A comparative approach shows differences in patterns of numt insertion during hominoid evolution.
A comparative approach shows differences in patterns of numt insertion during hominoid evolution.
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DOI：
10.1007/s00239-009-9243-4
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发表时间：
2009-06
影响因子：
3.9
通讯作者：
Anthony, N. M.
中科院分区：
文献类型：
--
作者：
Jensen-Seaman, M. I.;Wildschutte, J. H.;Soto-Calderon, I. D.;Anthony, N. M.
线粒体DNA的核整合广泛存在于真核生物中，尽管其发生率在不同的类群中有很大差异。大多数numt进化的知识来自于对单个物种的全基因组序列的分析，或者最近来自于跨越巨大系统发育距离的基因组比较。在这里，我们采用比较的方法，使用人类和黑猩猩的基因组序列数据来推断差异的模式和过程的基础numt整合。我们确定了66个numt，自人类-黑猩猩分歧以来，已经整合到黑猩猩核基因组中，这明显大于在人类中观察到的37个。通过比较这些密切相关的物种，我们准确地重建了整合前的靶位点序列，并推断出与numt整合相关的核苷酸变化。从100多个物种特异性numts中，我们量化了小插入，缺失，重复和微同源性实例的频率。大多数人类和黑猩猩的numt整合都伴随着微同源性和短插入缺失，这种插入缺失通常在DNA双链断裂修复的非同源末端连接途径中观察到。人类特有的numt已经整合到转座因子明显缺乏的区域，而在黑猩猩中没有发现同样的情况。从一个单独的数据集，我们还发现了证据，证明使用基于PCR的屏幕在人类和类人猿的最后一个共同祖先中numt插入率明显增加。最后，系统发育分析表明，numt序列必须至少为500 bp，最好大于1 kb的长度，以准确地重建古猿类的系统发育和恢复正确的numt插入点。
Nuclear integrations of mitochondrial DNA (numts) are widespread among eukaryotes although their prevalence differs greatly among taxa. Most knowledge of numt evolution comes from analyses of whole genome sequences of single species, or more recently from genomic comparisons across vast phylogenetic distances. Here, we employ a comparative approach using human and chimpanzee genome sequence data to infer differences in the patterns and processes underlying numt integrations. We identified 66 numts that have integrated into the chimpanzee nuclear genome since the human-chimp divergence, which is significantly greater than the 37 observed in humans. By comparing these closely related species, we accurately reconstructed the pre-integration target site sequence, and deduced nucleotide changes associated with numt integration. From over 100 species-specific numts, we quantified the frequency of small insertions, deletions, duplications, and instances of microhomology. Most human and chimpanzee numt integrations were accompanied by microhomology and short indels of the kind typically observed in the nonhomologous end-joining pathway of DNA double-strand break repair. Human-specific numts have integrated into regions with a significant deficit of transposable elements, while the same was not seen in chimpanzees. From a separate dataset, we also found evidence for an apparent increase in the rate of numt insertions in the last common ancestor of humans and the great apes using a PCR-based screen. Lastly, phylogenetic analyses indicate that mitochondrial-numt alignments must be at least 500bp, and preferably greater than 1kb in length, in order to accurately reconstruct hominoid phylogeny and recover the correct point of numt insertion.
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影响因子：
4.5
作者：
Hazkani-Covo E;Covo S
通讯作者：
Covo S
DOI：
10.1098/rstb.2002.1193
发表时间：
2003-01-29
影响因子：
6.3
作者：
Andersson, SGE;Karlberg, O;Kurland, CG
通讯作者：
Kurland, CG
影响因子：
4.4
作者：
Antunes, A;Ramos, MJ
通讯作者：
Ramos, MJ
影响因子：
10.7
作者：
Blanchard, JL;Schmidt, GW
通讯作者：
Schmidt, GW
影响因子：
10.7
作者：
Burgess, Ralph;Yang, Ziheng
通讯作者：
Yang, Ziheng