Large-scale copy number polymorphism in the human genome

The extent to which large duplications and deletions contribute to human genetic variation and diversity is unknown. Here, we show that large-scale copy number polymorphisms (CNPs) (about 100 kilobases and greater) contribute substantially to genomic variation between normal humans. Representational oligonucleotide microarray analysis of 20 individuals revealed a total of 221 copy number differences representing 76 unique CNPs. On average, individuals differed by 11 CNPs, and the average length of a CNP interval was 465 kilobases. We observed copy number variation of 70 different genes within CNP intervals, including genes involved in neurological function, regulation of cell growth, regulation of metabolism, and several genes known to be associated with disease.     

杨树肉桂醇脱氢酶基因序列和表达模式分析及CAD4酶活性检测

应用生物信息学方法从杨树基因组数据库中筛选出19个杨树肉桂醇脱氢酶基因,它们聚为3类.序列分析表明,杨树CAD基因家族主要通过全基因组加倍和串联复制的方式进行扩张.杨树和拟南芥CAD家族共6对旁系同源基因,在较强的净化选择压力下进化.19个基因在杨树不同组织中均有表达,表达量较高的是PoptrCAD17、PoptrCA...     

Human-specific changes of genome structure detected by genomic triangulation

Knowledge of the rhesus macaque genome sequence enables reconstruction of the ancestral state of the human genome before the divergence of chimpanzees. However, the draft quality of nonhuman primate genome assemblies challenges the ability of current methods to detect insertions, deletions, and copy-number variations between humans, chimpanzees, and rhesus macaques and hinders the identification of evolutionary changes between these species. Because of the abundance of segmental duplications, genome comparisons require the integration of genomic assemblies and data from large-insert clones, linkage maps, and radiation hybrid maps. With genomic triangulation, an integrative method that reconstructs ancestral states and the structural evolution of genomes, we identified 130 human-specific breakpoints in genome structure due to rearrangements at an intermediate scale (10 kilobases to 4 megabases), including 64 insertions affecting 58 genes. Comparison with a human structural polymorphism database indicates that many of the rearrangements are polymorphic.     

正选择驱动褪黑激素受体MT1与MT2基因的分化

【目的】研究褪黑激素受体（melatonin receptor,MTNR）基因的进化模式,为褪黑激素受体基因相关功能的研究提供理论参考。【方法】利用生物信息学的方法和软件对来自11个物种的褪黑激素受体1a（MT1）和褪黑激素受体1b（MT2）基因的系统发生关系、基因相似性、选择压力、选择方向等进行系统地分析。【结果】MT1和MT2基因可能由共同祖先基因通过基因重复产生, MT1可能保持着源基因的功能,MT2为新产生的功能基因。MT1基因在物种间的相似性极显著高于MT2基因（P＜0.01）;MT1基因主要受纯化选择,MT2基因受到显著的正选择;MT1与MT2基因均承受着较强的选择压力,且选择压力在2基因间无显著差异（P＞0.05）。【结论】MT1基因主要受纯化选择可能是MT1基因与动物季节性繁殖关联研究结论不统一的原因,MT2基因受正选择提示正选择可能是驱动MT2与MT1发生分化的重要动力。     

An abundance of rare functional variants in 202 drug target genes sequenced in 14,002 people

Rare genetic variants contribute to complex disease risk; however, the abundance of rare variants in human populations remains unknown. We explored this spectrum of variation by sequencing 202 genes encoding drug targets in 14,002 individuals. We find rare variants are abundant (1 every 17 bases) and geographically localized, so that even with large sample sizes, rare variant catalogs will be largely incomplete. We used the observed patterns of variation to estimate population growth parameters, the proportion of variants in a given frequency class that are putatively deleterious, and mutation rates for each gene. We conclude that because of rapid population growth and weak purifying selection, human populations harbor an abundance of rare variants, many of which are deleterious and have relevance to understanding disease risk.     

Human genome ultraconserved elements are ultraselected

Ultraconserved elements in the human genome are defined as stretches of at least 200 base pairs of DNA that match identically with corresponding regions in the mouse and rat genomes. Most ultraconserved elements are noncoding and have been evolutionarily conserved since mammal and bird ancestors diverged over 300 million years ago. The reason for this extreme conservation remains a mystery. It has been speculated that they are mutational cold spots or regions where every site is under weak but still detectable negative selection. However, analysis of the derived allele frequency spectrum shows that these regions are in fact under negative selection that is much stronger than that in protein coding genes.     

The evolutionary fate and consequences of duplicate genes

Gene duplication has generally been viewed as a necessary source of material for the origin of evolutionary novelties, but it is unclear how often gene duplicates arise and how frequently they evolve new functions. Observations from the genomic databases for several eukaryotic species suggest that duplicate genes arise at a very high rate, on average 0.01 per gene per million years. Most duplicated genes experience a brief period of relaxed selection early in their history, with a moderate fraction of them evolving in an effectively neutral manner during this period. However, the vast majority of gene duplicates are silenced within a few million years, with the few survivors subsequently experiencing strong purifying selection. Although duplicate genes may only rarely evolve new functions, the stochastic silencing of such genes may play a significant role in the passive origin of new species.     

Genome-wide Identification and Analysis of DNA Methyltransferases in Grape

DNA methylation is an important epigenetic regulation mechanism, which is catalyzed by DNA methyltransferases. In this study, eight DNA methyltransferase genes were identified in grape genome to analyze the selective pressure, gene expression and codon usage bias. The results showed grape DNA methyltransferase MET subfamily underwent relatively strong purifying selection during evolution, while chromomethylase CMT subfamily underwent positive selection during evolution. Under different abiotic(heat, drought or cold) stresses, the expression level of many grape DNA methyltransferase genes changed significantly. The expression level of these genes might be related with cis-regulatory elements of their promoters. The results of codon usage bias analysis showed that synonymous codon bias existed in grape DNA methyltransferase gene family, which might be affected by mutation pressure. These results laid a solid foundation for in-depth study of DNA methyltransferases in grape.     

梨火疫病病原菌（Erwinia amylovora）三型分泌系统的鉴别及Erwinia spp. HrpA的分析

 【目的】明确梨火疫病病原菌（Erwinia amylovora ）三型分泌系统（type Ⅲ secretion system,TTSS）的所在区域、相关基因及Erwinia spp.的HrpA（hypersensitive response and pathogenicity gene A）选择压水平。【方法】利用生物信息学方法,通过BLAST程序对梨火疫病菌基因组的核苷酸数据库进行同源比对,同时对Erwinia spp.与宿主互作的表面蛋白HrpA进行选择压分析。【结果】TTSS分析结果显示在40 kb大小的毒力岛上有27个TTSS相关基因。通过与看家基因及毒力岛上的致病性相关的重要基因HrpN的比较、选择压分析、多序列比较,发现HrpA基因处于较强的选择压作用下,且HrpA蛋白N端主要受正向选择,C端主要受净化选择。NJ法构建的HrpA系统发育树显示Erwinia spp.形成两个明显的分支,表明HrpA基因可能在种间分化后产生了不同的选择压变化。【结论】梨火疫病病原菌基因组3.14－3.18 Mb为其TTSS分布区域。该病原菌通过TTSS侵染寄主植物,在其病原菌表面有一种类鞭毛结构的TTSS蛋白HrpA,HrpA作为传输者起着将效应分子输送到宿主内部的功能,在进化上受到了较强的选择压影响。     

Genome-wide identification and function analysis of the sucrose phosphate synthase MdSPS gene family in apple

Sucrose phosphate synthase (SPS) is a rate-limiting enzyme that works in conjunction with sucrose-6-phosphate phosphatase (SPP) for sucrose synthesis, and it plays an essential role in energy provisioning during growth and development in plants as well as improving fruit quality. However, studies on the systematic analysis and evolutionary pattern of the SPS gene family in apple are still lacking. In the present study, a total of seven MdSPS and four MdSPP genes were identified from the Malus domestica genome GDDH13 v1.1. The gene structures and their promoter cis-elements, protein conserved motifs, subcellular localizations, physiological functions and biochemical properties were analyzed. A chromosomal location and gene-duplication analysis demonstrated that whole-genome duplication (WGD) and segmental duplication played vital roles in MdSPS gene family expansion. The Ka/Ks ratio of pairwise MdSPS genes indicated that the members of this family have undergone strong purifying selection during domestication. Furthermore, three SPS gene subfamilies were classified based on phylogenetic relationships, and old gene duplications and significantly divergent evolutionary rates were observed among the SPS gene subfamilies. In addition, a major gene related to sucrose accumulation (MdSPSA2.3) was identified according to the highly consistent trends in the changes of its expression in four apple varieties (‘Golden Delicious’, ‘Fuji’, ‘Qinguan’ and ‘Honeycrisp’) and the correlation between gene expression and soluble sugar content during fruit development. Furthermore, the virus-induced silencing of MdSPSA2.3 confirmed its function in sucrose accumulation in apple fruit. The present study lays a theoretical foundation for better clarifying the biological functions of the MdSPS genes during apple fruit development.     

Evolution and functional impact of rare coding variation from deep sequencing of human exomes

As a first step toward understanding how rare variants contribute to risk for complex diseases, we sequenced 15,585 human protein-coding genes to an average median depth of 111× in 2440 individuals of European (n = 1351) and African (n = 1088) ancestry. We identified over 500,000 single-nucleotide variants (SNVs), the majority of which were rare (86% with a minor allele frequency less than 0.5%), previously unknown (82%), and population-specific (82%). On average, 2.3% of the 13,595 SNVs each person carried were predicted to affect protein function of ~313 genes per genome, and ~95.7% of SNVs predicted to be functionally important were rare. This excess of rare functional variants is due to the combined effects of explosive, recent accelerated population growth and weak purifying selection. Furthermore, we show that large sample sizes will be required to associate rare variants with complex traits.     

Transitions to asexuality result in excess amino acid substitutions

Theory predicts that linkage between genetic loci reduces the efficiency of purifying selection. Because of the permanent linkage of all heritable genetic material, asexual lineages may be exceptionally prone to deleterious-mutation accumulation in both nuclear and organelle genes. Here, we show that the ratio of the rate of amino acid to silent substitution (Ka/Ks) in mitochondrial protein-coding genes is higher in obligately asexual lineages than in sexual lineages of the microcrustacean Daphnia pulex. Using a phylogeny-based approach to quantify the frequency of mutational-effect classes, we estimate that mitochondrial protein-coding genes in asexual lineages accumulate deleterious amino acid substitutions at four times the rate in sexual lineages. These results support the hypothesis that sexual reproduction plays a prominent role in reducing the mutational burden in populations.     

植物二氢吡啶二羧酸合成酶的功能分歧与进化分析

二氢吡啶二羧酸合成酶(DHDPS)是赖氨酸生物合成途径的关键酶,探讨DHDPS在不同植物中所受到的选择压力及其功能分歧,以期为阐明赖氨酸积累的分子机制奠定基础,并为植物逆境适应性研究提供线索。利用模式植物基因组数据库,通过生物信息学手段,鉴定并获得水稻、拟南芥和大豆等11个物种的DHDPS基因的核酸和蛋白全序列;利用Clustal X、PAML和DIVERGE等工具剖析了21条DHDPS基因的序列、功能分歧、选择压力及进化关系,并计算了相关参数。系统进化树揭示了植物DHDPS基因能被划分为5个类群,其中,杨树的2个DHDPS蛋白单独形成了E类群,剩余的4个类群至少包括2个物种的DHDPS蛋白。基于位点模型的选择压力检测显示,M8模型虽然能签定出正选择位点,但这些位点均未达到显著水平,说明植物DHDPS基因主要受控于纯净选择。类群间功能分歧研究显示:类群之间存在Ⅰ型功能分歧,不存在Ⅱ型功能分歧;总共鉴定了273个功能分歧位点,其中,Ⅰ型功能分歧位点214个,Ⅱ型功能分歧位点59个;似然比检测表明,Ⅰ型功能分歧位点均达到显著水平,但Ⅱ型功能分歧位点均不显著。因此,在长期进化过程中,DHDPS基因类群间发生Ⅰ型功能分化,同时,单个类群内纯净选择起着主导作用。     

A genome scan of recent positive selection signatures in three sheep populations

Domesticated sheep have been exposed to artificial selection for the production of fiber, meat, and milk as well as to natural selection. Such selections are likely to have imposed distinctive selection signatures on the sheep genome. Therefore, detecting selection signatures across the genome may help elucidate mechanisms of selection and pinpoint candidate genes of interest for further investigation. Here, detection of selection signatures was conducted in three sheep breeds, Sunite(n=66), German Mutton(n=159), and Dorper(n=93), using the Illumina Ovine SNP50 Genotyping Bead Chip array. Each animal provided genotype information for 43 273 autosomal single nucleotide polymorphisms(SNPs). We adopted two complementary haplotype-based statistics of relative extended haplotype homozygosity(REHH) and the cross-population extended haplotype homozygosity(XP-EHH) tests. In total, 707, 755, and 438 genomic regions subjected to positive selection were identified in Sunite, German Mutton, and Dorper sheep, respectively, and 42 of these regions were detected using both REHH and XP-EHH analyses. These genomic regions harbored many important genes, which were enriched in gene ontology terms involved in muscle development, growth, and fat metabolism. Fourteen of these genomic regions overlapped with those identified in our previous genome-wide association studies, further indicating that these genes under positive selection may underlie growth developmental traits. These findings contribute to the identification of candidate genes of interest and aid in understanding the evolutionary and biological mechanisms for controlling complex traits in Chinese and western sheep.     

Diversity of human copy number variation and multicopy genes

Copy number variants affect both disease and normal phenotypic variation, but those lying within heavily duplicated, highly identical sequence have been difficult to assay. By analyzing short-read mapping depth for 159 human genomes, we demonstrated accurate estimation of absolute copy number for duplications as small as 1.9 kilobase pairs, ranging from 0 to 48 copies. We identified 4.1 million "singly unique nucleotide" positions informative in distinguishing specific copies and used them to genotype the copy and content of specific paralogs within highly duplicated gene families. These data identify human-specific expansions in genes associated with brain development, reveal extensive population genetic diversity, and detect signatures consistent with gene conversion in the human species. Our approach makes ~1000 genes accessible to genetic studies of disease association.     

长期选择与群体某些参数的变化趋势初探

采用理论模拟与实地选种资料分析对比的方法,对长期选择作用下的群体变化特征作了初步探讨。实地选种资料取自南斯拉夫新杨工厂化养猪场,共15个世代的6245头纯繁长白母猪的繁殖记录。研究性状为头胎总产仔数和头胎断奶仔数。发现在群体均数、群体方差以及在群体分布的变化趋势方面理论模拟结果与实际分析结果颇为一致。还发现,仅由加性基因控制的性状同由加性和非加性(完全显性和超显性)、基因控制的性状,在群体均数与群体方差两者变化关系,以及选择反应的变化趋势方面各有特点。本研究表明,长期选择作用下的群体均数、群体方差、群体分布以及选择反应等参数的变化,其内在联系的本质在于控制所选性状基因频率的变化。若根据控制所选性状的各类基因数目、频率及其对表现作用的大小来估测选择后代的群体生产性能可能更准确,随着基因工程的不断发展,这将会得到实现。     

采用聚合杂交创新稻瘿蚊抗性育种材料

利用广西高抗稻瘿蚊的地方品种江潮为核心种质,与高抗稻瘿蚊的H71350和抗蚊青占进行抗抗聚合杂交,再用高产优质品种桂软占作轮回亲本进行回交,把来源于不同的抗源基因集合于优质高产品种中。通过聚合杂交、回交,低世代系谱选择、高世代集团选择方法,成功地将多种抗性基因聚合在一起,在后代群体中获得了3个抗性级别达0级的高抗品系,其抗性比各亲本更抗,实现了抗性基因重组聚合。     

Recent segmental duplications in the human genome

Primate-specific segmental duplications are considered important in human disease and evolution. The inability to distinguish between allelic and duplication sequence overlap has hampered their characterization as well as assembly and annotation of our genome. We developed a method whereby each public sequence is analyzed at the clone level for overrepresentation within a whole-genome shotgun sequence. This test has the ability to detect duplications larger than 15 kilobases irrespective of copy number, location, or high sequence similarity. We mapped 169 large regions flanked by highly similar duplications. Twenty-four of these hot spots of genomic instability have been associated with genetic disease. Our analysis indicates a highly nonrandom chromosomal and genic distribution of recent segmental duplications, with a likely role in expanding protein diversity.     

The origins of gene instability in yeast

Two unstable mutations at the his4 locus of yeast are due to the insertion of the transposable elements Ty912 and Ty917 into the his4 regulatory region. The two transposons are related, one being derived from the other by a substitution of 4000 base pairs of DNA. Element Ty912 includes identical terminal repeats, whereas the terminal repeats of Ty917 are not identical. Transposition of Ty912 or Ty917 generates 5-base-pair duplications of the target DNA at either end of the element. Expression and reversion of a his4 gene containing Ty912 or Ty917 is controlled by three unlinked regulatory genes. The properties of these regulatory genes are similar to those described for the controlling elements in maize.