QQ客服 官方微博 反馈留言

题名	基于二代测序技术的非人灵长类的基因组和转录组的比较研究
作者	张雁峰
学位类别	博士
答辩日期	2012-05
授予单位	中国科学院研究生院
授予地点	北京
导师	宿兵
关键词	非人灵长类 基因组 转录组 二代测序 单核苷酸多态性
其他题名	Genome and transcriptome comparisons of non-human primates based on next generation sequencing
学位专业	遗传学
中文摘要	非人灵长类是与人类进化关系最接近的物种。在很多人类疾病研究方面，非人灵长类是非常重要和不可替代的实验动物模型。然而，目前对非人灵长类基因组水平的比较研究非常有限。 尽管目前黑猩猩、大猩猩、印度猕猴等非人灵长类动物的基因组已经得到解析，但是这些灵长类物种在生物医学方面的研究受到很多限制。而另外两个非人灵长类物种——中国猕猴和食蟹猴在疾病动物模型研究方面有着非常广泛的应用，然而它们的基因组结构尚没有得到解析，也就无法从全基因组水平开展非人灵长类遗传差异的比较分析。有鉴于此，本论文的研究目的：（1）首先通过二代测序技术对一只中国猕猴进行了全基因组重测序，首次从全基因组水平开展了与印度猕猴参考基因组的遗传差异分析；（2）为进一步解析猕猴属物种之间的遗传差异，通过二代测序技术从头组装了中国猕猴和食蟹猴的全基因组，进而开展了猕猴属物种之间全基因组水平的差异比较。同时，我们还从转录组水平开展了对食蟹猴和印度猕猴基因表达差异的分析。 我们的研究发现，中国猕猴和印度猕猴尽管同属于一个物种，但是全基因组的比较分析揭示了这两个亚种之间存在着相当丰富的遗传多态性和结构性变异。我们一共找到了5.5百万个单核苷酸多态性（SNPs）位点。平均每kb区间内SNP的密度为2.08个。同时，我们还鉴定到了125,150个结构性变异（SVs），其中98.8%的SVs属于缺失型，并且通过PCR-直接测序的方法验证了中国猕猴和印度猕猴在SVs方面的差异程度。 我们深度测序了一只中国猕猴和一只食蟹猴基因组，分别达到了47X和54X的基因组覆盖度。通过从头组装两个物种的基因组，我们开展了猕猴属物种之间的遗传差异比较。结果表明，食蟹猴和印度猕猴之间的分歧程度最大，而中国猕猴和食蟹猴尽管属于两个不同的物种，却与中国猕猴和印度猕猴两个亚种的分歧程度非常接近。进一步的杂交模型分析表明，食蟹猴和中国猕猴存在着基因交流现象。这些基因交流的印记几乎遍及所有的染色体。另外，通过对疾病同源基因和药物作用靶点同源基因的注释分析提示了三只猴子之间在疾病和药物筛选模型方面作用相当。但是我们也发现个别例外的事例，其中最经典的是与HIV和SIV病毒复制相关的基因，TRIM5α。该基因在中国猕猴、印度猕猴和食蟹猴当中存在着6bp（编码Thr339 and Phe340两个氨基酸）缺失等位基因频率的差异，从而使得它们在SIV和HIV等逆转录病毒的抵制作用上存在显著性的不同，进一步提示了这些动物在开展病毒和免疫学方面的模型研究上需要考虑遗传背景的差异性。 最后，我们通过RNA-seq技术比较了食蟹猴和印度猕猴脑、肝脏和睾丸等组织的转录组，结果表明在睾丸组织中表达的基因分歧程度最大，这可能与灵长类物种受到性选择并发生快速进化导致基因表达差异相关。
英文摘要	As the closest relatives of humans, nonhuman primates are of great importance and irreplaceable as animal models. However, comparisons based on the genome sequences among nonhuman primates are still limited. Although the genome assemblies of chimpanzee, gorilla and Indian rhesus macaque (IR) have been released, the use of these primate species in biomedical research is rather limited. In constrast, the other two nonhuman primate species-Chinese rhesus macaque (CR) and crab-eating macaque (CE) are the most widely used nonhuman primate models, but their genomes are still undecoded. In this study, we aim to understand 1) the genetic difference beween CR and IR using the next-generation sequencing at the genome-wide level. Additionally, based on the de novo assembly of CR and CE genomes, we carried out genome comparison between the species/subspecies in the macaca genus, and we also conducted comparative transcriptome analysis among them. We uncovered a wealth of sequence diversity and structural variation (SV) between CR and IR, although they are classified as subspecies. Totally, we identified 5.5 million single nucleotide polymorphisms (SNPs) with density of 2.08 per kilobase (kb). Meanwhile, we also identified a total of 125,150 SVs, where 98.8% of them are deletions. Using PCR-direct sequencing verification, we confirmed the accuracy of the identified SVs between CR and IR. Next, using ultra-deep sequencing, we de novo assembled the CR and CE genomes (47X and 54X coverage, respectively). The results indicated the mostly diverged genomes are observed between CE and IR. The genetic divergence between CR and CE is close to that of CR and IR. Further hybridization model analysis suggested that the genetic introgression from CR to CE occurred long time ago. Moreover, comparison based on the disease-related genes and the druggable target orthologs indicated that these animal models are likely to be functionally equivalent. Nonetheless, we also discovered a few cases showing difference among species/subspecies. For example, TRIM5α, the gene encoding a protein performing restrictions in HIV and SIV replication contains a 6 bp deletion (encoding Thr339 and Phe340) polymorphism and the frequencies among the macaques are significantly different, suggesting that it is necessary to consider genetic divergence of macaques for constructing virus or immunological disease models. Finally, our comparative transcriptome analysis between CE and IR based on RNA-seq indicated that the gene expression parttern in testes is the mostly diverged among the tissues tested, implying the act of sexual selection leading to rapid evolution of the expression profile in these primate species.
语种	中文
公开日期	2012-08-01
内容类型	学位论文
源URL	[http://159.226.149.42:8088/handle/152453/6995]
专题	昆明动物研究所_比较基因组学
推荐引用方式 GB/T 7714	张雁峰. 基于二代测序技术的非人灵长类的基因组和转录组的比较研究[D]. 北京. 中国科学院研究生院. 2012.

个性服务

查看访问统计

相关权益政策

暂无数据

收藏/分享

除非特别说明，本系统中所有内容都受版权保护，并保留所有权利。