Factors affecting the relative abundance of nuclear copies of mitochondrial DNA (numts) in hominoids.
Factors affecting the relative abundance of nuclear copies of mitochondrial DNA (numts) in hominoids.
复制标题
影响类人猿线粒体 DNA (numts) 核拷贝相对丰度的因素。
DOI：
10.1007/s00239-012-9519-y
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发表时间：
2012
影响因子：
3.9
通讯作者：
Anthony,NM
中科院分区：
文献类型：
--
作者：
Soto-Calderon,ID;Lee,EJ;Jensen-Seaman,MI;Anthony,NM
虽然线粒体DNA的核拷贝（numts）可以来自线粒体基因组的任何部分，但来自人类的证据表明，线粒体基因组的更多可变部分，如线粒体控制区（MCR），在细胞核中的代表性不足。这种明显的缺陷可能是由于快速进化的线粒体序列引起的numts序列同一性的侵蚀。然而，线粒体序列特性在多大程度上影响基因组调查中检测到的numts的数量还没有得到评估。为了解决这个问题，我们：（1）在三个类人猿基因组中对MCR numt进行了详尽的BLAST搜索;（2）评估了四个MCR子域中的numt流行率（3）估计了它们在类人猿中的插入率（Hominoidea）;以及（4）研究了线粒体DNA变异性和numt流行率之间的关系，在序列起源于MCR和编码区的线粒体基因组结果表明，在所有三个物种的HV 2和MCRFMCR亚域的numts的显着赤字。这些MCR亚结构域表现出最高比例的可变位点和最低数量的检测numts每个线粒体位点。还观察到谱系之间MCR插入率的变化，在黑猩猩和猩猩的近期整合中出现了明显的爆发。无论年龄大小，均观察到HV 2/MCRF的numts不足，而HV 1仅在较老的numts（> 2500万年）中代表性不足。最后，更多的可变线粒体基因也表现出较低的同一性与核拷贝，因为这一点，似乎是在人类numt数据库中的代表性不足。
Although nuclear copies of mitochondrial DNA (numts) can originate from any portion of the mitochondrial genome, evidence from humans suggests that more variable parts of the mitochondrial genome, such as the mitochondrial control region (MCR), are under-represented in the nucleus. This apparent deficit might arise from the erosion of sequence identity in numts originating from rapidly evolving mitochondrial sequences. However, the extent to which mitochondrial sequence properties impacts the number of numts detected in genomic surveys has not been evaluated. In order to address this question, we: (1) conducted exhaustive BLAST searches of MCR numts in three hominoid genomes; (2) assessed numt prevalence across the four MCR sub-domains (HV1, CCD, HV2, and MCRF); (3) estimated their insertion rates in great apes (Hominoidea); and (4) examined the relationship between mitochondrial DNA variability and numt prevalence in sequences originating from MCR and coding regions of the mitochondrial genome. Results indicate a marked deficit of numts from HV2 and MCRFMCR sub-domains in all three species. These MCR sub-domains exhibited the highest proportion of variable sites and the lowest number of detected numts per mitochondrial site. Variation in MCR insertion rate between lineages was also observed with a pronounced burst in recent integrations within chimpanzees and orangutans. A deficit of numts from HV2/MCRFwas observed regardless of age, whereas HV1 is under-represented only in older numts (>25 million years). Finally, more variable mitochondrial genes also exhibit a lower identity with nuclear copies and because of this, appear to be under-represented in human numt databases.