The complete mitochondrial genome of Pleonexes koreana (Kim & Kim, 1988) (Crustacea: Amphipoda: Ampithoidae)

Abstract

The complete mitochondrial genome of an ampithoid amphipod, Pleonexes koreana, was sequenced for the first time. The total mitogenome length of P. koreana was 14,645 bp with 13 protein-coding genes, two rRNA genes, and 22 tRNA genes. Reconstruction of a phylogenetic tree confirmed that P. koreana belonged to the families Caprellidae in the same clade and to the suborder Senticaudata within Amphipoda. This is the first recorded complete mitochondrial genome sequence of the genus Pleonexes.

Keywords:

• Pleonexes koreana
• complete mitogenome
• Ampithoidae
• Amphipoda

The genus Pleonexes, established by Spence Bate in 1857, was previously considered to be a junior synonym of the genus Ampithoe. Recently conducted research, however, resurrected Pleonexes as a valid genus of family Ampithoidae (Peart and Ahyong 2016; Horton et al. 2018). Members of this genus have been known from Indian water (P. auriculata), eastern Atlantic Ocean (P. gammaroides and P. helleri), Pacific Islands (P. kaneohe, P. kulafi, P. poipu, P. kava and P. maxillissius), Australian water (P. maganae, P. parakava and P. rotunda), and Korean water (P. koreana). Pleonexes koreana was originally described by Kim and Kim in 1988, as Ampithoe koreana but was recently reassigned as P. koreana (Peart and Ahyong 2016). This amphipod species has only been reported in Korean waters so far. In the present study, we determined the complete mitochondrial genome for a herbivorous amphipod, P. koreana.

The specimen was collected from the southern coast of the East Sea, Gyeong Ju, Korea (35°48′25.7′′N, 129°30′32.6′′E), on July 11th, 2018, among algae in a tidal pool. The voucher specimen was deposited to the National Marine Biodiversity Institute of Korea. Subsequent to mtDNA enrichment procedures, mtDNA extraction, sequencing, assembly, analysis, annotation, and identification of all genes were performed, according to the same protocols and software as that of Lee et al. (2019).

The complete mitogenome of P. koreana was 14,645 bp in length (GenBank accession no. MK265245). It encoded 37 genes, 13 protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs), and 22 transfer RNA genes (tRNAs), with a non-coding region of 634 bp. The overall A–T content of the mitogenome was 73.2% (38.7% A, 16.8% C, 11.0% G, and 33.5% T). There were four types of PCGs start codons, ATT (cox1–2, nad2, and nad5), ATG (atp6, cytb, cox3, nad3–4, nad4L, and nad6), ATC (atp8) and TTG (nad1). TAA (cox3, cytb, atp6, atp8, nad1–2, nad4L, and nad5–6) and TAG (nad3) were used as stop codons. To avoid overlapping between the genes, the nucleotide ‘A’ located at the end of some PCGs (cox1–2, and nad4) was used, as in the study of Lee et al. (2019).

To confirm the phylogenetic position of P. koreana, 12 other species belonging to 10 families in the suborder Senticaudata available in GenBank were used, with a lysianassid species, Eurythenes maldoror, of the suborder Amphilochidea as an outgroup (all the species were registered in the NCBI). A phylogenetic tree was reconstructed based on the concatenated data set of 13 PCGs, using the neighbor-joining (NJ) method, with the Kimura 2-parameter model with MEGA7 software (Kumar et al. 2016). As a result, P. koreana was grouped with the family Caprellidae in the same clade. The tree clearly supports phylogenetic relationships of the suborder Senticaudata within the Amphipoda (Figure 1).

Figure 1. A phylogenetic tree built using a concatenated data set of 13 protein-coding genes by the neighbor-joining (NJ) method, with the Kimura 2-parameter model. Bootstrap values were calculated from 1000 replicates. The tree was reconstructed based on 14 mitogenome sequences, including that of Pleonexes koreana examined in the present study. The herbivorous amphipod, Pleonexes koreana is highlighted in black.

This is the first recorded complete mitochondrial genome sequence of the genus Pleonexes belonging to the family Ampithoidae. It provides useful genetic information not only for evolutionary research on herbivorous amphipods but also for future phylogenetic studies on amphipods.

Disclosure statement

The authors declare no conflict of interest. The authors alone are responsible for the content and writing of the paper.

Additional information

Funding

This study was financially supported by the National Marine Biodiversity Institute Research Program (2018M00100 and 2018E00100).