Characterization of the Complete Mitochondrial Genome of the Elongate Loach and Its Phylogenetic Implications in Cobitidae
Zhenlin Ke,
Kangqi Zhou,
Mengdan Hou,
Hui Luo,
Zhe Li,
Xianhui Pan,
Jian Zhou,
Tingsen Jing,
Hua Ye
Affiliations
Zhenlin Ke
Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, College of Fisheries, Southwest University, Chongqing 402460, China
Kangqi Zhou
Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning 530021, China
Mengdan Hou
Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, College of Fisheries, Southwest University, Chongqing 402460, China
Hui Luo
Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, College of Fisheries, Southwest University, Chongqing 402460, China
Zhe Li
Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning 530021, China
Xianhui Pan
Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning 530021, China
Jian Zhou
Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu 611731, China
Tingsen Jing
Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, College of Fisheries, Southwest University, Chongqing 402460, China
Hua Ye
Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, College of Fisheries, Southwest University, Chongqing 402460, China
The elongate loach is an endemic fish in China. Previous studies have provided some insights into the mitochondrial genome composition and the phylogenetic relationships of the elongate loach inferred using protein-coding genes (PCGs), yet detailed information about it remains limited. Therefore, in this study we sequenced the complete mitochondrial genome of the elongate loach and analyzed its structural characteristics. The PCGs and mitochondrial genome were used for selective stress analysis and genomic comparative analysis. The complete mitochondrial genome of the elongate loach, together with those of 35 Cyprinidae species, was used to infer the phylogenetic relationships of the Cobitidae family through maximum likelihood (ML) reconstruction. The results showed that the genome sequence has a full length of 16,591 bp, which includes 13 PCGs, 22 transfer RNA genes (tRNA), 2 ribosomal RNA genes (rRNA), and 2 non-coding regions (CR D-loop and light chain sub-chain replication origin OL). Overall, the elongate loach shared the same gene arrangement and composition of the mitochondrial genes with other teleost fishes. The Ka/Ks ratios of all mitochondrial PCGs were less than 1, indicating that all of the PCGs were evolving under purifying selection. Genome comparison analyses showed a significant sequence homology of species of Leptobotia. A significant identity between L. elongata and the other five Leptobotia species was observed in the visualization result, except for L. mantschurica, which lacked the tRNA-Arg gene and had a shorter tRNA-Asp gene. The phylogenetic tree revealed that the Cobitidae species examined here can be grouped into two clades, with the elongate loach forming a sister relationship with L. microphthalma. This study could provide additional inferences for a better understanding of the phylogenetic relationships among Cobitidae species.
