| 其他摘要 | 树鼩（中缅树鼩）目前隶属攀缘目，广泛分布于南亚，东南亚和中国西南地区。由于其独特的特点，如体型小，脑-体重比例高，生殖周期短，寿命短、饲养成本低及与灵长类亲缘关系近等，树鼩被认为是可替代灵长类动物的新型实验动物。目前已在很多疾病研究方面尝试建立树鼩的动物模型，比如乙型肝炎病毒、丙型肝炎病毒、近视、抑郁症等。对于成年树鼩脑部的研究亦可为衰老和行为学研究提供可靠的医学模型。尽管树鼩在动物模型开发方面具有显著的优势，但目前却仅有少数实验室对其展开研究，这主要是由于树鼩还有没有建立良好纯种家系和有限的使用权限。总之，对于树鼩的研究目前还存在很多的阻碍。由于缺乏高质量的基因组和基因表达谱全景图，很多问题都无法解决，比如：1）树鼩与灵长类的亲缘关系究竟如何；2）作为灵长类的近亲，树鼩的关键通路是否与灵长类相似；3）树鼩拥有怎样的生物学特征。相信这些问题的解答将为树鼩动物模型可行性，设计和发展新型疾病模型，药物筛选与安全检测等方面提供重要信息。我们选取了一只来自云南的雄性中缅树鼩进行基因组测序，得到了大小为2.86G的高质量树鼩基因组序列。通过比较美国Broad研究发布的北树鼩基因组与我们的中缅树鼩基因组，我们的树鼩基因组无论在组装质量，还是在基因注释的完整度上都有明显的提升。通过基因组注释得到了22,121个编码基因，4,143,138个转座因子和2,754个非编码RNA。这些信息为解析树鼩基因组秘密提供了重要的遗传基础。为了确定树鼩在灵长总目的系统发育地位，我们利用树鼩与14种哺乳动物的（包括6种灵长类动物）的2,177个单拷贝基因的CDS序列和氨基酸序列进行系统发育树重构，皆显示树鼩与灵长类的亲缘关系最为接近。我们进一步对树鼩基因组中的重要基因进行了挖掘。我们鉴定了28个树鼩与灵长类特有的共同基因，这些基因意味着树鼩与灵长类拥有着某些共同的的表型特征。同时，我们鉴定了11个树鼩中缺失的基因和144个假基因，其中一些重要基因的改变，提示了树鼩特有的生物学功能变化。针对一些树鼩特有的生物学特点，比如快速跳跃能力和酒精耐受能力，我们对相关基因进行了解析，发现树鼩TNNC2、MYH4和ACTN2等基因的快速进化可能促使其拥有更强的爆发力和跳跃能力，而拥有许多特异变异位点的ALDH2基因可能影响了树鼩酒精代谢系统。最后，我们对于树鼩神经系统、免疫系统和药物靶点等关键基因进行解析，发现其中绝大部分基因与人具有很高的同源性，为相关的动物模型创建和药物试验提供了重要的遗传学数据。为了使研究人员能够快速方便的地获得树鼩基因组的注释信息，我们搭建了树鼩基因组数据库（Tree shrew Database）。树鼩基因组数据库整合树鼩基因的基本信息、序列信息、功能注释信息、同源基因信息和表达信息，提供友好界面，建立一键式检索服务。此外，为了方便研究人员做一些序列分析与进化分析，我们整合了一些常用软件包括Blast、Muscle、Gbrowse、Genewise和codeml等，而且自主开发了正选择分析流程（PSAP）和一些小工具，如ExtractSeq、ReverseSeq和TranslateCDS。相信树鼩基因组数据库（http://www.treeshrewdb.org）会成为广大研究人员了解树鼩遗传特性与创建树鼩动物模型的一个有力平台。综上所述，基于对树鼩基因组的分析，我们发现树鼩与灵长类的关系最近，解决了关于树鼩与灵长总目系统发育关系的长期争论。并且，我们提供了公开完整的树鼩基因组注释信息，为了解其独特的生物学特性和其动物模型创建的可行性提供了重要的遗传学基础。; The tree shrew (Tupaia belangeri), currently placed in the order Scandentia, has a wide distribution in South Asia, Southeast Asia and Southwest China. For several decades, due to a variety of unique characteristics ideal for an experimental animal (e.g. small adult body size, high brain-to-body mass ratio, short reproductive cycle and life span, low-cost of maintenance, and most importantly, a claimed close affinity to primates), the tree shrew has been proposed as a viable animal model alternative to primates in biomedical research and drug safety testing.Currently, there are many attempts to employ tree shrew to create animal models for studying hepatitis C virus and hepatitis B virus infections, myopia, as well as social stress and depression. Recent studies of aged tree shrew brain suggested tree shrew is also a valid model for aging research and learning behaviors. Despite marked progress in using tree shows as an animal model, tree shrews are studied only in a handful of laboratories worldwide, partially because there is no pure breed of this animal, limited access to this animal resource and lack of specific reagents. Moreover, a great number of obstacles to furthering these studies remain, especially the lack of a high-quality genome and an overall view of gene expression profiling which leave several key questions unanswered: a) How closely related are tree shrews to primates; b) do tree shrews share similarity of key signaling pathways to primates and be fully used as an adjunct to primates; and c) what are the unique biological features of the tree shrew? The answers to these questions provide the necessary information needed to expedite current efforts in making the Chinese tree shrew a viable model animal, and to design and develop new animal models for human diseases, drug screening and safety testing.In this study, we conducted whole genome sequencing on a male Chinese tree shrew from Yunnan Province of China, and yielded a high-quality reference genome about 2.86 Gb. Compared to the previous version released by Broad Institute, we found that our version has a apparent improvement on assembly and annotation. We annotated 22,121coding genes, 4,143,138 transposable element and 2,754 ncRNA, these data provide important genetic basis of this animal as an animal model for biomedical research. To identify the phylogenetic position of tree shrew in Euarchontoglires, we compared the 2,117 single-copy genes in tree shrew and 14 other species, including 6 primate species, and found the tree shrew was clustered with primate species with a high bootstrap support by all phylogenetic signals, including coding sequences with all codon positions and peptide sequences.Moreover, we analysed some important genes in tree shrew. We identified 28 genes previously considered as primate specific genes also present in tree shrew genome. These genes may encode functional proteins that shape similar phenotypic characters between tree shrews and primates. We also identified a total of 11 lost genes and 144 pseudo-genes in the tree shrew genome. These genes may suggests some important biological function changed in tree shrew. Basis on some biological features of tree shrew such as speed jumping ability and ethanol tolerance, we analyzed the related genes and found some positively selected genes TNNC2, MYH4 and ACTN2 in tree shrew. These changes may improve explosive power and jumping ability. ALDH2 with so many speical mutation sites may influence alcohol metabolism in tree shrew. We likewise characterized the key classes of molecules relevance to the tree shrew nervous and immune systems, and found most of these genes are highly conserved in amino acid sequences with their human counterparts. These data provided important genetic basis of this animal as a rising model for biomedical research.With the aim to making the access to an extensively annotated genome database straightforward and easy, we have created the Tree shrew Database (TreeshrewDB). This is a web-based platform that integrates the currently available data from the tree shrew genome, including basic information, sequence, functional annotation, ortholog gene and mRNA expression levels of all the genes. In addition, to assist with automatic gene sequence analysis, we have integrated the common programs Blast, Muscle, GBrowse, GeneWise and codeml, into TreeshrewDB. We have also developed a pipeline for the analysis of positive selections and some small tool such as ExtractSeq, ReverseSeq and TranslateCDS. The user-friendly interface of TreeshrewDB, which is available at http://www.treeshrewdb.org, will undoubtedly be a powerful platform for understanding the unique genitic fearture of tree shrew and help in many areas of biological research into the tree shrew.In summary, we showed that tree shrews had a relatively closer affinity to non-human primates, settling a long-running dispute regarding the phylogenetic position of tree shrew within the Euarchontoglires clade. The publicly available annotated genome sequence of the Chinese tree shrew we generated offers an opportunity to understand unique biological fearture of this animal and decipher the genetic basis of the tree shrews’ suitability as an animal model. |
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