Identification of Mitochondrial DNA (NUMTs) in the Nuclear Genome of Daphnia magna.
Identification of Mitochondrial DNA (NUMTs) in the Nuclear Genome of Daphnia magna.
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DOI：
10.3390/ijms21228725
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发表时间：
2020-11-18
影响因子：
5.6
通讯作者：
Ślaska B
中科院分区：
文献类型：
--
作者：
Kowal K;Tkaczyk A;Pierzchała M;Bownik A;Ślaska B
这是第一次对大型蚤（Daphnia magna，D.分析从GenBank数据库获得的大）核基因组（nDNA）的线粒体起源的假基因序列。迄今为止，还没有关于D中定位的假基因的信息。大基因组本研究的目的是确定NUMT，它们的长度，同源性和位置在进化研究中的潜在用途，并检查它们的发生是否会导致线粒体基因组（mtDNA）分析过程中的共扩增。生物信息学分析表明，该菌mtDNA共有1909个片段。其中1630个位于nDNA的10个连锁群（LG）上。已经鉴定了两个mt-tRNA基因的最佳匹配NUMT，其覆盖>90%的基因序列，并且它们可能是功能性核RNA分子。在mtDNA研究中分离总DNA，在扩增整个tRNA基因以及其他基因片段的情况下，不太可能共扩增nDNA片段。据观察，TRNA-MET片段具有最高水平的序列同源性，因此它们在进化上可能是最年轻的。在D环衍生的假基因中发现同源性最低。它可能是最古老的NUMT纳入nDNA;然而，进一步的分析是必要的。
This is the first study in which the Daphnia magna (D. magna) nuclear genome (nDNA) obtained from the GenBank database was analyzed for pseudogene sequences of mitochondrial origin. To date, there is no information about pseudogenes localized in D. magna genome. This study aimed to identify NUMTs, their length, homology, and location for potential use in evolutionary studies and to check whether their occurrence causes co-amplification during mitochondrial genome (mtDNA) analyses. Bioinformatic analysis showed 1909 fragments of the mtDNA of D. magna, of which 1630 were located in ten linkage groups (LG) of the nDNA. The best-matched NUMTs covering >90% of the gene sequence have been identified for two mt-tRNA genes, and they may be functional nuclear RNA molecules. Isolating the total DNA in mtDNA studies, co-amplification of nDNA fragments is unlikely in the case of amplification of the whole tRNA genes as well as fragments of other genes. It was observed that TRNA-MET fragments had the highest level of sequence homology, thus they could be evolutionarily the youngest. The lowest homology was found in the D-loop-derived pseudogene. It may probably be the oldest NUMT incorporated into the nDNA; however, further analysis is necessary.
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