共查询到19条相似文献，搜索用时 46 毫秒
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基因组变异作为生物遗传多样性产生的核心,对解析生命演化、揭示物种内个体差异、探究疾病机制等方面有重要影响,而参考基因组作为遗传研究中的参考框架,其序列表征能力会直接影响遗传变异的准确识别。当前广泛应用的人类参考基因组主要由西方人群样本组成,对中国人群特异性遗传变异解析能力不足,亟需构建有中国人遗传特性的新参考基因组,以促进对中国人群遗传和进化机制的深入研究。本研究提出一种基于人群基因组变异的参考基因组改造方法,利用单核苷酸变异(SNV)、短插入删除变异(Indel)以及结构变异(SV)三种类型的东亚人群变异数据对GRCh38版本人类参考基因组进行改造,经过多层筛选、修订,建立了一系列包含不同变异频率、变异类型的中国人参考基因组。通过选取不同地域的中国人样本测序数据对所改造的中国人参考基因组进行序列比对测试,选取变异频率超过2/3,1/2,1/2的东亚人SV,Indel和SNV变异改造GRCh38参考基因组时分别获得了最佳比对效果。最终整合上述对应变异频率下的全部变异改造参考基因组时,得到了最优的中国人参考基因组。本研究所建立的中国人参考基因组将有望提升大规模中国人群基因组变异识别的能力,为后续中国人参考基因组构建工作提供有效方法。方法详见:https://github.com/azheasir/Chinese-specific-reference-genome-construction。 相似文献
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基因组注释是识别出基因组序列中功能组件的过程,其可以直接对序列赋予生物学意义,由此方便研究者探究和分析基因组功能.基因组注释可以帮助研究从三个层次上理解基因组,一种是在核苷酸水平的注释,主要确定DNA序列中基因、RNA、重复序列等组件的物理位置,包括转录起始,翻译起始,外显子边界等具体位置信息.同时可以注释得到变异在不... 相似文献
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大肠杆菌分布广泛,是微生物遗传学和分子遗传学重要的研究对象,对大肠杆菌遗传学研究的许多重要发现,加学了我们在分子水平上对生物遗传机制的理解;同时由于我们对大肠杆菌遗传背景有较深的了解,大肠杆菌在基因工程研究中占据着不可替代的重要地位。本文拟将大肠杆菌基因组图谱研究方向的进展作一简要综述。 大肠杆菌基因组是由超螺旋的环状DNA分子所组成,其长度为4710.4千碱基对(kb)。大肠杆菌基因组图谱有下列三种表现形式。 相似文献
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人基因组分析是现代生物学研究的前沿之一,其目标是分析人基因组3×10~9bp的全核苷酸序列,识别所有基因的位置和功能,基因组分析的第一步是要进行物理图谱分析,然后才能分段进行序列分析,最后将全部序列连成人基因组的全序列。由于人基因组之巨大,传统的图谱分析如cosmid,由于其克隆容量只有40Kb;而经典的分析方法如遗传连锁(geneticlinkage)分析的分辩力太低(1cM,相当于1Mb,megabase,百万碱基对),不宜于作为人基因组分析的第一克隆工具。1987年,美国华盛顿大学的M.Olson小组首次在成功地将长达数百Kb的人染色体片段以YAC(Yeast Artificial Chromosome)形式克隆到酵母细胞中, 相似文献
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权静;肖艳群;卢大儒;鲍芸 《遗传》2025,(4):428-436
随着基因组研究的不断深入,越来越多的研究发现结构变异(structural variantions,SVs)在人类进化及疾病发生发展中发挥着重要作用,由此SVs也引起了临床研究的广泛关注。近年来,基因组光学图谱技术(optical genome mapping,OGM)作为一种高分辨率、超长读长、自动化的新型非测序基因检测技术凸显了在SVs研究中的优势。与核型(karotyping)、荧光原位杂交(fluorescence in situ hybridization,FISH)、染色体微阵列分析(chromosomal microarray analysis,CMA)及高通量测序技术相比,OGM可一次性检测全基因组范围内的结构和数目异常,包括染色体非整倍体、插入、缺失、重复、倒位、平衡易位以及复杂结构变异等,且OGM检测分辨率高至500 bp,因其分辨率高和分析片段长度长的检测特性,又被称为下一代细胞遗传学技术,对基因组结构变异检测具有重大应用价值。本文主要对OGM检测方法及其在疾病相关SVs诊断中的应用研究进行了综述,旨在为SVs在疾病诊断领域中的研究提供参考和借鉴。 相似文献
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人类基因组结构变异 总被引：2，自引：0，他引：2
基因组结构变异通常是指基因组内大于1 kb的DNA片段缺失、插入、重复、倒位、易位以及DNA拷贝数目变化(CNVs)。人类基因组结构变异涉及数千片段不连续的基因组区域, 含数百万DNA碱基对, 可含数个基因及调控序列, 多种基因功能因此缺失或改变, 导致机体表型变化、疾病易感性改变或发生疾病。对基因组结构变异的研究, 有助于用动态的观点全面分析基因组遗传变异得到整合的基因型, 理解结构变异的潜在医学作用及机体整体功能的复杂性。文章从人类基因组结构变异的类型、研究方法, 对个体表型、疾病及生物进化的影响等方面综合阐述人类基因组结构变异的最新研究进展。 相似文献
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高通量测序技术和生物信息学的发展极大的促进了山羊分子生物学研究。山羊参考基因组的不断完善以及基因组重测序技术的应用,在全基因组水平上发现了大量的遗传变异信息(SNP、Indel和CNV),丰富了山羊分子群体遗传学研究利用的分子标记。综述了山羊参考基因组组装和全基因组变异图谱的构建及其在山羊上的研究进展,以期为进一步利用分子遗传标记进行山羊的各种性状的遗传基础研究和遗传资源保护利用提供科学依据和参考。 相似文献
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随着三代测序组装的高质量参考基因组的陆续发布,以及大规模重测序和群体遗传学分析的广泛进行,研究人员发现来自单一个体的参考基因组远不能涵盖整个物种的所有遗传序列,大量缺失序列导致群体遗传变异图谱不完整,而构建来自多个个体的泛基因组能很好地解决这一缺陷,其研究内容包括负责基本生物学功能及该物种主要表型特征的核心基因组以及与物种的遗传多样性和个体独特性相关的可变基因组。根据核心和可变基因组所占比例的不同,泛基因组存在开放型和闭合型两种类型。本文主要综述了细菌、真菌和动植物的泛基因组学研究进展,讨论了其在各生物类群中的特征,其中哺乳动物泛基因组是相对闭合的,而目前已知的微生物、被子植物和部分低等动物的泛基因组倾向于开放,通过泛基因组的构建可以完善现有参考基因组并获取整个物种的完整变异信息,将有助于深入研究遗传多样性和表型变异产生的分子机制。 相似文献
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结构变异作为人类基因组上的一种大规模的变异类型,对分子与细胞进程、调节功能、基因表达调控、个体表型具有重要的影响,检测群体中基因组结构变异有助于绘制群体基因组变异图谱,刻画群体遗传进化特征,为疾病诊治、精准医疗的发展提供支撑。本研究提出一种面向高通量测序的群体基因组结构变异检测工作流,该工作流通过使用多种高性能基因组结构变异检测算法实现全面、精准的结构变异挖掘,使用多层融合与过滤获得高精度群体结构变异候选集合,利用基因型重新校正、变异修剪、类型校对,最终完整绘制群体基因组结构变异图谱。基于该工作流对由267个样本组成的人群进行群体结构变异检测,检测出了96 202个结构变异,其变异种类和频率分布与其他国际基因组计划相符,这些结果证明了本工作流具有良好的群体结构变异检测能力。同时,工作流通过并行的方式在内存可控的基础上显著降低了分析时间,为大规模人群基因组结构变异的高效检测提供了重要支撑。 相似文献
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Ingerid J. Hagen Sigbjrn Lien Anna M. Billing Tore O. Elgvin Cassandra Trier Alina K. Niskanen Maja Tarka Jon Slate Glenn‐Peter Stre Henrik Jensen 《Molecular ecology resources》2020,20(2):544-559
The house sparrow is an important model species for studying physiological, ecological and evolutionary processes in wild populations. Here, we present a medium density, genome wide linkage map for house sparrow (Passer domesticus) that has aided the assembly of the house sparrow reference genome, and that will provide an important resource for ongoing mapping of genes controlling important traits in the ecology and evolution of this species. Using a custom house sparrow 10 K iSelect Illumina SNP chip we have assigned 6,498 SNPs to 29 autosomal linkage groups, based on a mean of 430 informative meioses per SNP. The map was constructed by combining the information from linkage with that of the physical position of SNPs within scaffold sequences in an iterative process. Averaged between the sexes; the linkage map had a total length of 2,004 cM, with a longer map for females (2,240 cM) than males (1,801 cM). Additionally, recombination rates also varied along the chromosomes. Comparison of the linkage map to the reference genomes of zebra finch, collared flycatcher and chicken, showed a chromosome fusion of the two avian chromosomes 8 and 4A in house sparrow. Lastly, information from the linkage map was utilized to conduct analysis of linkage disequilibrium (LD) in eight populations with different effective population sizes (Ne) in order to quantify the background level LD. Together, these results aid the design of future association studies, facilitate the development of new genomic tools and support the body of research that describes the evolution of the avian genome. 相似文献
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Elucidating the forces responsible for genomic variation is critical for understanding evolution. Under standard conditions, X-linked diversity is expected to be three-quarters the level of autosomal diversity. Empirical data often deviate from this prediction, but the reasons for these departures are unclear. We demonstrate that population size changes can greatly alter relative levels of X-linked and autosomal variation: population size reductions lead to particularly low X-linked diversity, whereas growth elevates X-linked relative to autosomal diversity. Genetic variation from a diverse array of taxa supports an important role for this effect in accounting for population differences in the ratio of X-linked to autosomal diversity. Consideration of this effect may improve the inference of population history and other evolutionary processes. 相似文献
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Chunxian Chen Kim D. Bowman Young A Choi Phat M. Dang Madhugiri Nageswara Rao Shu Huang Jaya R. Soneji T. Greg McCollum Fred G. Gmitter Jr. 《Tree Genetics & Genomes》2008,4(1):1-10
The segregation of 141 polymorphic expressed sequence tag-simple sequence repeat (EST-SSR) markers in an F1 intergeneric citrus population was studied to build the first extensive EST maps for the maternal sweet orange and paternal Poncirus genomes. Of these markers, 122 were found segregating in sweet orange, 59 in Poncirus, and 40 in both. Eleven linkage groups with 113 markers in sweet orange, 8 with 45 markers in Poncirus, and 13 with 123 markers in the cross pollinator (CP) consensus of both, were constructed. About 775.8 cM of sweet orange genome and 425.7 cM of Poncirus genome were covered. Through comparison of shared markers, three cases were found where two linkage groups in one map apparently were colinear with one group of the other map; Poncirus linkages Ar1a and Ar1b and consensus linkages CP1a and CP1b, were both collinear with one sweet orange linkage, Sa1, as were sweet orange Sa3a and Sa3b with Poncirus Ar3 and consensus CP3, and sweet orange Sa7a and Sa7b, and consensus CP7a and CP7b with Poncirus Ar7. These EST-SSR markers are particularly useful for constructing comparative framework maps for related genera because they amplify orthologous genes to provide anchor points across taxa. All SSR primers are freely available to the citrus community. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
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Zhenglin Du Liang Ma Hongzhu Qu Wei Chen Bing Zhang Xi Lu Weibo Zhai Xin Sheng Yongqiao Sun Wenjie Li Meng Lei Qiuhui Qi Na Yuan Shuo Shi Jingyao Zeng Jinyue Wang Yadong Yang Qi Liu Yaqiang Hong Lili Dong Zhewen Zhang Dong Zou Yanqing Wang Shuhui Song Fan Liu Xiangdong Fang Hua Chen Xin Liu Jingfa Xiao Changqing Zeng 《基因组蛋白质组与生物信息学报(英文版)》2019,17(3):229-247
To unravel the genetic mechanisms of disease and physiological traits,it requires comprehensive sequencing analysis of large sample size in Chinese populations.Here,we report the primary results of the Chinese Academy of Sciences Precision Medicine Initiative(CASPMI) project launched by the Chinese Academy of Sciences,including the de novo assembly of a northern Han reference genome(NH1.0) and whole genome analyses of 597 healthy people coming from most areas in China.Given the two existing reference genomes for Han Chinese(YH and HX1) were both from the south,we constructed NH1.0,a new reference genome from a northern individual,by combining the sequencing strategies of Pac Bio,10? Genomics,and Bionano mapping.Using this integrated approach,we obtained an N50 scaffold size of 46.63 Mb for the NH1.0 genome and performed a comparative genome analysis of NH1.0 with YH and HX1.In order to generate a genomic variation map of Chinese populations,we performed the whole-genome sequencing of597 participants and identified 24.85 million(M) single nucleotide variants(SNVs),3.85 M small indels,and 106,382 structural variations.In the association analysis with collected phenotypes,we found that the T allele of rs1549293 in KAT8 significantly correlated with the waist circumference in northern Han males.Moreover,significant genetic diversity in MTHFR,TCN2,FADS1,and FADS2,which associate with circulating folate,vitamin B12,or lipid metabolism,was observed between northerners and southerners.Especially,for the homocysteine-increasing allele of rs1801133(MTHFR 677 T),we hypothesize that there exists a ‘‘comfort\" zone for a high frequency of 677 T between latitudes of 35–45 degree North.Taken together,our results provide a high-quality northern Han reference genome and novel population-specific data sets of genetic variants for use in the personalized and precision medicine. 相似文献
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Melanie E. F. LaCava Ellen O. Aikens Libby C. Megna Gregg Randolph Charley Hubbard C. Alex Buerkle 《Molecular ecology resources》2020,20(2):360-370
Advances in DNA sequencing have made it feasible to gather genomic data for non‐model organisms and large sets of individuals, often using methods for sequencing subsets of the genome. Several of these methods sequence DNA associated with endonuclease restriction sites (various RAD and GBS methods). For use in taxa without a reference genome, these methods rely on de novo assembly of fragments in the sequencing library. Many of the software options available for this application were originally developed for other assembly types and we do not know their accuracy for reduced representation libraries. To address this important knowledge gap, we simulated data from the Arabidopsis thaliana and Homo sapiens genomes and compared de novo assemblies by six software programs that are commonly used or promising for this purpose (ABySS , CD‐HIT , Stacks , Stacks2 , Velvet and VSEARCH ). We simulated different mutation rates and types of mutations, and then applied the six assemblers to the simulated data sets, varying assembly parameters. We found substantial variation in software performance across simulations and parameter settings. ABySS failed to recover any true genome fragments, and Velvet and VSEARCH performed poorly for most simulations. Stacks and Stacks2 produced accurate assemblies of simulations containing SNPs, but the addition of insertion and deletion mutations decreased their performance. CD‐HIT was the only assembler that consistently recovered a high proportion of true genome fragments. Here, we demonstrate the substantial difference in the accuracy of assemblies from different software programs and the importance of comparing assemblies that result from different parameter settings. 相似文献
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从十九世纪中期孟德尔的豌豆杂交工作开始;直到二十世纪的今天;在遗传基因信息传递上;遗传学工作者只发现了3条规律。这就是孟德尔发现的分亭律和自申零章律和摩尔根等人发现的李锁辛冬律。此外;再没有人发现具有象这3条定律在高等动植物中普遍存在的遗传规律了。然而;这3条规律的发现无一不是通过经典遗传学的方法;即根据杂交后子;代与子．代的结果（或用隐性亲代与子:代回交的数据）和统计的方法推算出来的。至于说直观的证据;只是在研究性细胞（配子）的减数分裂的意义之后;人们才逐渐领会到的。 相似文献
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Population genetic studies in nonmodel organisms are often hampered by a lack of reference genomes that are essential for whole‐genome resequencing. In the light of this, genotyping methods have been developed to effectively eliminate the need for a reference genome, such as genotyping by sequencing or restriction site‐associated DNA sequencing (RAD‐seq). However, what remains relatively poorly studied is how accurately these methods capture both average and variation in genetic diversity across an organism's genome. In this issue of Molecular Ecology Resources, Dutoit et al. (2016) use whole‐genome resequencing data from the collard flycatcher to assess what factors drive heterogeneity in nucleotide diversity across the genome. Using these data, they then simulate how well different sequencing designs, including RAD sequencing, could capture most of the variation in genetic diversity. They conclude that for evolutionary and conservation‐related studies focused on the estimating genomic diversity, researchers should emphasize the number of loci analysed over the number of individuals sequenced. 相似文献
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Reto Burri 《Molecular ecology》2017,26(15):3853-3856
Selection has a deep impact on the distribution of genetic diversity and population differentiation along the genome (the genomic landscapes of diversity and differentiation), reducing diversity and elevating differentiation not only at the sites it targets, but also at linked neutral sites. Fuelled by the high‐throughput sequencing revolution, these genomic footprints of selection have been extensively exploited over the past decade with the aim to identify genomic regions involved in adaptation and speciation. However, while this research has shown that the genomic landscapes of diversity and differentiation are usually highly heterogeneous, it has also led to the increasing realization that this heterogeneity may evolve under processes other than adaptation or speciation. In particular, instead of being an effect of selective sweeps or barriers to gene flow, accentuated differentiation can evolve by any process reducing genetic diversity locally within the genome (Charlesworth, 1998 ), including purifying selection at linked sites (background selection). In particular, in genomic regions where recombination is infrequent, accentuated differentiation can evolve as a by‐product of diversity reductions unrelated to adaptation or speciation (Cruickshank & Hahn, 2014 ; Nachman & Payseur, 2012 ; Noor & Bennett, 2009 ). In such genomic regions, linkage extends over physically larger genome stretches, and selection affects a particularly high number of linked neutral sites. Even though the effects of selection on linked neutral diversity (linked selection) within populations are well documented (Cutter & Payseur, 2013 ), recent observations of diversity and differentiation landscapes that are highly correlated even among independent lineages suggest that the effects of long‐term linked selection may have a deeper impact on the evolution of the genomic landscapes of diversity and differentiation than previously anticipated. The study on Saxicola stonechats by Van Doren et al. ( 2017 ) reported in the current issue of Molecular Ecology lines in with a rapidly expanding body of evidence in this direction. Correlations of genomic landscapes extending from within stonechats to comparisons with Ficedula flycatchers add to recent insights into the timescales across which the effects of linked selection persist. Absent and inverted correlations of genomic landscapes in comparisons involving an island taxon, on the other hand, provide important empirical clues about the role of demographic constraints in the evolution of the genomic landscapes of diversity and differentiation. 相似文献