Quantification and evolution of mitochondrial genome rearrangement in Amphibians.

Affiliation

Zhang J(1)(2)(3)(4)(5), Miao G(6), Hu S(6), Sun Q(6), Ding H(7), Ji Z(8), Guo P(9), Yan S(6), Wang C(6), Kan X(10), Nie L(11).
Author information:
(1)School of Biological Engineering, Huainan Normal University, Huainan, Anhui, 232001, People's Republic of China. [Email]
(2)College of Life Science, Anhui Normal University, Wuhu, Anhui, 241000, People's Republic of China. [Email]
(3)Anhui Key Laboratory of Low Temperature Co-Fired Materials, Huainan Normal University, Huainan, 232001, People's Republic of China. [Email]
(4)Key Laboratory of Industrial Dust Prevention and Control and Occupational Health and Safety, Ministry of Education, Huainan, 232001, People's Republic of China. [Email]
(5)Anhui Shanhe Pharmaceutical Excipients Co., Ltd., Huainan, 232001, People's Republic of China. [Email]
(6)School of Biological Engineering, Huainan Normal University, Huainan, Anhui, 232001, People's Republic of China.
(7)College of Life Science, Anhui Normal University, Wuhu, Anhui, 241000, People's Republic of China.
(8)Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, 21205, USA.
(9)Life Science and Food Engineering College, Yibin University, Yibin, Sichuan, 644000, People's Republic of China.
(10)College of Life Science, Anhui Normal University, Wuhu, Anhui, 241000, People's Republic of China. [Email]
(11)College of Life Science, Anhui Normal University, Wuhu, Anhui, 241000, People's Republic of China. [Email]

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.