Comparative Analysis of the Complete Mitochondrial Genomes for Development Application
Comparative Analysis of the Complete Mitochondrial Genomes for Development Application
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完整线粒体基因组的比较分析用于开发应用
DOI：
10.3389/fgene.2018.00651
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发表时间：
2019-03
影响因子：
3.7
通讯作者：
Dashi Qi
中科院分区：
文献类型：
--
作者：
Nwobodo Alex;er Kenechukwu;Man Li;Cailin Wang;Chenyao Feng;Miaomiao Cui;Saijun Du;Yuting Ga;Xueyan Cao;Li Wang;Sijin Zhong;Dashi Qi
本研究通过对强壮丽鱼和背带颊丽鱼线粒体基因组全序列的比较分析和蛋白质编码基因的系统发育分析，探讨了它们在慈鲷科鱼类中的系统发育关系。线粒体基因组的S。robustus和B.背带绦虫的基因组长度分别为16，583和16，580个碱基对，包括13个蛋白质编码基因（PCG）、2个核糖体RNA基因、22个转运RNA基因和一个控制区（D-loop），分别为888和887个碱基对，与其它已阐明的慈鲷科鱼类有丝分裂基因组的基因顺序和基因或区域数目相同。然而，除了细胞色素c氧化酶亚基-1（考克斯-1）基因外，所有鉴定的PCG都是由ATG密码子启动的。结构上，B中有11个tRNA基因。背带绦虫（S. robustus物种，折叠成典型的三叶草二级结构，由tRNA内的自我互补区域产生。这两个物种的22个tRNA基因都缺少可变环。此外，包括12个蛋白质编码基因的28个基因在H链上编码，包括1个蛋白质编码基因的其余9个基因在L链上编码。利用MUSCLE比对了13个串联的线粒体蛋白编码基因序列，并利用最大似然法和贝叶斯推断进行了系统发育分析，结果表明，S。robustus和B.背带绦虫的系统发育关系较广。这些结果可能是一个有用的工具，在解决更高层次的关系，在生物体和有用的数据集研究的慈鲷科线粒体基因组的进化，因为慈鲷是众所周知的模式物种在进化生物学研究，因为他们极端的形态，地理，父母照顾的行为，卵和幼虫和系统发育的差异。
This present research work reports the comparative analysis of the entire nucleotide sequence of mitochondrial genomes of Serranochromis robustus and Buccochromis nototaenia and phylogenetic analyses of their protein-coding genes in order to establish their phylogenetic relationship within Cichlids. The mitochondrial genomes of S. robustus and B. nototaenia are 16,583 and 16,580 base pairs long, respectively, including 13 protein-coding genes (PCGs), 2 ribosomal RNA genes, 22 transfer RNA genes, and one control region (D-loop) which is 888 and 887 base pairs long, respectively, showing the same gene order and identical number of gene or regions with other well-elucidated mitogenomes of Cichlids. However, with exception of cytochrome-c oxidase subunit-1 (COX-1) gene, all the identified PCGs were initiated by ATG-codons. Structurally, 11 tRNA genes in B. nototaenia species and 9 tRNA genes in S. robustus species, folded into typical clover-leaf secondary structure created by the regions of self-complementarity within tRNA. All the 22 tRNA genes in both species lack variable loop. Moreover, 28 genes which include 12-protein-coding genes are encoded on the H-strand and the remaining 9 genes including one protein-coding gene are encoded on the L-strand. Thirteen sequences of concatenated mitochondrial protein-coding genes were aligned using MUSCLE, and the phylogenetic analyses performed using maximum likelihood and Bayesian inference showed that S. robustus and B. nototaenia had a broad phylogenetic relationship. These results may be a useful tool in resolving higher-level relationships in organisms and a useful dataset for studying the evolution of the Cichlidae mitochondrial genome, since Cichlids are well-known model species in the study of evolutionary biology, because of their extreme morphological, biogeographical, parental care behavior for eggs and larvae and phylogenetic diversities.
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