摘要
线粒体基因频繁的向细胞核中转移,产生了一些与线粒体基因同源并且没有表达功能的序列。这种序列就被称为线粒体假基因,即Numts (nuclear mitochondrial DNA segments,简称Numts)。线粒体假基因目前在植物、昆虫和哺乳动物中研究较为广泛,但对于鸟类核基因组中的线粒体假基因研究却很少。随着聚合酶链式反应(PCR)和DNA测序技术的发展,线粒体DNA (mtDNA)已成为鸟类系统学和进化研究的理想分子标记。目前公共数据库(GenBank)中,鸟类仅有6个目(雁形目、鸽形目、隼形目、鸻形目、鸡形目和雀形目)存在线粒体假基因共244条(包括实验室前期获得的35条numts序列)。
利用GenBank上9个物种的线粒体基因组的数据(家鸡(Gallus gallus,NC_001323)、小鼠(Mus musculus,NC_001665)、大鼠(Rattus norvegicus,NC_005089)、猪(Sus scrofa,NC_000845)、家牛(Bos taurus,NC_006853)、家狗(Canis familiaris,NC_002008)、猕猴(Rhesus macaque,NC_005943)、黑猩猩(Pan troglodytes,NC_001643)、人(Homo sapiens,NC_001807))为诱饵序列,在NCBI中分别与其核基因组序列进行做Blastn同源性序列比对,推断同源性较高的为线粒体假基因(numts),对其线粒体序列和numts侧翼序列分析。结果如下:家鸡、小鼠、大鼠、猪、牛、狗、猕猴、黑猩猩和人类核基因组中存在的numts数量分别为15、44、17、21、39、69、92、159及147条;在猕猴、黑猩猩和人的核基因组中的线粒体假基因序列分别涵盖了其各自线粒体基因组的全部序列;9个物种中线粒体rRNA基因向核内转移的次数最多。分析numts侧翼序列的重复元件发现:家鸡核基因组序列中仅有不到5 %的序列含有重复序列,并认为家鸡中的任何一条numt都是独立插入到核基因组中。Numts侧翼序列GC含量均小于44 %。对numts侧翼序列的分析有助于进一步了解线粒体基因向核基因组转移的机制。
Content: Mitochondrial DNA sequences are frequently transferred to the nucleus giving rise to the so-called NUMT (nuclear mitochondrial DNA segments) which not only homologous to mtDNA but also no expression functions. Mitochondrial pseudogenes are greatly researched in plants, insects and mammals, however, which in Aves has a less research. With the concurrent developments of polymerase chain reaction (PCR) and DNA sequencing technology, the mitochondrial DNA (mtDNA) has become a very useful molecular marker for studying avian systematics and evolutionary biology. Currently, there are only 244 numts containing gained by lab in six orders (Anseriformes, Columbiformes, Falconiformes, Galliformes, Charadriiformes and Passeriformes) of Aves in public database (GenBank).
NCBI-BLASTN was carried out with mitochondrial and corresponding nuclear genome of nine species in vertebrates (Gallus gallus (NC_001323), Mus musculus (NC_001665), Rattus norvegicus (NC_005089), Sus scrofa (NC_000845), Bos Taurus (NC_006853), Canis familiaris (NC_002008), Rhesus macaque (NC_005943), Pan troglodytes (NC_001643), Homo sapiens (NC_001807)). The sequences with high homology were considered as‘numts’. In our findings, the number of numts in Gallus gallus, Mus musculus, Rattus norvegicus, Sus scrofa, Bos Taurus, Canis familiaris, Rhesus macaque, Pan troglodytes and Homo sapiens were 15, 44, 17, 21, 39, 69, 92, 159 and 147, respectively. The sequences of numts in Rhesus macaque, Pan troglodytes and Homo sapiens span 100 % of the entire mammalian mitochondrial genome. The reconstructed frequency of mitochondrial gene transfer to nucleus shows rRNA gene has more frequency than other mitochondrial gene. Using the RepeatMasker program, we detected the transposable elements in the flanking regions of each numt. The result shows less than 5 % of nuclear sequence were repetitive elements. Furthermore, these numts are considered to independent insertion from the mitochondria into the nucleus in Gallus gallus. The GC content of 5' and 3' - flanking region of numts in nine species is less than 44 %. The analysis of numts flanking sequences provides a valuable understand for future study in mechanism of motichondrial transfer to nucleus and the site of numt integration.
引文
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