Characterization of the complete mitochondrial genome of Macrotocinclus affinis (Siluriformes; Loricariidae) and phylogenetic studies of Siluriformes
Characterization of the complete mitochondrial genome of Macrotocinclus affinis (Siluriformes; Loricariidae) and phylogenetic studies of Siluriformes
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Macrotocinclus affinis（鲶形目；Loricariidae）完整线粒体基因组的表征和鲶形目的系统发育研究
DOI：
10.1007/s11033-020-06120-z
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发表时间：
2021-01-13
影响因子：
2.8
通讯作者：
Liu, Bingjian
中科院分区：
文献类型：
--
作者：
Zhang, Kun;Liu, Yifan;Liu, Bingjian
脊椎动物线粒体基因组通常是由14，000至16，000 bp组成的环状分子，包括13个蛋白质编码基因（PCG），22个转运RNA基因（tRNA），两个核糖体RNA基因（12 s rRNA和16 s rRNA）和一个控制区。与核DNA相比，线粒体DNA具有更高的突变率，是鱼类遗传学研究中最有效、最可靠的分子标记之一。Macrotocinclus affinis是Macrotocinclus中唯一的物种（过去被归类为Otocinclus），目前缺乏遗传信息。目前的研究大多是基于线粒体Cytb基因和RAG 1、RAG 2核基因对鲇形目鱼类进行系统发育分析。因此，本研究提供了近缘巨鲶线粒体基因组的特征，首次基于COI重建了鲶形目的系统发育关系。本研究旨在利用常规PCR技术对近缘巨孔绦虫的线粒体基因组进行全序列测定，并利用线粒体COI序列阐明其在鲶形目中的系统发育地位。在这项研究中，我们对该物种的线粒体全基因组进行了测序，得到了一个由典型的脊椎动物线粒体特征组成的16，632 bp的环状组装体。它包含13个蛋白质编码基因，两个rRNA基因，22个tRNA基因，一个假定的控制区，和一个轻链上的复制起点。总碱组成包括A（30.07%）、T（24.43%）、C（29.43%）和G（16.01%）。基因组组成是A + T偏置的（54.5%），并表现出AT偏置（0.1036）和GC偏置（-0.2962）。此外，13个PCG共编码3850个氨基酸。系统发育树的结果支持近缘大孔霍皮法尔。这些结果将有助于了解近缘巨鲶线粒体基因组的特征，并为甲鲶科的进化关系提供分子基础。
The vertebrate mitochondrial genome is typically circular molecules made up of 14,000 to 16,000 bp, including 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (12 s rRNA and 16 s rRNA) and a control region. Compared with nuclear DNA, mitochondrial DNA has a higher mutation rate, so it is one of the most effective and reliable molecular markers in fish phylogeny. Macrotocinclus affinis was the only species in Macrotocinclus (it was classified as Otocinclus in the past) and currently lacks genetic information. Most of the current researches are based on the mitochondrial Cytb gene and RAG1 and RAG2 nuclear genes to study the phylogenetic analysis of Siluriformes. So, the study provides the characteristic features of the Macrotocinclus affinis mitochondrial genome and this is the first time that the phylogenetic relationship of Siluriformes has been reconstructed based on COI. We aimed to sequence the entire mitochondrial genome of Macrotocinclus affinis using conventional PCR techniques and to clarify its phylogenetic status in Siluriformes by using the COI sequence of mitochondria. In this study, we sequenced the whole mitochondrial genome of this species yielding a 16,632 bp circular assembly composed of the typical vertebrate mitochondrial features. It contains 13 protein-coding genes, two rRNA genes, 22 tRNA genes, a putative control region, and one origin of replication on the light-strand. The overall base composition includes A (30.07%), T (24.43%), C (29.43%) and G (16.01%). The genome composition is A + T biased (54.5%), and exhibits AT-skew (0.1036) and GC-skew (−0.2962). Moreover, the 13 PCGs encode 3850 amino acids in total. The result of the phylogenetic tree supports Macrotocinclus affinis has a closest relationship with Otocinclus cf. hoppei far. These results will help to understand the characteristics of the mitochondrial genome of Macrotocinclus affinis and provide molecular basis for the evolutionary relationship of Loricariidae.