Complete mitochondrial genome of the mudskipperBoleophthalmus pectinirostris(Perciformes, Gobiidae): Repetitive sequences in the control region

Abstract

The mudskipper, Boleophthalmus pectinirostris (Perciformes, Gobiidae), is an amphibious gobioid fish. In this paper, the complete mitochondrial genome of B. pectinirostris was firstly determined. The mitogenome (17,111 bp) comprises 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and 1 putative control region. 130-bp tandem repeat was identified in the control region, which was almost identical among the 10 individuals examined, and three different frequencies of the repeat unit (five, six or seven) were found among these individuals.

Variations existing in protein-coding genes of the complete mitochondrial genomes of two highly morphological similarity fish: Periophthalmus magnuspinnatus and P. modestus (Perciformes, Gobiidae)

“…Periophthalmus magnuspinnatus used TAG, TAA and T, but P. modestus preferred TAA, TA and T. The content A þ T was 55.6% and 55.4% for P. modestus and P. magnuspinnatus, respectively. The phenomenon of A þ T content higher than G þ C content was similar to those of B. pectinirostris (Liu et al 2012) and Odontobutis potamophila (Li & Liu 2016). Analysis showed that ND4 and ND5 had the largest number of mutation loci, indicating that they would be better molecular markers than Cyt b gene in examining intraspecific population genetic diversity such as P. magnuspinnatus and P. modestus.…”

“…The genomic DNA was extracted from pectoral fin using phenol/chloroform procedure (Sambrook & Russell, 2001). Primers were designed according to Boleophthalmus pectinirostris (Liu et al 2012). Then we used DNA baser V.3.5.4 to assemble the whole sequence.…”

“…All transfer RNA genes were reappraised by tRNA Scan-SE version 1.21 (Lowe & Eddy, 1997). To detect tandem repeat as existed in the control region of B. pectinirostris (Liu et al 2012), we examined ten individuals for P. magnuspinnatus and P. modestus, respectively. In order to analyse the phylogenetic relationships, we downloaded 23 mtDNA of relative species.…”

Complete mitochondrial genome and phylogenic analysis of the mudskipper Scartelaos gigas (Perciformes, Gobiidae)

“…We found one termination-associated sequence (TAS) and two conserved sequence block (CSB1 and CSB2) domains in S. gigas, while three conserved sequence block (CSB1, CSB2, and CSB3) domains were found in other fish (Sbisà et al, 1997;Walberg & Clayton, 1981) in the control region, which indicates that the two domains (CSB1 and CSB2) are more conserved than the domain (CSB3) in fishes. We did not find the 131-bp tandem repeat which is found in the Boleophthalmus boddarti (Perciformes, Gobiidae) and Boleophthalmus pectinirostris (Perciformes, Gobiidae) (Liu et al, 2012;Zhang et al, 2014), probably because the control region varies between fishes and this tandem repeat region may be lost due to gene mutation in some fishes.…”

“…This region should be the origin of L-strand replication (OL) in S. gigas, as in most vertebrates (Zardoya et al, 1995). The 22 tRNA genes were identified by the online software tRNAScan-SE 1.21 (Lowe & Eddy, 1997) except the tRNA Ser gene that lacks a dihydrouridine arm, which is common among fishes (Chang et al, 2013a,b;Jin et al, 2013;Liu et al, 2012). The control region was located between tRNA Pro and tRNA Phe genes.…”