The complete mitochondrial genome of loliginid squid (Uroteuthis chinensis) from Minnan–Taiwan bank fishing ground

Abstract

The squid Uroteuthis chinensis is commercially important fishery species in many coastal regions of Asia. In this study, we described the complete mitochondrial genome of U. chinensis. The genome is 17,353 bp in length, encoding the standard set of 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, with circular organization. The overall base composition of the whole mitochondrial genome was A (39.56%), T (31.71%), G (9.05%) and C (19.68%) with an AT bias of 71.27%. The longest protein-coding genes of these species was ND5, whereas the shortest ATP8.

Uroteuthis chinensis (Gray, 1849) is a large-sized Indo-Pacific species extending from the western Pacific to Indian Ocean (Natsukari and Tashiro 1991). It was formerly classified under the genus Loligo (Lamarck, 1798), as Loligo chinensis. Uroteuthis chinensis support a very important commercial fisheries industry in China on the continental shelf off Guangdong, southern Fujian and around the Pescadores Islands in the Taiwan Strait (Voss and Williamson 1971). Uroteuthis chinensis accounts for up to 90% of the loliginid catch in several parts of China and 15–40% of the trawl catch in the Gulf of Thailand. Here, we sequenced and annotate mitogenome of U. chinensis form Minnan–Taiwan bank fishing ground (South China Sea) to provide molecular information for genetically understanding of loliginid squid.

The specimens of U. chinensis were collected from Minnan–Taiwan bank fishing ground (South China Sea) (22°30′N, 118°45′E) in 19th September, 2018. Whole genomic DNA was extracted from muscle tissue of one specimen of U. chinensis using TIANamp Marine Animals DNA Kit (TIANGEN, China). The concentration for use as a PCR template was adjusted to an A₂₆₀ of about 0.05 to 0.2. The collected specimen and extracted DNA were stored in Guangdong Provincial Key Laboratory of Fishery Ecology and Environment (specimen accession number: MT2018-A-22). The complete mitochondrial genomes of U. chinensis was sequenced using PCR primers designed from highly conserved regions of transfer RNA (tRNA) sequences of related species (Jiang et al. 2016) with additional specific primers designed as required from sequences already obtained. Long-PCR amplifications were performed by thermo-cycling using five pairs of primers and PCR amplicons were subjected to build up genomic library and pair-end sequencing by MiSeq. The COI sequence of U. chinensis was used as reference seeds for iterative assembly by MITObim v.1.8 (Hahn et al. 2013). SeqMan v.7.1.0 was used for the mitogenome assembly and annotation (Swindell and Plasterer 1997). Transfer RNA genes were predicted using online software tRNAScan-SE 1.21 (Lowe and Eddy 1997). All protein-coding gene (PCGs) are aligned independently, then concatenated to be applied for phylogenetic reconstruction with other cephalopods in MrBayes v 3.12 (Ronquist and Huelsenbeck 2003) using relaxed clock model.

The U. chinensis mitochondrial genome forms a 17,353 bp closed loop (GenBank accession number MN687903). The overall base composition of the whole mitochondrial genome was A (39.56%), T (31.71%), G (9.05%) and C (19.68%) with an AT bias of 71.27%. This mitochondrial genome represents a typical Uroteuthis mitochondrial genome and matches with the U. duvaucelii genome (Jiang et al. 2016), in which it comprises 13 protein-coding genes, 22 transfer RNA genes and 2 ribosomal RNA genes (12S rRNA and 16S rRNA). The ATG initiation codon are used in all protein-coding genes except ND2, ND6 and ND5 (ATT), and the stop codons of all the 13 protein-coding genes were complete. Ten protein-coding genes (ND3, CYTB, ND6, ND1, ND2, COX1, COX2, ATP8, ATP6, and COX3) use TAA as the termination codon; three protein-coding genes (ND4, ND5, ND4L) use TAG as the termination codon. Meanwhile, the longest protein-coding genes of these species was ND5 (1644 bp), whereas the shortest ATP8 (153 bp). lrRNA and srRNA genes are 1398 bp and 929 bp in length separately. All the 22 typical tRNAs possess a complete clover leaf secondary structure, ranging from 65 bp to 79 bp. The Bayesian inference phylogenetic tree showed that U. chinensis firstly grouped with species of U. edulls (Figure 1). We have the confidence to construct phylogenetic trees, based on the complete the mitochondrial genomes, but the evolution history of marine cephalopod still needs future research to be clearly resolved.

Figure 1.

The Bayesian inference phylogenetic tree for Cephalopoda based on mitochondrial PCGs and rRNAs concatenated dataset. The gene’s accession numbers for tree construction are listed as follows: Loliolus japonica (KU568467), Heterololigo bleekeri (AB029616), Uroteuthis edulis (AB675081), Loliolus uyii (KP265013), Uroteuthis duvaucelii (KR051264), Doryteuthis opalescens (KP336703), Loliolus beka (KT254309), Sepioteuthis lessoniana (KM878671), Illex argentines (KP336702), Dosidicus gigas (EU068697), Spirula spirula (KU893141), Bathyteuthis abyssicola (AP012225), Todarodes pacificus (AB158364), Architeuthis dux (KC701764).

Funding Statement

Support was obtained from Fund of Guangdong Provincial Key Laboratory of Fishery Ecology and Environment [FEEL-2019-9].

Disclosure statement

No potential conflict of interest was reported by the authors.