|
1
|
Ke Z, Zhou K, Hou M, Luo H, Li Z, Pan X, Zhou J, Jing T, Ye H. Characterization of the Complete Mitochondrial Genome of the Elongate Loach and Its Phylogenetic Implications in Cobitidae. Animals (Basel) 2023; 13:3841. [PMID: 38136877 PMCID: PMC10740543 DOI: 10.3390/ani13243841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 12/01/2023] [Accepted: 12/02/2023] [Indexed: 12/24/2023] Open
Abstract
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.
Collapse
Affiliation(s)
- 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; (Z.K.); (M.H.); (H.L.); (T.J.)
- Key Laboratory of Aquatic Science of Chongqing, Chongqing 400175, China
| | - Kangqi Zhou
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning 530021, China; (K.Z.); (Z.L.); (X.P.)
| | - 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; (Z.K.); (M.H.); (H.L.); (T.J.)
- Key Laboratory of Aquatic Science of Chongqing, Chongqing 400175, 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; (Z.K.); (M.H.); (H.L.); (T.J.)
- Key Laboratory of Aquatic Science of Chongqing, Chongqing 400175, China
| | - Zhe Li
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning 530021, China; (K.Z.); (Z.L.); (X.P.)
| | - Xianhui Pan
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning 530021, China; (K.Z.); (Z.L.); (X.P.)
| | - 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; (Z.K.); (M.H.); (H.L.); (T.J.)
- Key Laboratory of Aquatic Science of Chongqing, Chongqing 400175, 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; (Z.K.); (M.H.); (H.L.); (T.J.)
- Key Laboratory of Aquatic Science of Chongqing, Chongqing 400175, China
| |
Collapse
|
|
2
|
Chen Q, Lian X, Li Y, Liu Z, Shen Y. Complete mitochondrial genome of Acrossocheilus yunnanensis (Cypriniformes: Cyprinidae: Acrossocheilus) and its phylogenetic analysis. Mitochondrial DNA B Resour 2022; 7:1764-1765. [PMID: 36237204 PMCID: PMC9553164 DOI: 10.1080/23802359.2020.1780973] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Acrossocheilus yunnanensis is an endemic species in China. In this study, the complete mitochondrial genome of A. yunnanensis was determined. It was 16,587 bp in length, containing 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and a putative control region. Phylogenetic analysis showed that A. yunnanensis was clustered with A. monticola.
Collapse
Affiliation(s)
- Qiliang Chen
- Chongqing Key Laboratory of Animal Biology, School of Life Sciences, Chongqing Normal University, Chongqing, China
| | - Xiaolong Lian
- Chongqing Key Laboratory of Animal Biology, School of Life Sciences, Chongqing Normal University, Chongqing, China
| | - Yingwen Li
- Chongqing Key Laboratory of Animal Biology, School of Life Sciences, Chongqing Normal University, Chongqing, China
| | - Zhihao Liu
- Chongqing Key Laboratory of Animal Biology, School of Life Sciences, Chongqing Normal University, Chongqing, China
| | - Yanjun Shen
- Chongqing Key Laboratory of Animal Biology, School of Life Sciences, Chongqing Normal University, Chongqing, China,CONTACT Yanjun Shen Chongqing Key Laboratory of Animal Biology, School of Life Sciences, Chongqing Normal University, Chongqing, China
| |
Collapse
|