Abstract
BackgroundAlthough more than one thousand complete mitochondrial DNA (mtDNA) sequences have been determined in teleostean fishes, only a few gene rearrangements have been observed, and genome-scale rearrangements are even rarer. However, flatfishes (Pleuronectiformes) have been identified as having diverse types of mitochondrial gene rearrangements. It has been reported that tongue soles and the blue flounder mitogenomes exhibit different types of large-scale gene rearrangements.ResultsIn the present study, the complete mitochondrial genome of another flatfish, Samariscus latus, was sequenced, and genome-scale rearrangements were observed. The genomic features of this flounder are different from those of any other studied vertebrates, including flatfish species too. The mitogenome of S. latus is characterized by the duplication and translocation of the control region (CR). The genes located between the two CRs are divided into two clusters in which their relative orders are maintained.ConclusionsWe propose a “Double Replications and Random Loss” model to explain the rearrangement events in S. latus mitogenome. This model consists of the following steps. First, the CR was duplicated and translocated. Subsequently, double replications of the mitogenome were successively initiated from the two CRs, leading to the duplication of the genes between the two CRs. Finally, one of each pair of duplicated genes was lost in a random event.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-352) contains supplementary material, which is available to authorized users.
Highlights
More than one thousand complete mitochondrial DNA sequences have been determined in teleostean fishes, only a few gene rearrangements have been observed, and genome-scale rearrangements are even rarer
Most of the genes are encoded on the H-strand, except for ND6 and ten of the transfer RNAs (tRNAs) genes (Table 1, Figure 1)
The typical gene order of vertebrate mitogenomes and that of S. latus mitogenome are shown in Figure 1A and F, respectively
Summary
More than one thousand complete mitochondrial DNA (mtDNA) sequences have been determined in teleostean fishes, only a few gene rearrangements have been observed, and genome-scale rearrangements are even rarer. The vertebrate mitochondrial genome typically codes for 37 genes, including 13 protein-coding genes, 22 transfer RNAs (tRNAs) and two ribosomal RNAs (rRNAs). (2) Another commonly accepted hypothesis is the Tandem Duplication and Random Loss (TDRL) model, which posits that rearrangements of the mitochondrial gene order have occurred via tandem duplications of some genes, followed by the random deletion of some of the duplications [18,19]. This model is widely used to explain gene rearrangements in vertebrate mtDNA [4,11,20,21]. This model is widely used to explain gene rearrangements in vertebrate mtDNA [4,11,20,21]. (3) The other two models are seldom used; one is the Tandem Duplication and Non-Random Loss (TDNL)
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