Abstract
We determined the complete mitochondrial genome sequence of Squalidus chankanensis tsuchigae (Cypriniformes: Cyprinidae). It is 16,603 bp long, with 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNA genes, and 1 control region, which is 927 bp long, located between tRNApro and tRNAphe. The overall base composition is as follows: 29.98% A, 16.86% G, 25.44% T, and 27.72% C, with a slight AT bias. These results provide necessary data for phylogenetic studies on Squalidus species.
Keywords: Mitochondrial genome, phylogenetic analysis, Squalidus chankanensis tsuchigae
Squalidus (Cypriniformes: Cyprinidae) genus consists of 18 species (Froese and Pauly 2017), widely distributed in East Asia. Of those, Squalidus chankaensis tsuchigae, Squalidus multimaculatus, Squalidus japonicus coreanus, and Squalidus gracilis majimae are distributed in South Korea as endemic species (Kim and Park 2007). As ecological and genetic information about S. chankaensis tsuchigae is limited (Kim 1997), we determined its mitochondrial genome sequence to analyze phylogenetic relationship within the genus.
S. chankaensis tsuchigae was collected from the Nakdonggang River near Gyeongcheonseom Island (36°44.606′N, 128°26.113′E). The voucher specimen (NNIBR-MPL2017GSC0007) has been preserved at the Molecular Phylogenetics Laboratory collection in Nakdonggang National Institute of Biological Resources, Sangju-si, Korea. The mtDNA sequence was extracted from the whole-genome sequencing data (unpublished data) using the Illumina HiSeq4000 platform by GnCBio (Daejeon, Korea). Totally, 42 Gb raw reads were obtained and assembled using Platanus assembler version 1.2.4 (http://platanus.bio.titech.ac.jp/). A total of 231,108 reads were extracted to reconstruct the mitochondrial genome using Deconseq version 0.4.3 (http://deconseq.sourceforge.net/) and annotated using gsMapper version 2.8 (Roche Inc) with fishMito DB as the reference.
The complete mitochondrial genome of S. chankaensis tsuchigae (GeneBank accession no. MK840863) is 16,603 bp long, with 13 protein-coding genes, 22 transfer RNAs (tRNAs), 2 ribosomal RNA, and 1 control region, which is 927 bp long, located between the tRNApro and tRNAphe. The start codon of the 12 protein-coding genes is ATG and that of COXI is GTG. Four genes (ND1, COX1, ND4L, and ND5) end in the TAA codon. Three genes (ND4, ND1, and ND2) contain TAG as the stop codon, whereas seven genes (ND2, COX2, COX3, ATPase6, ND3, ND4, and Cytb) share the incomplete stop codon T or TA. The tRNA sequence is 67–75 bp and has a three-leafed clover structure, except tRNA-SerUCG. Two rRNAs are 12S rRNA (958 bp) and 16S rRNA (1688 bp). The overall base composition is as follows: 29.98% A, 16.86% G, 25.44% T, and 27.72% C, with a slight AT bias (55.41%).
To examine the phylogenetic position of S. chankaensis tsuchigae, the mitochondrial genome sequence of five Squalidus species was downloaded from the GeneBank. The phylogenic tree was constructed using the neighbor-joining (NJ) method with the sequence of the 13 protein-coding genes. A close relationship was observed between S. gracilis and S. chankaensis tsuchigae (KT948082.1 and in this study) (Figure 1). Reports on ecology, phylogeny, and genetic studies on S. chankaensis tsuchigae in English are limited; thus, further studies are necessary to establish more information. Our results will help elucidate the phylogenetic relationship among Squalidus species.
Figure 1.
Phylogenetic relationships among five Squalidus species based on the 13 coding gene sequence of complete mitochondrial genome sequences in the GenBank were inferred using the neighbor-joining (NJ) method. The numbers at the nodes are bootstrap values computed using 10,000 replications and Kimura’s 2-parameter distance model. The scale bar indicates 0.02 substitutions per nucleotide position.
Funding Statement
This work was supported by a grant [NNIBR201901110] from the Nakdonggang National Institute of Biological Resources (NNIBR) funded by the Ministry of Environment (MOE), Republic of Korea.
Disclosure statement
No potential conflict of interest was reported by the authors.
References
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