The Complete Mitochondrial Genome of a Rare Cavefish (Sinocyclocheilus cyphotergous) and Comparative Genomic Analyses in Sinocyclocheilus
The Complete Mitochondrial Genome of a Rare Cavefish (Sinocyclocheilus cyphotergous) and Comparative Genomic Analyses in Sinocyclocheilus
Xiaoping Gao1, Yanping Li2*, Renyi Zhang3, Yunyun Lv2, Yongming Wang2, Jinrong Shi2, Jiang Xie2, Chiping Kong1 and Lekang Li1
ABSTRACT
The Sinocyclocheilus cyphotergous, belonging to the family Cyprinidae, is endemic to the Karst area of the Yunnan-Guizhou Plateau. Here, we determined the complete mitogenome of S. cyphotergous using an Illumina Hiseq X Ten sequencer. This mitogenome’s structure is typical circular with 16,611 bp in length, consisting of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and a control region. The overall base composition of S. cyphotergous is 31.33% A, 25.89% T, 26.49% C, and 16.29% G with a slight AT bias of 57.22%. Most mitochondrial genes except ND6 and eight tRNAs were encoded on the heavy strand. All tRNA genes fold into the typical cloverleaf secondary structures, except for tRNA-Ser (AGY) that lacked the dihydrouracil arm. 15 of 22 tRNA genes were found to have 29 G-U mismatches in their secondary structures, which formed a weak bond. In addition, mismatches of A-C, C-C, U-U, and A-A were also found in their tRNA secondary structures. Result of substitution rate estimation among the mitochondrial protein coding genes (PCGs) showed ATP8 had the largest average Ka and Ka/Ks, while COI had the lowest, which implied that ATP8 might evolve more quickly than the other mitochondrial protein coding genes. Phylogenetic analyses based on Bayesian inference (BI) and maximum likelihood (ML) revealed all Sinocyclocheilus species in this research formed a solid monophyletic group and grouped into two major clades with strong support excluded S. jii. Additionally, S. cyphotergous in this study was closely related to S. multipunctatus and S. punctatus. In summary, this study provided novel insights into the phylogeny of the Sinocyclocheilus fishes, conducive to the conservation genetics and cave adaptation for S. cyphotergous.
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