误差限<0.15)。研究表明,利用多重长PCR靶向捕获技术结合二代测序技术为高同源区段的SNP分型提供一个准确、快速、大样本检测方案。
基金supported by the Chinese Academy of Sciences Scientific Research Equipment (Grant No YZ200823)
文摘As one of the most powerful tools in biomedical research,DNA sequencing not only has been improving its productivity at an exponential growth rate but has also been evolving into a new layout of technological territories toward engineering and physical disciplines over the past three decades.In this technical review,we look into technical characteristics of the next-generation sequencers and provide insights into their future development and applications.We envisage that some of the emerging platforms are capable of supporting the USD1000 genome and USD100 genome goals if given a few years for technical maturation.We also suggest that scientists from China should play an active role in this campaign that will have a profound impact on both scientific research and societal healthcare systems.
文摘With the rapid development of medicine,the studies of genes have become increasingly concerned by more people and being the contend of a great of researches.The next generation sequencing with its own advantages has been widely used in gene research nowadays.It has almost replaced the traditional sequencing methods(such as Sanger sequencing method),and played an important role in a variety of complex disease researches,including breast cancer.The next generation sequencing technology has the advantages of high speed,high throughput and high accuracy.It has been widely used in various cancers(such as prostate cancer,lung cancer,pancreatic cancer,liver cancer,etc.),especially in breast cancer.Moreover,the use of the next generation sequencing technology to make DNA sequence analysis and risk prediction has made a great contribution to the research of breast cancer.We will focus on the application of whole genome sequencing,exon sequencing and targeted gene sequencing in breast cancer gene research.
文摘Background： Congenital cataract （CC） is the leading cause of visual impairment or blindness in children worldwide. Because of highly genetic and clinical heterogeneity, a molecular diagnosis of the lens disease remains a challenge. Methods： In this study, we tested a three-generation Chinese family with autosomal dominant CCs by targeted sequencing of 45 CC genes on next generation sequencing and evaluated the pathogenicity of the detected mutation by protein structure, pedigree validation, and molecular dynamics （MD） simulation. Results： A novel 15 bp deletion on GJA8 （c.426_440delGCTGGAGGGGACCCT or p. 143147delLEGTL） was detected in the family. The deletion, concerned with an in-frame deletion of 5 amino acid residues in a highly evolutionarily conserved region within the cytoplasmic loop domain of the gap junction channel protein connexin 50 （CxS0）, was in full cosegregation with the cataract phenotypes in the family but not found in 1100 control exomes. MD simulation revealed that the introduction of the deletion destabilized the Cx50 gap junction channel, indicating the deletion as a dominant-negative mutation, Conclusions： The above results support the pathogenic role of the 15 bp deletion on GJA8 in the Chinese family and demonstrate targeted genes sequencing as a resolution to molecular diagnosis of CCs.
文摘Family Cortinariaceae currently includes only one genus,Cortinarius,which is the largest Agaricales genus,with thousands of species worldwide.The species are important ectomycorrhizal fungi and form associations with many vascular plant gen-era from tropicals to arctic regions.Genus Cortinarius contains a lot of morphological variation,and its complexity has led many taxonomists to specialize in particular on infrageneric groups.The previous attempts to divide Cortinarius have been shown to be unnatural and the phylogenetic studies done to date have not been able to resolve the higher-level classification of the group above section level.Genomic approaches have revolutionized our view on fungal relationships and provide a way to tackle difficult groups.We used both targeted capture sequencing and shallow whole genome sequencing to produce data and to perform phylogenomic analyses of 75 single-copy genes from 19 species.In addition,a wider 5-locus analysis of 245 species,from the Northern and Southern Hemispheres,was also done.Based on our results,a classification of the family Cortinariaceae into ten genera-Cortinarius,Phlegmacium,Thaxterogaster,Calonarius,Aureonarius,Cystinarius,Volvanarius,Hygronarius,Mystinarius,and Austrocortinarius-is proposed.Seven genera,10 subgenera,and four sec-tions are described as new to science and five subgenera are introduced as new combinations in a new rank.In addition,41 section names and 514 species names are combined in new genera and four lecto-and epitypes designated.The position of Stephanopus in suborder Agaricineae remains to be studied.Targeted capture sequencing is used for the first time in fungal taxonomy in Basidiomycetes.It provides a cost-efficient way to produce-omics data in species-rich groups.The-omics data was produced from fungarium specimens up to 21 years old,demonstrating the value of museum specimens in the study of the fungal tree of life.This study is the first family revision in Agaricales based on genomics data and hopefully many others will soon follow.
