【摘 要】
:
线粒体DNA(mtDNA)由于具有母系遗传、缺乏重组及突变速率快等特点作为最常用的分子标记之一,已广泛应用在家养动物的遗传多样性评估、群体进化历史解析等诸多研究中。家
【机 构】
:
中国科学院昆明动物研究所,昆明650204
【出 处】
:
中国”西南地区农业动物种质资源挖掘与创新利用“学术研讨会
论文部分内容阅读
线粒体DNA(mtDNA)由于具有母系遗传、缺乏重组及突变速率快等特点作为最常用的分子标记之一,已广泛应用在家养动物的遗传多样性评估、群体进化历史解析等诸多研究中。家养动物mtDNA 系统发育基因组学研究的基础是构建系统发育关系,目前已有大量的mtDNA基因组序列被测定并提交到公共数据库,然而,由于缺少一个统一的参考标准,家养动物的mtDNA 世系划分和命名依旧十分混乱,严重阻碍了不同研究之间的比较。同时相关数据的质量也没有得到系统有效的评估。在人类mtDNA单倍型类群树研究中,Phylotree很好解决了之前人类mtDNA 研究中由于不同研究者采用不同划分标准或者不同命名习惯导致的混乱。同时也提出了一系列关于数据质量控制和分析的方法。基于此,我们借鉴人类mtDNA 工作的相关经验,对来自8 种家养动物(家犬、家牛、牦牛、家猪、马、山羊、绵羊和家鸡)共计1342条mtDNA基因组序列进行了系统的评估,用基于mtDNA单倍型类群树(haplogroup tree)的系统发育分析策略,一共发现194 条存在质量问题的序列。相关问题可归结于人为重组(artificialrecombination),突变过多(surplus of mutations)和幻影突变(phantom mutation)。值得注意的是,幻影突变在由二代测序产生的数据中普遍存在。通过上述的数据质控,我们整合质量合格的mtDNA 基因组序列,分别构建和完善了8 种家养动物(家犬、家牛、牦牛、家猪、马、山羊、绵羊和家鸡)mtDNA 单倍型类群树,为相关mtDNA 研究提供统一的单倍型类群命名系统和划分标准。同时基于构建的家养动物mtDNA 单倍型类群树,我们提供了一个用于多种家养动物mtDNA 基因组数据分析的软件MitoToolpy,为家养动物mtDNA 数据的计算提供支援,推进加速家养动物mtDNA 系统发育基因组学的发展。
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