Unusual mitochondrial genome structure of the freshwater gobyOdontobutis platycephala: rearrangement of tRNAs and an additional non‐coding region

Abstract

Mitochondrial DNA was isolated from the Korean freshwater gobioid fish Odontobutis platycephala by long-polymerase chain reaction with conserved primers and this mtDNA was sequenced by primer walking using flanking sequences as sequencing primers. The resultant O. platycephala mtDNA sequence was found to be 17 588 bp in size with a mostly conserved structural organization when compared with that of other teleost fish. Rearrangements of tRNAs (tRNA-Ser, tRNA-Leu, tRNA-His) and an additional non-coding region (533 bp) were present between the ND4 and ND5 genes. In the present paper, the basic characteristics of the O. platycephala mitochondrial genome is reported, including its structural organization, base composition of rRNAs, tRNAs and protein-encoding genes, characteristics of mitochondrial tRNAs and the peculiar rearrangement features of some parts of the mtDNA. Phylogenetic analysis performed using the cytochrome b gene sequences of 16 Korean freshwater fishes (15 gobioids) with the Bayesian algorithm showed that O. platycephala forms a clade (1Á00 of posterior probability) with other species of Odontobutis. This suggests that the observed rearrangement between the ND4 and ND5 genes in the O. platycephala mitogenome reflects independent events.

Phylogeographical Analysis of a Cold-Temperate Freshwater Fish, the Amur Sleeper (Perccottus glenii) in the Amur and Liaohe River Basins of Northeast Asia

“…Phylogenetic relationships among haplotypes were reconstructed using the Bayesian method, implemented in MrBayes 3.2.1 (Ronquist et al, 2012). Three species of the genus Odontobutis (O. obscura, O. potamophila, and O. platycephala) were selected as outgroup taxa, and their sequences were obtained from previous studies (Akihito et al, 2000;Thacker and Hardman, 2005;Ki et al, 2008) with GenBank accession number AB021243, AY722247, and DQ010651. Three partitions according to the codon frame were selected as the best partitioning scheme under the Bayesian Information Criterion (BIC) using heuristic search algorithms by PartitionFinder (Lanfear et al, 2012).…”

An unusual mitochondrial genome structure of the tonguefish, Cynoglossus trigrammus: Control region translocation and a long additional non-coding region inversion

“…As we did not find a similar sequence using NCBI Blast, the function of these repeat sequences in the NR of the C. trigrammus mt genome is unknown. An inversion of an additional non-coding region (N 300 bp) has been found in various fish taxa, such as Odontobutis sinensis (Ma et al, 2013), O. platycephala (Ki et al, 2008), and Samariscus latus (Shi et al, 2014). Ki et al (2008) reported an additional non-coding region (533 bp) between the ND4 and ND5 genes in the O. platycephala mt genome and thought that an unknown mechanism resulted in the incorporation of the non-coding region compared with already characterized mechanisms.…”

“…An inversion of an additional non-coding region (N 300 bp) has been found in various fish taxa, such as Odontobutis sinensis (Ma et al, 2013), O. platycephala (Ki et al, 2008), and Samariscus latus (Shi et al, 2014). Ki et al (2008) reported an additional non-coding region (533 bp) between the ND4 and ND5 genes in the O. platycephala mt genome and thought that an unknown mechanism resulted in the incorporation of the non-coding region compared with already characterized mechanisms. Shi et al (2014) proposed a "Double Replications and Random Loss model (DRRL)" to describe the D-loop rearrangement events in the S. latus mt genome.…”

“…We found 10 * 34 bp tandem repeat sequences (5′-TTACATTATGTAATTACTCTATATATGCATGATT-3′) in the D-loop of the C. trigrammus mt genome, which forms a stable secondary structure that may be related to transcription and replication processes (Fig. 3B) (Lunt et al, 1998;Ki et al, 2008). Each repeat sequence contains a conserved TAS motif, TACAT, and the reverse complement cTAS motif ATGTA, which may lead to the formation of stable hairpin loops as a sequence-specific signal for the termination of mtDNA replication (Saccone et al, 1991).…”

“…Furthermore, some structural features, such as gene rearrangements, could exist in some fish, which are typically explained by the recombination model, tandem duplication and random loss model (Dowton et al, 2003). Although more than one thousand complete mtDNA sequences have been reported in teleostean fish (http://www.ncbi.nlm.nih.gov/ genomes/ORGANELLES/taxtree.cgi?db=Mito&taxid=2759&result= frame&complete=All&initrankid=1) and the organization in most fish mtDNA genomes is quite conserved (Manchado et al, 2007), only a few reports have appeared on gene rearrangements in fish mt genomes, such as flatfishes (Inoue et al, 2004;Papetti et al, 2007;Ki et al, 2008;Kong et al, 2009;Shi et al, 2014;Fonseca et al, 2014). These studies revealed that the gene rearrangements and their variations could be very useful to better understand the molecular genetics and evolution of mt genomes and to infer evolutionary relationships (SanMauro et al, 2006;Amer and Kumazawa, 2007).…”