面向大规模人群的基因组注释系统

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...     

大肠杆菌基因组图谱研究进展

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。     

人基因组的STS图谱分析

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,     

人类基因组结构变异

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。     

山羊基因组与遗传变异图谱研究进展

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。     

泛基因组：高质量参考基因组的新标准

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。     

群体基因组结构变异检测工作流

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。     

中国科学家绘制籼稻高质量参考基因组序列图谱

2005年多国合作的国际水稻(Oryza sativa)基因组测序项目绘制了粳稻(O.sativa subsp.japonica)品种日本晴的参考基因组序列。最近,中国科学家发布了2个籼稻(O.sativa subsp.indica)品种(明恢63和珍汕97)的高质量参考基因组序列,为籼稻的功能基因组学研究和分子育种应用提供了便利。     

动物线粒体基因组变异研究进展

动物mtDNA大多是共价闭合的环状双链分子,一般由2个非编码区和37个编码基因组成,不同动物线粒体基因组大小变异明显.孑遗疟虫(Plasmodium reichenowi)的线粒体基因组最小,仅为5966bp;领鞭毛虫(Monosiga brevicollis)的最大,达76568bp.动物线粒体基因组大小变异的原因主要有:控制区串联重复元件的变异;基因重复;基因重叠与基因间隔区大小的差异;基因缺失和增加.     

EST-SSR genetic maps for Citrus sinensis and Poncirus trifoliata

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.     

A chromosome-level reference genome and pangenome for barn swallow population genomics

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Origin matters: Using a local reference genome improves measures in population genomics

Genome sequencing enables answering fundamental questions about the genetic basis of adaptation, population structure and epigenetic mechanisms. Yet, we usually need a suitable reference genome for mapping population-level resequencing data. In some model systems, multiple reference genomes are available, giving the challenging task of determining which reference genome best suits the data. Here, we compared the use of two different reference genomes for the three-spined stickleback (Gasterosteus aculeatus), one novel genome derived from a European gynogenetic individual and the published reference genome of a North American individual. Specifically, we investigated the impact of using a local reference versus one generated from a distinct lineage on several common population genomics analyses. Through mapping genome resequencing data of 60 sticklebacks from across Europe and North America, we demonstrate that genetic distance among samples and the reference genomes impacts downstream analyses. Using a local reference genome increased mapping efficiency and genotyping accuracy, effectively retaining more and better data. Despite comparable distributions of the metrics generated across the genome using SNP data (i.e. π, Tajima's D and F_ST), window-based statistics using different references resulted in different outlier genes and enriched gene functions. A marker-based analysis of DNA methylation distributions had a comparably high overlap in outlier genes and functions, yet with distinct differences depending on the reference genome. Overall, our results highlight how using a local reference genome decreases reference bias to increase confidence in downstream analyses of the data. Such results have significant implications in all reference-genome-based population genomic analyses.     

Small‐ and large‐scale heterogeneity in genetic variation across the collard flycatcher genome: implications for estimating genetic diversity in nonmodel organisms

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.     

A genome‐wide linkage map for the house sparrow (Passer domesticus) provides insights into the evolutionary history of the avian genome

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 (N_e) 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.     

A reference genome of the Chinese hamster based on a hybrid assembly strategy

Accurate and complete genome sequences are essential in biotechnology to facilitate genome‐based cell engineering efforts. The current genome assemblies for Cricetulus griseus, the Chinese hamster, are fragmented and replete with gap sequences and misassemblies, consistent with most short‐read‐based assemblies. Here, we completely resequenced C. griseus using single molecule real time sequencing and merged this with Illumina‐based assemblies. This generated a more contiguous and complete genome assembly than either technology alone, reducing the number of scaffolds by >28‐fold, with 90% of the sequence in the 122 longest scaffolds. Most genes are now found in single scaffolds, including up‐ and downstream regulatory elements, enabling improved study of noncoding regions. With >95% of the gap sequence filled, important Chinese hamster ovary cell mutations have been detected in draft assembly gaps. This new assembly will be an invaluable resource for continued basic and pharmaceutical research.     

Gender and age-specific reference intervals of common biochemical analytes in Chinese population: Derivation using real laboratory data

BackgroundIndirect sampling methods are not only inexpensive but also efficient for establishing reference intervals (RIs) using clinical data. This study was conducted to select fully normal records to establish ageand gender-specific RIs for common biochemical analytes by laboratory data mining.MethodsIn total, 280,206 records from 2014 to 2018 were obtained from Peking Union Medical College Hospital. Common biochemical analytes total protein, albumin, total bilirubin (TBil), direct bilirubin (DBil), alanine aminotransferase (ALT), glutamyltranspeptidase (GGT), alkaline phosphatase (ALP), aspartate aminotransferase (AST), lactate dehydrogenase (LDH), potassium, sodium, chlorine, calcium, urea, glucose, uric acid (UA), inorganic phosphorus, creatinine (Cr), total cholesterol, triglyceride, high-density lipoprotein cholesterol, and low-density lipoprotein cholesterol] were measured using an automatic analyzer. Sources of variation were identified by multiple regression analysis. The 2.5th and 97.5th percentiles were calculated as the lower and upper limits of the RIs, respectivelyResultsGender was the major source of variation among the 13 common biochemical analytes with an rp > 0.15. In contrast to the value listed in the WS/T 404, nearly all RIs established in this study were significantly narrower. Furthermore, age-specific RIs should be determined for DBil, LDH, and urea, whereas gender-specific RIs are suggested for GGT, LDH, and urea.ConclusionsWe recommend that gender-specific RIs should be established for ALT, AST, GGT, DBil, TBil, UA, and Cr as well as genderand age-specific RIs for urea and ALP. Through indirect sampling, ageand gender-specific RIs for common biochemical analytes were established and analyzed.     

TESS3: fast inference of spatial population structure and genome scans for selection

Geography and landscape are important determinants of genetic variation in natural populations, and several ancestry estimation methods have been proposed to investigate population structure using genetic and geographic data simultaneously. Those approaches are often based on computer‐intensive stochastic simulations and do not scale with the dimensions of the data sets generated by high‐throughput sequencing technologies. There is a growing demand for faster algorithms able to analyse genomewide patterns of population genetic variation in their geographic context. In this study, we present TESS3 , a major update of the spatial ancestry estimation program TESS . By combining matrix factorization and spatial statistical methods, TESS3 provides estimates of ancestry coefficients with accuracy comparable to TESS and with run‐times much faster than the Bayesian version. In addition, the TESS3 program can be used to perform genome scans for selection, and separate adaptive from nonadaptive genetic variation using ancestral allele frequency differentiation tests. The main features of TESS3 are illustrated using simulated data and analysing genomic data from European lines of the plant species Arabidopsis thaliana.     

Chromosome-scale scaffolds for the Chinese hamster reference genome assembly to facilitate the study of the CHO epigenome

The Chinese hamster genome serves as a reference genome for the study of Chinese hamster ovary (CHO) cells, the preferred host system for biopharmaceutical production. Recent re-sequencing of the Chinese hamster genome resulted in the RefSeq PICR meta-assembly, a set of highly accurate scaffolds that filled over 95% of the gaps in previous assembly versions. However, these scaffolds did not reach chromosome-scale due to the absence of long-range scaffolding information during the meta-assembly process. Here, long-range scaffolding of the PICR Chinese hamster genome assembly was performed using high-throughput chromosome conformation capture (Hi-C). This process resulted in a new “PICRH” genome, where 97% of the genome is contained in 11 mega-scaffolds corresponding to the Chinese hamster chromosomes (2n = 22) and the total number of scaffolds is reduced by three-fold from 1,830 scaffolds in PICR to 647 in PICRH. Continuity was improved while preserving accuracy, leading to quality scores higher than recent builds of mouse chromosomes and comparable to human chromosomes. The PICRH genome assembly will be an indispensable tool for designing advanced genetic engineering strategies in CHO cells and enabling systematic examination of genomic and epigenomic instability through comparative analysis of CHO cell lines on a common set of chromosomal coordinates.     

A physical map of the highly heterozygous Populus genome: integration with the genome sequence and genetic map and analysis of haplotype variation

As part of a larger project to sequence the Populus genome and generate genomic resources for this emerging model tree, we constructed a physical map of the Populus genome, representing one of the few such maps of an undomesticated, highly heterozygous plant species. The physical map, consisting of 2802 contigs, was constructed from fingerprinted bacterial artificial chromosome (BAC) clones. The map represents approximately 9.4-fold coverage of the Populus genome, which has been estimated from the genome sequence assembly to be 485 ± 10 Mb in size. BAC ends were sequenced to assist long-range assembly of whole-genome shotgun sequence scaffolds and to anchor the physical map to the genome sequence. Simple sequence repeat-based markers were derived from the end sequences and used to initiate integration of the BAC and genetic maps. A total of 2411 physical map contigs, representing 97% of all clones assigned to contigs, were aligned to the sequence assembly (JGI Populus trichocarpa , version 1.0). These alignments represent a total coverage of 384 Mb (79%) of the entire poplar sequence assembly and 295 Mb (96%) of linkage group sequence assemblies. A striking result of the physical map contig alignments to the sequence assembly was the co-localization of multiple contigs across numerous regions of the 19 linkage groups. Targeted sequencing of BAC clones and genetic analysis in a small number of representative regions showed that these co-aligning contigs represent distinct haplotypes in the heterozygous individual sequenced, and revealed the nature of these haplotype sequence differences.