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Zhang J, Miao G, Hu S, Sun Q, Ding H, Ji Z, Guo P, Yan S, Wang C, Kan X, Nie L. Quantification and evolution of mitochondrial genome rearrangement in Amphibians. BMC Ecol Evol 2021; 21:19. [PMID: 33563214 PMCID: PMC7871395 DOI: 10.1186/s12862-021-01755-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 01/28/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Rearrangement is an important topic in the research of amphibian mitochondrial genomes ("mitogenomes" hereafter), whose causes and mechanisms remain enigmatic. Globally examining mitogenome rearrangements and uncovering their characteristics can contribute to a better understanding of mitogenome evolution. RESULTS Here we systematically investigated mitogenome arrangements of 232 amphibians including four newly sequenced Dicroglossidae mitogenomes. The results showed that our new sequenced mitogenomes all possessed a trnM tandem duplication, which was not exclusive to Dicroglossidae. By merging the same arrangements, the mitogenomes of ~ 80% species belonged to the four major patterns, the major two of which were typical vertebrate arrangement and typical neobatrachian arrangement. Using qMGR for calculating rearrangement frequency (RF) (%), we found that the control region (CR) (RF = 45.04) and trnL2 (RF = 38.79) were the two most frequently rearranged components. Forty-seven point eight percentage of amphibians possessed rearranged mitogenomes including all neobatrachians and their distribution was significantly clustered in the phylogenetic trees (p < 0.001). In addition, we argued that the typical neobatrachian arrangement may have appeared in the Late Jurassic according to possible occurrence time estimation. CONCLUSION It was the first global census of amphibian mitogenome arrangements from the perspective of quantity statistics, which helped us to systematically understand the type, distribution, frequency and phylogenetic characteristics of these rearrangements.
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Affiliation(s)
- Jifeng Zhang
- School of Biological Engineering, Huainan Normal University, Huainan, Anhui, 232001, People's Republic of China.
- College of Life Science, Anhui Normal University, Wuhu, Anhui, 241000, People's Republic of China.
- Anhui Key Laboratory of Low Temperature Co-Fired Materials, Huainan Normal University, Huainan, 232001, People's Republic of China.
- Key Laboratory of Industrial Dust Prevention and Control and Occupational Health and Safety, Ministry of Education, Huainan, 232001, People's Republic of China.
- Anhui Shanhe Pharmaceutical Excipients Co., Ltd., Huainan, 232001, People's Republic of China.
| | - Guopen Miao
- School of Biological Engineering, Huainan Normal University, Huainan, Anhui, 232001, People's Republic of China
| | - Shunjie Hu
- School of Biological Engineering, Huainan Normal University, Huainan, Anhui, 232001, People's Republic of China
| | - Qi Sun
- School of Biological Engineering, Huainan Normal University, Huainan, Anhui, 232001, People's Republic of China
| | - Hengwu Ding
- College of Life Science, Anhui Normal University, Wuhu, Anhui, 241000, People's Republic of China
| | - Zhicheng Ji
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Pen Guo
- Life Science and Food Engineering College, Yibin University, Yibin, Sichuan, 644000, People's Republic of China
| | - Shoubao Yan
- School of Biological Engineering, Huainan Normal University, Huainan, Anhui, 232001, People's Republic of China
| | - Chengrun Wang
- School of Biological Engineering, Huainan Normal University, Huainan, Anhui, 232001, People's Republic of China
| | - Xianzhao Kan
- College of Life Science, Anhui Normal University, Wuhu, Anhui, 241000, People's Republic of China.
| | - Liuwang Nie
- College of Life Science, Anhui Normal University, Wuhu, Anhui, 241000, People's Republic of China.
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Mu X, Yang Y, Liu Y, Luo D, Xu M, Wei H, Gu D, Song H, Hu Y. Retraction Note to: The complete mitochondrial genomes of two freshwater snails provide new protein-coding gene rearrangement models and phylogenetic implications. Parasit Vectors 2017; 10:350. [PMID: 28732528 PMCID: PMC5522592 DOI: 10.1186/s13071-017-2287-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 07/13/2017] [Indexed: 12/03/2022] Open
Affiliation(s)
- Xidong Mu
- Key Laboratory of Tropical&Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Xingyu Road1, Guangzhou, 510380, China
| | - Yexin Yang
- Key Laboratory of Tropical&Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Xingyu Road1, Guangzhou, 510380, China
| | - Yi Liu
- Key Laboratory of Tropical&Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Xingyu Road1, Guangzhou, 510380, China
| | - Du Luo
- Key Laboratory of Tropical&Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Xingyu Road1, Guangzhou, 510380, China
| | - Meng Xu
- Key Laboratory of Tropical&Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Xingyu Road1, Guangzhou, 510380, China
| | - Hui Wei
- Key Laboratory of Tropical&Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Xingyu Road1, Guangzhou, 510380, China
| | - Dangen Gu
- Key Laboratory of Tropical&Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Xingyu Road1, Guangzhou, 510380, China
| | - Hongmei Song
- Key Laboratory of Tropical&Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Xingyu Road1, Guangzhou, 510380, China
| | - Yinchang Hu
- Key Laboratory of Tropical&Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Xingyu Road1, Guangzhou, 510380, China.
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