Quantification and evolution of mitochondrial genome rearrangement in Amphibians

BackgroundRearrangement 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.ResultsHere 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 similar to 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.ConclusionIt 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.

Automated summary

This study systematically investigated mitogenome arrangements of 232 amphibians, including newly sequenced Dicroglossidae mitogenomes. The results revealed that around 80% of species belonged to four major arrangement patterns, with the control region and trnL2 being the most frequently rearranged components. The typical neobatrachian arrangement may have appeared in the Late Jurassic according to possible estimation.