Abstract
Complete mitochondrial (mt) genome sequences with duplicate control regions (CRs) have been detected in various animal species. In Testudines, duplicate mtCRs have been reported in the mtDNA of the Asian big-headed turtle, Platysternon megacephalum, which has three living subspecies. However, the evolutionary pattern of these CRs remains unclear. In this study, we report the completed sequences of duplicate CRs from 20 individuals belonging to three subspecies of this turtle and discuss the micro-evolutionary analysis of the evolution of duplicate CRs. Genetic distances calculated with MEGA 4.1 using the complete duplicate CR sequences revealed that within turtle subspecies, genetic distances between orthologous copies from different individuals were 0.63% for CR1 and 1.2% for CR2app:addword:respectively, and the average distance between paralogous copies of CR1 and CR2 was 4.8%. Phylogenetic relationships were reconstructed from the CR sequences, excluding the variable number of tandem repeats (VNTRs) at the 3′ end using three methods: neighbor-joining, maximum likelihood algorithm, and Bayesian inference. These data show that any two CRs within individuals were more genetically distant from orthologous genes in different individuals within the same subspecies. This suggests independent evolution of the two mtCRs within each P. megacephalum subspecies. Reconstruction of separate phylogenetic trees using different CR components (TAS, CD, CSB, and VNTRs) suggested the role of recombination in the evolution of duplicate CRs. Consequently, recombination events were detected using RDP software with break points at ≈290 bp and ≈1,080 bp. Based on these results, we hypothesize that duplicate CRs in P. megacephalum originated from heterological ancestral recombination of mtDNA. Subsequent recombination could have resulted in homogenization during independent evolutionary events, thus maintaining the functions of duplicate CRs in the mtDNA of P. megacephalum.
Highlights
Gene content, genomic architecture and gene strand asymmetry have all been reported to be stable in the mitochondrial genomes of deuterostomes, the vertebrates, according to the genome stabilization theory [1]
Because control regions are large noncoding regions (LNR) that may participate in mitochondrial genome replication and regulation of transcription, genetic variances such as duplication or degeneration occurring within CRs have significant evolutionary value in the mitochondria [3]
Despite the increasing reports of concerted evolution of CRs, contradictory data have been reported in the mt genome of the Amazona parrot, albatross, and three related sea birds belonging to the family Sulidae [15,16,17]
Summary
Genomic architecture and gene strand asymmetry have all been reported to be stable in the mitochondrial (mt) genomes of deuterostomes, the vertebrates, according to the genome stabilization theory [1]. Eberhard documented the concerted evolution of CR within Amazona parrots and reported that both paralogous copies of duplicate CRs in an individual were more closely related to each other than orthologous copies of same CR in different individuals [15]. Contrasting evolutionary patterns have been reported in the albatross, Thalassarche albatrosses, where one part of CRs evolved independently while the other showed concerted evolution [16]. The 51 bp at the 59 end of the sea birds’ CRs exhibited independent evolutionary signals but the duplicate CRs evolved concertedly as a whole. These conflicting evolutionary patterns of CR duplication warrant further investigation to clarify the phylogenetic relationships by investigating multiple recombination sites [16,17]. We discuss the possible mechanisms by which the duplicate CRs may have originated and evolved in P. megacephalum mtDNA
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