Seven complete mitochondrial genome sequences of bushtits (Passeriformes, Aegithalidae, Aegithalos): the evolution pattern in duplicated control regions

Abstract

The control region (CR) of the mitochondrial DNA exhibits important functions in replication and transcription, and duplications of the CR have been reported in a wide range of animal groups. In most cases, concerted evolution is expected to explain the high similarity of duplicated CRs. In this paper, we present seven complete mitochondrial genome sequences from the bushtits (genus Aegithalos), in which we discovered two duplicated CRs, and try to survey the evolution pattern of these duplicated CRs. We also found that the duplicated CRs within one individual were almost identical, and variations were concentrated in two sections, one located between a poly-C site and a potential TAS (termination associated sequence) element, the other one located at the 3′ end of the duplicated CRs. The phylogenetic analyses of paralogous CRs showed that the tree topology were depending on whether the two high variable regions at the upstream of TAS element and the 3′end of duplicated CRs: when they were concluded, the orthologous copies were closely related; when they were excluded, the paralogous copies in the same lineages were closely related. This may suggest the role of recombination in the evolution of duplicated CRs. Consequently, the recombination was detected, and the breakpoints were found at ∼120 bp (the upstream of the potential TAS element) and ∼1150 bp of the alignment of duplicated CRs. According to these results, we supposed that homologous recombination occurred between paralogous CRs from different mtDNA molecule was proposed as the most suitable mechanism for concerted evolution of the duplicated CRs, and the recombination took place in every replication cycle, so that most part of the duplicated regions remain identical within an individual, while the 5′ and 3′end of the duplicated CRs were not involved in recombination, and evolved independently.

• Aegithalos
• concert evolution
• duplicated control regions
• mitochondrial genome

Acknowledgements

We are grateful to Zuohua Yin, Chuanyin Dai who have assisted with field specimen collections. We own many thanks to Hongli Zhang and Gang Song for their valuable comments and suggestions.

Declaration of interest

The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the article. This research was supported by grants from Shaanxi Normal University (No. 2013CXB008), National Natural Science Foundation of China (No. 31201711), Strategic Priority Research Program of the Chinese Academy of Sciences (No. XDB13020300), the Major International (Regional) Joint Research Project (No. 31010103901), State Key Program of NSFC (No. 31330073) and the Key Laboratory of the Zoological Systematics and Evolution of the Chinese Academy of Sciences (No. O529YX5105).

Supplementary material available online

Supplementary Appendix A–E