Comparative mitogenomic and phylogenetic analysis of Apalone spinifera and Apalone ferox (Testudines: Trionychidae)
Comparative mitogenomic and phylogenetic analysis of Apalone spinifera and Apalone ferox (Testudines: Trionychidae)
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Apalone spinifera 和 Apalone ferox（陆龟目：鳖科）的比较线粒体基因组和系统发育分析
DOI：
10.1007/s10709-019-00059-1
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发表时间：
2019-04-01
期刊：
影响因子：
1.5
通讯作者：
Zhang, Jun
中科院分区：
文献类型：
--
作者：
Yu, Peng;Yang, Xiaoli;Zhang, Jun
软壳海龟Apalone Spinifera（AS）和Apalone Ferox（AF）是两个重要的经济物种。 AF在中国黄河中发现，是Trionychidae家族的确认成员。但是，AS在争议中的分类。线粒体基因组（有丝分裂组）已被广泛用于物种鉴定以及种群和系统发育分析。为了了解AS和AF的系统发育和有丝分裂的特征，在本研究中对完整的有丝分裂组进行了测序，注释和分析。 AS和AF的完整有丝分裂组分别为16,817bp和16,756bp。两个有丝分裂组都有37个基因，七个短基因间隔剂和两个长的基因间间隔物。比较分析表明，两个有丝分裂组之间有1,137个变异位点（6.79％）。 AS和AF有丝分裂组都在核苷酸，密码子和氨基酸方面均显示出使用偏好。此外，非同义替代率/同义替代率表明所有蛋白质编码基因（PCG）都经历了强烈的纯化选择。由13个PCG构建的系统发育树显示了软壳海龟的系统发育关系，并表明与Apalone属的AF的姊妹物种一样。数据可能有助于进一步研究物种鉴定，人群分析和软壳海龟的有丝分裂特征。
The soft-shell turtles Apalone spinifera (AS) and Apalone ferox (AF) are two important economic species. AF is found in the Yellow River of China, and is a confirmed member of the Trionychidae family. However, the classification of AS was in dispute. Mitochondrial genomes (mitogenomes) have been widely used for species identification, as well as population and phylogenetic analysis. In order to understand the phylogenetic and mitogenomic features of AS and AF, the complete mitogenomes were sequenced, annotated and analyzed in this study. The complete mitogenomes of AS and AF are 16,817 bp and 16,756 bp in length, respectively. Both mitogenomes contain 37 genes, seven short intergenic spacers and two long intergenic spacers. Comparative analysis showed that there are 1,137 variation sites (6.79%) between the two mitogenomes. AS and AF mitogenomes both show a usage preference in terms of nucleotides, codons and amino acids. In addition, the non-synonymous substitution rate/synonymous substitution rate indicates that all protein-coding genes (PCGs) have undergone a strong purifying selection. Phylogenetic trees constructed by 13 PCGs show a clear phylogenetic relationship of the soft-shell turtles and suggest that AS is a sister species to AF of the genus Apalone. The data could be useful for further research of species identification, population analysis and the mitogenomic features of soft-shell turtles.