利用转录组数据探究高山倭蛙原适应性机制和大额牛的系统发育地位

	利用转录组数据探究高山倭蛙原适应性机制和大额牛的系统发育地位
其他题名	High-altitude adaptation of Nanorana parkeri and phylogeny of Bos frontalis revealed by RNA-seq
	涂小龙
学位类型	硕士
导师	车静，吴东东
	2014-05
学位授予单位	中国科学院研究生院
学位授予地点	北京
学位专业	遗传学
关键词	转录组高山倭蛙高原适应大额牛系统发育
摘要	探讨生物如何适应高原极端环境的分子机制是目前进化领域的热点问题。青藏高原被誉为“世界屋脊”，是开展此项研究的理想场所。尤其随着高通量测序及基因组分析方法的发展，使基于全基因组信息开展此类研究成为可能。然而，过去大部分的研究对象是恒温动物，如哺乳类和鸟类，其高原适应遗传机制也有很好的了解，而对种类和数量更多的变温动物目前却仍缺乏系统研究，变温动物的高原适应性的遗传机制尚不清楚。本文中，我们选择青藏高原特有两栖物种高山倭蛙（Nanorana parkeri）作为研究对象，通过比较转录组学在表达水平方面探究变温动物高原适应的遗传机制。通过与近缘物种的差异表达分析，我们发现高山倭蛙肝脏组织中表达上调的基因在能量代谢相关通路显著富集，这也是恒温动物高原适应采取的一种策略。而在卵巢组织中，表达上调的基因在脂肪合成代谢，碳水化合物代谢等营养代谢通路显著富集，与高山倭蛙顺利渡过高原上较长的冬眠相关。在皮肤组织中，我们发现ASTKD1和STK17A基因的表达上调与细胞的紫外应答和存活相关。高通量RNA-seq数据不仅可以进行差异表达分析，还可以用于系统发育分析。牛作为一种反刍动物，能将饲料等低阶营养物质转化为营养丰富的肉奶，具有良好的经济价值而在世界范围内保持着丰富的物种多样性。大额牛（Bos frontalis）是牛属特殊的一员，在我国主要分布于怒江和独龙江流域，是一种半野生半家养的珍贵品种，它的起源问题仍存在很大争议，主要集中在3种假说：（1）由印度野牛（Bos gaurus）驯化而来；（2）由雄性印度野牛和雌性普通牛（Bos taurus）或瘤牛（Bos indicus）杂交成种；（3）起源于印度野牛的某种现已灭绝的近亲。本文中，我们利用RNA-seq技术，对获取的大额牛血样进行了转录组测序和拼装，通过与普通牛、瘤牛、牦牛（Bos grunniens）、山羊（Capra hircus）和野猪（Sus scrofa）预测直系同源基因，结合“串联”和“并联”等数据分析方法，分别构建了最大似然树，贝叶斯树，并由单基因树推断物种树，结果显示大额牛最先分化出来，与牦牛、普通牛和瘤牛是姐妹群关系，支持大额牛是一个独立的物种和独立起源的，为日后大额牛及其近缘物种的进化研究提供了科学依据。
其他摘要	Investigation on the molecular mechanism of how organism adapt to the plateau extreme environment is one of the hot issues in the field of evolution. The Qinghai-Tibet Plateau is known as "the roof of the world", which became the ideal area for conducting such researches. Especially with the development of high-throughput sequencing and genome analysis method, which make it is possible to carry out such research base on whole genome information. However, at present, most of the research object is warm-blooded, like mammals and birds, and the genetic mechanisms of their high-altitude adaptations had a good understanding. However, the ectothermic animals that have larger amount and more diversity are still lack of systematic study, and we are still unclear on the genetic mechanism underlying their high-elevation adaptations. This article, we choose the Tibetan frog Nanorana parkeri as the research object to explore the genetic mechanism of ectotherm’s high-elevation adaptation, through comparing the gene expression levels with its low-altitude relatives. Analyses found that the up-regulated genes in the liver tissue are significantly enriched in energy metabolism related pathways, which is also a common strategy utilized by warm-blooded animals. In ovary tissue, genes with higher expression are significantly enriched in the nutrition metabolic pathway, such as, synthesis of fat metabolism, carbohydrate metabolism and so on. That is related to the get through a long hibernation in plateau. In skin tissue, we found the higher expression of ASTKD1 and STK17A gene is associated with the ultraviolet response and survival of cells. High throughput RNA-seq data can not only carry on different expression analysis, but also be used for the analysis of phylogeny. Cattle as a kind of ruminants, is able to convert low-grade forage into nutrition-rich muscle and milk, has good economic value and maintained abundant species diversity throughout the world. Bos frontalis is a special member in Bos，which mainly distributed in the Nu and Dulong rivers basin in China, and is a kind of precious semi-wild / semi-domesticated animal. It still exist with great debate about the origin of Bos frontalis，which is mainly concentrated in three kinds of hypothesis: (1) domestic type of Bos gaurus; (2) hybrid descendant of male Bos gaurus and female Bos indicus or Bos taurus; and (3) the descendant of an extinct wild Indian cattle, which is close related to Bos gaurus. In this thesis, we used the RNA-seq technology, carry out transcriptome sequencing and assembly for the blood tissue of Bos frontalis, and predict orthologous genes with Bos taurus, Bos indicus, Bos grunniens, Capra hircus, Sus scrofa. Combining with "concatenation" and "parallel" data analysis methods, maximum likelihood tree and bayesian tree have been constructed respectively, and further more, species tree has been constructed base on single gene tree. Analyses show that Bos frontalis first separated, with Bos grunniens, Bos taurus and Bos indicus cluster as sister group relationship，supporting that Bos frontalis is an independent species and origin independently. and provide a scientific basis for the evolution study of Bos frontalis and its related species.
语种	中文
文献类型	学位论文
条目标识符	http://ir.kiz.ac.cn/handle/152453/7917
专题	科研部门_两栖爬行类多样性与进化（车静）科研部门_进化与发育转录组学（吴东东）
作者单位	中国科学院昆明动物研究所
推荐引用方式 GB/T 7714	涂小龙. 利用转录组数据探究高山倭蛙原适应性机制和大额牛的系统发育地位[D]. 北京. 中国科学院研究生院,2014.

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