Complete mitochondrial genome of the Loligo japonica

Abstract

In this study, we determined the complete mitochondrial genome of Loligo japonica. The genome was 17,232 bp in length and contained 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and 3 main non-coding regions. The overall base composition of L. japonica is A 39.60%, C 18.22%, T33.38% and G 8.80%, with a highly A + T bias of 72.98%. All of the three control regions (CR) contain termination-associated sequences and conserved sequence blocks. Here, we describe a phylogenetic analysis of 11 species Cephalopoda based on the complete mitochondrial genome, and the result showed that the Loligo Beka and Loligo uyii are most closely related to L. japonica. This mitogenome sequence data would play an important role in the investigation of phylogenetic relationship, taxonomic resolution and phylogeography of the Cephalopoda.

Loligo japonica, which belongs to Loliginidae, Teuthoidea, Coleoidea (Cephalopoda) and Animalia (Mollusca) (Dong 1988), is one of the most economically marine cephalopod. It mainly distributes in the Sea of Japan and China Sea (Dong 1988). In order to provide useful information for the future research of genetic diversity and phylogenetics, we determined the complete mitochondrial genome of L. japonica (GenBank accession number KU568467).

L. japonica were obtained from the otter trawl from Hakodate (41°47′N, 140°44′E). Initially, the squid were identified based on both the morphologic features and the COI mitochondrial gene. Tissue samples for molecular analysis were reserved in 95% ethanol. Whole genomic DNA was extracted from muscle tissue of individual specimens using the phenol–chloroform method. The DNA of the sample is stored in the lab of National Engineering Research Center of Marine Facilities Aquaculture, College of Marine Science, Zhejiang Ocean University, Zhoushan, Zhejiang Province, China; polymerase chain reaction (PCR) was performed. The PCR products were sequenced by Sangon Biotech (Shanghai, China).

Sequences were assembled using Geneious 4.5.3 (http://www.geneious.com). BioEdit 7.0 (Hall 1999) was used for sequence alignment. The neighbour joining (NJ) methods were used to construct the phylogenetic tree. The NJ trees were obtained with 10,000 bootstrap replications using MEGA5.0 (Kimura, 1980).

The complete mitochondrial genome of L. japonica is 17,232 bp in length and consists of 13 protein-coding genes, 22 transfer RNA genes (tRNA), 2 ribosomal RNA genes (rRNA) and 3 control regions (CR). The mitogenome base composition was A 39.60%, C 18.22%, T33.38% and G 8.80%, and A + T content (72.98%) was much higher than the G + C content, in common with other invertebrate mitogenomes.

Thirteen protein-coding genes can be classified into two categories: CYTB, COI, ND5 and ND4L were encoded by the light strand, and the rests including COIII, ND3, ND2, ND4, ND4L, COII, ATP8 and ATP6 were encoded by the heavy strand. Seven protein-coding genes (COIII, ND3, ND2, COI, COII, ATP8 and ATP6) start with an ATG initiation codon, ND4 and ND6 start with an TTA initiation codon, and CYTB and ND1 share CTA as the initiation codon, while ND5 uses CTA as the initiation codon, and ND4L uses CTA as the initiation codon. Six protein-coding genes (COIII, ND2, COI, COII, and ATP6) use TAA as the termination codon; five protein-coding genes (CYTB, ND6, ND1, ND5 and ND4L) use CAT as the termination codon, while ND4 uses CTA as the termination codon; ATP8 uses TAG as the termination codon. There are two ribosomal RNA genes: 16SrRNA (1437 bp) is located between tRNA^Ile and tRNA^Val genes, and 12SrRNA (987 bp) is located between tRNA^Val and tRNA^Trp genes. The complete mitochondrial genome of L. japonica has three non-coding regions, and they were 508 bp, 510 bp and 513 bp, respectively, in length and contain termination-associated sequences and conserved sequence blocks: one was located between tRNA^Gln and tRNA^Ile, one was located between tRNA^Trp and tRNA^Lys, and the other one was located between tRNA^Gly and tRNA^Ala.

In this study, Loligo beka is most closely related to L. japonica, and Octopus ocellatus was placed at the most basal position forming an individual clade, while other species formed a large cluster (Figure 1). L. japonica is one of the economically marine cephalopod. We expect that the present result will facilitate the further investigations of phylogenetic relationship, taxonomic resolution and phylogeography of the cephalopod.

Figure 1.

Molecular phylogenetic tree based on the complete mitochondrial genome sequences. GenBank accession numbers: Loligo beka: KT254309, L. japonica: KU568467, Loliolus uyii: NC026724, Loligo duvaucelii: KR051264, Loligo edulis: AB675081, Sepioteuthis lessoniana: AB240154, Loligo bleekeri: NC002507, Loligo opalescence: KP336703, Illex argentines: KP336702, Sepia aculeata: KF690633 and Octopus ocellatus: NC007896.

Disclosure statement

The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.