Characterization of complete mitochondrial genome of coonstriped shrimp Pandalus hypsinotus (Decapoda: Pandalidae)

Abstract

The complete mitochondrial genome of the coonstriped, Pandalus hypsinotus was determined by the MiSeq sequencing platform. The mitogenome of P. hypsinotus (15,909 bp) encoded the 13 protein-coding genes, 22 tRNA genes, two rRNA genes, non-coding, control region (D-Loop). Phylogenetic analysis based on the full mitochondrial genome sequences showed that P. hypsinotus is most closely related to P. borealis (86%) clustering together with Chlorotocus crassicornis in Pandalidae. The complete mitogenome sequence of P. hypsinotus would contribute to the scientific management for conservation of its resources in East/Japan Sea.

Keywords:

• Next-generation sequencing
• decapoda
• mitogenome
• Dokdo
• Pandalidae

Pandalus hypsinotus, commonly called coonstriped shrimp, is among the most valuable Pandalid shrimp in Korea for its sweet taste and large size. P. hypsinotus is widely distributed from Alaska and Bering Sea to northern East/Japan Sea (Holthuis 1980; Komai 1999). In Korea, commercial-sized P. hypsiontus (29–30 mm in carapace length) is caught at the bottom of the deep sea (200 m–300 m) around Ulleungdo and Dokdo islands. Due to the low amount of its catch and patch spatial distribution, the population study of P. hypsiontus resource has been difficult.

In this study, full mitochondrial genome sequence of P. hypsinotus was determined by next-generation sequencing (NGS) platform. Specimen was collected near from Ulleungdo Island (37° 21′ 22N, 131° 27′ 06 E) and stored at Pukyong National University, Korea. Species identification of the specimen was confirmed by both its morphological characteristics and DNA sequence identity in COI region (GenBank Accession number: EU600101). Mitochondrial DNA isolation kit (Abcam, UK) was used for extracting the mitochondrial DNA (mtDNA) and purified mtDNA was fragmented into smaller sizes (∼350 bp) by Covaris M220 Focused-Ultrasonicator (Covaris Inc., USA). A library for MiSeq sequencing was constructed by TruSeq® RNA library preparation kit V2 (Illumina, USA) and its quality and the quantity was analysed by 2100 Bioanalyzer (Agilent Technologies, USA). DNA sequencing was conducted by Illumina MiSeq sequencer (2 × 300 bp pair ends).

The complete mitochondrial genome of P. hypsinotus was 15,909 bp in length (GenBank accession No. MH920259), which was similar to Pandalus borealis (15,905 bp) (Viker et al. 2006). The mitochondrial genome contains 13 protein-coding genes, 22 tRNA genes, and two rRNA (12S and 16S) as well as a non-coding control region (D-Loop). Five proteins initiated with ATG (COX2, ATP6, COX3, ND6 and Cytb), while unusual start codons including ATT (ND2, ND4, ND4L), AGA (COX1), ATA (ND3 and ND5), and TTG (ND1) were also identified. Ten protein-coding genes contained complete stop codons and incomplete ‘T’ was identified in COX2, ATP8 and Cytb. According to the prediction by ARWEN (Laslett and Canbäck 2008), all 21 tRNA genes (63 bp to 73 bp) were able to be folded into the typical clover secondary structures except for tRNA-Ser^(TCT). The gene arrangement of P. hypsinotus was same to those from other decapods such as Charybdis bimaculata (Kim et al. 2018) and Penaeus acehensis (Sektiana et al. 2018). The putative control region (1041 bp) was located between 12S rRNA and tRNA-Ile gene. The 12S rRNA (801 bp) and 16S rRNA (1316 bp) were located between tRNA-Leu^(TAG) and control region and tRNA-Val, respectively. The phylogenetic analysis of P. hypsinotus by MEGA7 (Kumar et al. 2016) with minimum evolutionary (ME) algorithm was the most closely related to P. borealis (86%) clustering with Chlorotocus crassicornis (77%) as Family Pandalidae (Figure 1). This mitogenome P. hypsinotus would be the useful information for the further studies of Pandalid shrimp resources.

Figure 1. Phylogenetic tree of Pandalus hypsinotus within Suborder Pleocyemata. Phylogenetic tree of P. hypsinotus complete genome was constructed by MEGA7 software with Minimum Evolution (ME) algorithm with 1000 bootstrap replications. GenBank Accession numbers were shown followed by each scientific name. The sequence data for phylogenetic analyses used in this study were as follows: P. hypsinotus (MH920259), P. borealis (LC341266), Chlorotocus crassicornis (NC035828), Alpheus japonicus (NC038116), Macrobrachium rosenbergii (NC006880), Macrobrachium nipponense (NC015073), Nautilocaris sainlauentae (NC021971), Alvinocaris chelys (NC018778), Caridina indistinca (MH189850), Halocaridinides fowleri (NC035412), Laurentaeglyphea neocaledonic (NC035679), Enoplometopus occidentalis (NC020027), and Neoglyphea inopinata (KT984197).

Disclosure statement

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

Additional information

Funding

This work was supported by Dokdo Fisheries Research Center, National Institute of Fisheries Science (R2018027).