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The Complete Mitochondrial Genome of a Rare Cavefish (Sinocyclocheilus cyphotergous ) and Comparative Genomic Analyses in Sinocyclocheilus
Author(s):
1. Xiaoping Gao: Jiujiang Academy of Agricultural Sciences, Jiujiang, 332101, China
2. Yanping Li: Key Laboratory of Sichuan Province for Fishes Conservation and Utilization in the Upper Reaches of the Yangtze River, College of Life Sciences, Neijiang Normal University, Neijiang, 641100, China
3. Renyi Zhang: Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern China, School of Life Science, Guizhou Normal University, Guiyang, Guizhou, 550001, China
4. Yunyun Lv: Key Laboratory of Sichuan Province for Fishes Conservation and Utilization in the Upper Reaches of the Yangtze River, College of Life Sciences, Neijiang Normal University, Neijiang, 641100, China
5. Yongming Wang: Key Laboratory of Sichuan Province for Fishes Conservation and Utilization in the Upper Reaches of the Yangtze River, College of Life Sciences, Neijiang Normal University, Neijiang, 641100, China
6. Jinrong Shi: Key Laboratory of Sichuan Province for Fishes Conservation and Utilization in the Upper Reaches of the Yangtze River, College of Life Sciences, Neijiang Normal University, Neijiang, 641100, China
7. Jiang Xie: Key Laboratory of Sichuan Province for Fishes Conservation and Utilization in the Upper Reaches of the Yangtze River, College of Life Sciences, Neijiang Normal University, Neijiang, 641100, China
8. Chiping Kong: Jiujiang Academy of Agricultural Sciences, Jiujiang, 332101, China
9. Lekang Li: Jiujiang Academy of Agricultural Sciences, Jiujiang, 332101, China
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..
Page(s): 2245-2254
Published: Journal: Pakistan Journal of Zoology, Volume: 56, Issue: 5, Year: 2024
Keywords:
Phylogenetic relationship , Annotation , Sinocyclocheilus cyphotergous , Mitogenome assembly , Evolution analysis
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