Identification of species-specific nuclear insertions of mitochondrial DNA (numts) in gorillas and their potential as population genetic markers.
Identification of species-specific nuclear insertions of mitochondrial DNA (numts) in gorillas and their potential as population genetic markers.
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DOI：
10.1016/j.ympev.2014.08.018
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发表时间：
2014-12
影响因子：
4.1
通讯作者：
Anthony, Nicola Mary
中科院分区：
文献类型：
--
作者：
Dario Soto-Calderon, Ivan;Clark, Nicholas Jonathan;Wildschutte, Julia Vera Halo;DiMattio, Kelly;Jensen-Seaman, Michael Ignatius;Anthony, Nicola Mary
线粒体控制区（MCR）的第一高变区（HV 1）已被广泛用作群体遗传学的分子工具，但大猩猩线粒体DNA核易位拷贝（numts）的无意扩增已经损害了线粒体DNA在群体遗传学研究中的应用。在过去的十年中，已经发现了至少三类（I，II，III）大猩猩特异性HV 1 MCR numts。然而，大猩猩和其他猿类中numt基因座的数量、大小和位置完全未知。此外，迄今为止，很少有工作评估numts作为候选群体遗传标记的效用。在本研究中，我们筛选了黑猩猩和大猩猩的细菌人工染色体（BAC）基因组文库，以比较两个类群中的全细胞插入模式。我们对大猩猩基因组中的numt基因进行了密集的BLAST搜索，并将来自MCR的numt基因座的流行率与其他类人猿分类群进行了比较。通过BAC文库筛选或使用来自五个无关大猩猩的基因组DNA的扩增-PCR（A-PCR）扩增来检索另外的大猩猩特异性MCR numts。设计位点特异性引物鉴定numt插入多态性，并评价其作为群体遗传标记的潜力。对黑猩猩和大猩猩BAC的线粒体范围调查表明，这两个分类群之间的numt数量没有差异。然而，黑猩猩的MCR数量比其他类人猿要多。我们确定并绘制了67个假定的大猩猩特异性numt，包括两个包含整个HV 1结构域的numt，与两个numt类别（I，IIb）的序列聚类，并可能使用大多数已发表的HV 1引物与线粒体序列共扩增。然而，系统发育分析加上线粒体变异的事后分析可以成功地区分核序列。插入多态性是明显的，在三个五numts检查，表明其潜在的效用作为分子标记。总之，这些发现证明了numts在揭示大猩猩和其他哺乳动物的种群历史方面可能具有强大的洞察力。
The first hyper-variable region (HV1) of the mitochondrial control region (MCR) has been widely used as a molecular tool in population genetics, but inadvertent amplification of nuclear translocated copies of mitochondrial DNA (numts) in gorillas has compromised the use of mitochondrial DNA in population genetic studies. At least three putative classes (I, II, III) of gorilla-specific HV1 MCR numts have been uncovered over the past decade. However, the number, size and location of numt loci in gorillas and other apes are completely unknown. Furthermore, little work to date has assessed the utility of numts as candidate population genetic markers. In the present study, we screened Bacterial Artificial Chromosome (BAC) genomic libraries in the chimpanzee and gorilla to compare patterns of mitochondrial-wide insertion in both taxa. We conducted an intensive BLAST search for numts in the gorilla genome and compared the prevalence of numt loci originating from the MCR with other great ape taxa. Additional gorilla-specific MCR numts were retrieved either through BAC library screens or using an anchored-PCR (A-PCR) amplification using genomic DNA from five unrelated gorillas. Locus-specific primers were designed to identify numt insertional polymorphisms and evaluate their potential as population genetic markers. Mitochondrial-wide surveys of chimpanzee and gorilla BACs showed that the number of numts does not differ between these two taxa. However, MCR numts are more abundant in chimpanzees than in other great apes. We identified and mapped 67 putative gorilla-specific numts, including two that contain the entire HV1 domain, cluster with sequences from two numt classes (I, IIb) and will likely co-amplify with mitochondrial sequences using most published HV1 primers. However, phylogenetic analysis coupled with post-hoc analysis of mitochondrial variation can successfully differentiate nuclear sequences. Insertional polymorphisms were evident in three out of five numts examined, indicating their potential utility as molecular markers. Taken together, these findings demonstrate the potentially powerful insight that numts could make in uncovering population history in gorillas and other mammals.
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影响因子：
4.5
作者：
Mailund T;Halager AE;Westergaard M;Dutheil JY;Munch K;Andersen LN;Lunter G;Prüfer K;Scally A;Hobolth A;Schierup MH
通讯作者：
Schierup MH
影响因子：
2.4
作者：
Jensen-Seaman, MI;Sarmiento, EE;Kidd, KK
通讯作者：
Kidd, KK
影响因子：
4.1
作者：
Garner, KJ;Ryder, OA
通讯作者：
Ryder, OA
影响因子：
4.9
作者：
Greenwood, AD;Pääbo, S
通讯作者：
Pääbo, S
影响因子：
4.4
作者：
Calvignac, Sebastien;Konecny, Lara;Douady, Christophe J.
通讯作者：
Douady, Christophe J.