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.     

The origins of genomic duplications in Arabidopsis

Large segmental duplications cover much of the Arabidopsis thaliana genome. Little is known about their origins. We show that they are primarily due to at least four different large-scale duplication events that occurred 100 to 200 million years ago, a formative period in the diversification of the angiosperms. A better understanding of the complex structural history of angiosperm genomes is necessary to make full use of Arabidopsis as a genetic model for other plant species.     

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.     

Single-copy inverted repeats associated with regional genetic duplications in gamma fibrinogen and immunoglobulin genes

We have found that a portion (150 base pairs) of the seventh exon of the human gamma fibrinogen gene is duplicated in the preceding intron. This duplicated sequence, termed a "pseudoexon," is flanked on each side by a single-copy inverted repeat sequence consisting of 102 base pairs. Frequencies of point substitutions indicate that both the pseudoexon and the inverted repeat sequence arose approximately 10 to 20 million years ago. The generality of this type of duplication is suggested by the occurrence of a similar duplication in the mouse immunoglobulin mu-delta region. As in the fibrinogen pseudoexon, the portion of the immunoglobulin mu-delta region containing the duplication and the inverted repeat was reported to be single-copy in the mouse genome. Since both of the first two single-copy inverted repeats to be sequenced are associated with regional duplications, it is likely that many of the single-copy inverted repeat sequences, which make up 1 to 2 percent of the genome, are also associated with regional duplications.     

Dynamics of mammalian chromosome evolution inferred from multispecies comparative maps

The genome organizations of eight phylogenetically distinct species from five mammalian orders were compared in order to address fundamental questions relating to mammalian chromosomal evolution. Rates of chromosome evolution within mammalian orders were found to increase since the Cretaceous-Tertiary boundary. Nearly 20% of chromosome breakpoint regions were reused during mammalian evolution; these reuse sites are also enriched for centromeres. Analysis of gene content in and around evolutionary breakpoint regions revealed increased gene density relative to the genome-wide average. We found that segmental duplications populate the majority of primate-specific breakpoints and often flank inverted chromosome segments, implicating their role in chromosomal rearrangement.     

Natural selection shapes genome-wide patterns of copy-number polymorphism in Drosophila melanogaster

The role that natural selection plays in governing the locations and early evolution of copy-number mutations remains largely unexplored. We used high-density full-genome tiling arrays to create a fine-scale genomic map of copy-number polymorphisms (CNPs) in Drosophila melanogaster. We inferred a total of 2658 independent CNPs, 56% of which overlap genes. These include CNPs that are likely to be under positive selection, most notably high-frequency duplications encompassing toxin-response genes. The locations and frequencies of CNPs are strongly shaped by purifying selection, with deletions under stronger purifying selection than duplications. Among duplications, those overlapping exons or introns, as well as those falling on the X chromosome, seem to be subject to stronger purifying selection.     

A mutation in the TRPC6 cation channel causes familial focal segmental glomerulosclerosis

Focal and segmental glomerulosclerosis (FSGS) is a kidney disorder of unknown etiology, and up to 20% of patients on dialysis have been diagnosed with it. Here we show that a large family with hereditary FSGS carries a missense mutation in the TRPC6 gene on chromosome 11q, encoding the ion-channel protein transient receptor potential cation channel 6 (TRPC6). The proline-to-glutamine substitution at position 112, which occurs in a highly conserved region of the protein, enhances TRPC6-mediated calcium signals in response to agonists such as angiotensin II and appears to alter the intracellular distribution of TRPC6 protein. Previous work has emphasized the importance of cytoskeletal and structural proteins in proteinuric kidney diseases. Our findings suggest an alternative mechanism for the pathogenesis of glomerular disease.     

The influence of CCL3L1 gene-containing segmental duplications on HIV-1/AIDS susceptibility

Segmental duplications in the human genome are selectively enriched for genes involved in immunity, although the phenotypic consequences for host defense are unknown. We show that there are significant interindividual and interpopulation differences in the copy number of a segmental duplication encompassing the gene encoding CCL3L1 (MIP-1alphaP), a potent human immunodeficiency virus-1 (HIV-1)-suppressive chemokine and ligand for the HIV coreceptor CCR5. Possession of a CCL3L1 copy number lower than the population average is associated with markedly enhanced HIV/acquired immunodeficiency syndrome (AIDS) susceptibility. This susceptibility is even greater in individuals who also possess disease-accelerating CCR5 genotypes. This relationship between CCL3L1 dose and altered HIV/AIDS susceptibility points to a central role for CCL3L1 in HIV/AIDS pathogenesis and indicates that differences in the dose of immune response genes may constitute a genetic basis for variable responses to infectious diseases.     

Rare structural variants disrupt multiple genes in neurodevelopmental pathways in schizophrenia

Schizophrenia is a devastating neurodevelopmental disorder whose genetic influences remain elusive. We hypothesize that individually rare structural variants contribute to the illness. Microdeletions and microduplications >100 kilobases were identified by microarray comparative genomic hybridization of genomic DNA from 150 individuals with schizophrenia and 268 ancestry-matched controls. All variants were validated by high-resolution platforms. Novel deletions and duplications of genes were present in 5% of controls versus 15% of cases and 20% of young-onset cases, both highly significant differences. The association was independently replicated in patients with childhood-onset schizophrenia as compared with their parents. Mutations in cases disrupted genes disproportionately from signaling networks controlling neurodevelopment, including neuregulin and glutamate pathways. These results suggest that multiple, individually rare mutations altering genes in neurodevelopmental pathways contribute to schizophrenia.     

DNA synthesis generates terminal duplications that seal end-to-end chromosome fusions

End-to-end chromosome fusions that occur in the context of telomerase deficiency can trigger genomic duplications. For more than 70 years, these duplications have been attributed solely to breakage-fusion-bridge cycles. To test this hypothesis, we examined end-to-end fusions isolated from Caenorhabditis elegans telomere replication mutants. Genome-level rearrangements revealed fused chromosome ends having interrupted terminal duplications accompanied by template-switching events. These features are very similar to disease-associated duplications of interstitial segments of the human genome. A model termed Fork Stalling and Template Switching has been proposed previously to explain such duplications, where promiscuous replication of large, noncontiguous segments of the genome occurs. Thus, a DNA synthesis-based process may create duplications that seal end-to-end fusions, in the absence of breakage-fusion-bridge cycles.     

猪源新城疫病毒SP13株的F基因克隆及序列分析

采用RT-PCR方法对猪源新城疫病毒(NDV)SP13株的F基因进行了扩增与克隆,并测定出F基因的核苷酸全序列,推导出氨基酸序列.F基因全长为1662 bp,单一的开放阅读框,编码553个氨基酸的长肽,裂解位点的氨基酸序列为112G-R-Q-G-R-L117,与弱毒株在这一区域的序列(112G-R/K-Q-G/S-R-L117)相符;F蛋白有6个潜在的糖基化位点和13个Cys残基位点,其疏水构型有3个强疏水区.通过同源率、系统发育、致病性、疏水性和抗原性等比较分析的结果表明,SP13与LaSota、Clone 30株不但同源性达到99.9%,而且在致病性、疏水性和抗原性等方面也极为相似.     

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.     

The Release 5.1 annotation of Drosophila melanogaster heterochromatin

The repetitive DNA that constitutes most of the heterochromatic regions of metazoan genomes has hindered the comprehensive analysis of gene content and other functions. We have generated a detailed computational and manual annotation of 24 megabases of heterochromatic sequence in the Release 5 Drosophila melanogaster genome sequence. The heterochromatin contains a minimum of 230 to 254 protein-coding genes, which are conserved in other Drosophilids and more diverged species, as well as 32 pseudogenes and 13 noncoding RNAs. Improved methods revealed that more than 77% of this heterochromatin sequence, including introns and intergenic regions, is composed of fragmented and nested transposable elements and other repeated DNAs. Drosophila heterochromatin contains "islands" of highly conserved genes embedded in these "oceans" of complex repeats, which may require special expression and splicing mechanisms.     

猪繁殖与呼吸综合征病毒17-ZJ-HZ毒株的分离鉴定与分子流行病学分析

杭州某猪场断奶仔猪群出现高热、呼吸困难等症状,疑似猪繁殖与呼吸综合征病毒(porcine reproductive and respiratory syndrome virus,PRRSV)感染,3头病猪肺脏病变样本送本实验室检测,通过RT-PCR方法检测其病原核酸。肺脏匀浆液无菌处理接种到MARC-145细胞,细胞病变观察、Western-blot、间接免疫荧光等方法验证PRRSV病毒分离情况;RT-PCR方法分五段扩增获得全长病毒基因组序列,采用MEGA等软件分析该毒株的核苷酸序列以及GP5、NSP2氨基酸序列;分离病毒接种3日龄PRRSV阴性仔猪,评价该病毒的毒力。结果表明:该场送检样品为PRRSV阳性;成功分离得到17-ZJ-HZ病毒;获得15 325 bp的 PRRSV全基因组序列。序列分析表明,该毒株与经典北美株的NSP2存在典型的29+1个氨基酸的缺失,且进化分析归于HP-PRRSV亚群。攻毒60 h后猪只出现典型的PRRSV临床症状和病理变化,以上结果表明该毒株为高致病性PRRSV(highly pathogenic PRRSV, HP-PRRSV)的北美株。     

陕西杨陵葡萄黑痘病病原菌的分离与鉴定

采用常规组织法对陕西杨陵葡萄黑痘病病原菌进行分离、纯化,共获得病原菌菌株24个,并对菌株YL018进行形态学鉴定、致病性测定及病原菌DNA同源性分析。利用ITS区域通用引物ITS1-F/ITS4进行病原菌DNA PCR扩增,将获得的病原菌rDNA-ITS区域的DNA序列进行Blast比较分析。结果发现,菌株YL018与GenBank登录号分别为AY826763、AY826762和AY826764的Elsinoe ampelina位于一个分支上。从而证明分离到了陕西杨陵葡萄黑痘病病原菌。也为进一步研究在病原菌侵染葡萄过程中,植物防御系统中酶类物质的变化及作用做好了前期基础。     

黑豆NBS类抗病基因同源片段的克隆与分析

根据已克隆的抗病基因保守结构域设计简并引物,以湖南黑豆（HH）为试材,通过RT-PCR,从cDNA中扩增抗病基因同源序列,测序鉴定出2个含有通读阅读框的DNA片段：FNBSl、FNBS3。FNBS1大小为534bp,编码178个氨基酸;FNBS3大小为513bp,编码169个氨基酸。BLASTP分析表明,2个片段均具有NB-ARC结构域（与植物抗病有关）,并且包含p-loop、Kinase-2、HD等结构域。基因FNBSl与大豆基因RPMl-like编码的氨基酸序列的同源性为98％,基因FNBS3与大豆基因N-like 编码的氨基酸序列的同源性为99％,推测FNBS1、FNBS3可能是黑豆NBS-LRR类抗病基因的核心区域。     

Characterization and chromosomal localization of a cDNA encoding brain amyloid of Alzheimer's disease

Four clones were isolated from an adult human brain complementary DNA library with an oligonucleotide probe corresponding to the first 20 amino acids of the beta peptide of brain amyloid from Alzheimer's disease. The open reading frame of the sequenced clone coded for 97 amino acids, including the known amino acid sequence of this polypeptide. The 3.5-kilobase messenger RNA was detected in mammalian brains and human thymus. The gene is highly conserved in evolution and has been mapped to human chromosome 21.     

Structural dynamics of eukaryotic chromosome evolution

Large-scale genome sequencing is providing a comprehensive view of the complex evolutionary forces that have shaped the structure of eukaryotic chromosomes. Comparative sequence analyses reveal patterns of apparently random rearrangement interspersed with regions of extraordinarily rapid, localized genome evolution. Numerous subtle rearrangements near centromeres, telomeres, duplications, and interspersed repeats suggest hotspots for eukaryotic chromosome evolution. This localized chromosomal instability may play a role in rapidly evolving lineage-specific gene families and in fostering large-scale changes in gene order. Computational algorithms that take into account these dynamic forces along with traditional models of chromosomal rearrangement show promise for reconstructing the natural history of eukaryotic chromosomes.