Complete mitochondrial genome sequence of Acoptolabrus changeonleei Ishikawa et Kim, 1983 (Coleoptera: Carabidae)

Abstract

Acoptolabrus changeonleei Ishikawa et Kim, 1983 (Coleoptera: Carabidae) has been listed as an endangered insect in South Korea. The complete mitochondrial genome (mitogenome) of the species was 16,831-bp long with a typical set of genes (13 protein-coding genes [PCGs], 2 rRNA genes, and 22 tRNA genes) and one non-coding region, with the arrangement identical to that observed in most insect genomes. Twelve PCGs had the typical ATN start codon, whereas ND1 had the atypical TTG codon. The 1,712-bp long A+T-rich region was composed of 88.6% A/T nucleotides and had no long repeat sequences. Phylogenetic analyses with concatenated sequences of the 13 PCGs and the lrRNA gene placed A. changeonleei as a sister to the within-subfamilial species Damaster mirabilissimus in Carabinae, with the highest nodal support by both analyses.

Keywords:

• Mitochondrial genome
• Carabidae
• Acoptolabrus changeonleei
• endangered species
• phylogeny

Acoptolabrus changeonleei Ishikawa et Kim, 1983 (Coleoptera: Carabidae) is an endemic species distributed only in Mt. Jiri, which is located in the southern-mid portion of the Korean Peninsula, and listed as an endangered insect in South Korea (Kim et al. 2013). It occurs once a year from May to September, overwinters as adults, and is found in primeval forests (Kim et al. 2013).

An adult male A. changeonleei was collected from Hamyang-gun, Gyeongsangnam-do Province (35°21′55.92″N, 127°37′24.58″E), South Korea in 2017. This voucher specimen was deposited at the Chonnam National University, Gwangju, Korea, under the accession no. CNU7048. Using DNA extracted from the hind legs, two long overlapping fragments (LFs; COI-CytB and CytB-COI) were amplified using two sets of primers designed from the available mitogenomes of Carabidae in Coleoptera (Song et al. 2010; Wan et al. 2012; Linard et al. 2016; López-López and Vogler 2017). Subsequently, these LFs were used as templates to amplify 30 short fragments. The sequence data have been deposited in GenBank under the accession number MG253028.

Phylogenetic analysis was performed using the concatenated nucleotide sequences of 13 protein-coding genes (PCGs) and the lrRNA gene of 16 mitogenome sequences from Carabidae in Coleoptera, including that of A. changeonleei. Bayesian inference (BI) and maximum-likelihood (ML) methods that were implemented in CIPRES Portal v. 3.1 (Miller et al. 2010) were used for phylogenetic analyses. An optimal partitioning scheme (six partitions) and substitution model (GTR + Gamma + I) were determined using PartitionFinder 2 and the Greedy algorithm (Lanfear et al. 2012, 2014, 2016).

The complete 16,831 bp long mitogenome of A. changeonleei is composed of typical sets of genes (2 rRNAs, 22 tRNAs, 13 PCGs, and 1 A + T-rich region). The arrangement of this genome is identical to the typically observed genomes of other insects (Cameron 2014). The A/T content of the whole mitogenome was 79.4%; however, it varied among the genes as follows: A + T-rich region, 88.6%; srRNA, 81.6%; lrRNA, 81.5%; and PCGs, 77.2%. Twelve PCGs had the typical ATN start codon, whereas ND1 had the atypical TTG codon. Twelve of the 13 PCGs had a complete stop codon (nine TAA and three TAG); however, COII had an incomplete stop codon, T. Unlike other coleopteran A + T-rich regions, which have long repeat regions (Kim et al. 2012; Kim et al. 2014), the 1712 bp long A + T-rich region of A. changeonleei does not harbor any long repeat sequences; however, it does harbor a few poly-T stretches and multiple runs of TA sequences.

Phylogenetic analysis resulted in a sister relationship between A. changeonleei and Damaster mirabilissimus, a species within the subfamily, with the highest nodal support by both BI and ML methods (Bayesian posterior probabilities [BPP] = 1; Bootstrap [BS] = 100; Figure 1). The three subfamilies in Carabidae represented by more than one species formed strong monophyletic groups (BPP = 1; BS = 100; Figure 1). Currently, the complete mitogenome sequences in Carabidae are available limitedly. Considering the taxonomic diversity of this family, more mitogenome sequences are required for further comprehensive phylogenetic inference, which is compatible with those obtained using other molecular markers.

Figure 1. The Bayesian inference (BI) method-based phylogenetic tree constructed for the family Carabidae using the concatenated sequences of 13 protein coding genes (PCGs) and lrRNA. The numbers at each node indicate the bootstrap support using the Maximum Likelihood (ML) method (above nodes) and Bayesian posterior probabilities (BPP; below nodes) using the BI method. The scale bar indicates the number of substitutions per site. Four species belonging to the family Dytiscidae in Coleoptera were used as outgroups. The GenBank accession numbers are as follows: Habrodera capensis, JX412824 (Timmermans et al. 2015); Cicindela anchoralis, MG253029 (Wang et al. 2018); Australicapitona hopei, MF497816 (López-López and Vogler 2017); Pogonostoma subtiligrossum, MF497820 (López-López and Vogler 2017); Omus cazieri, MF497813 (López-López and Vogler 2017); Platychile pallida, MF497814 (López-López and Vogler 2017); Manticora tibialis, MF497821 (López-López and Vogler 2017); Pterostichus sp., KT876909 (Linard et al. 2016); Stomis sp., KT876914 (Linard et al. 2016); Abax parallelepipedus, KT876877 (Linard et al. 2016); Scarites buparius, MF497821 (López-López and Vogler 2017); Promecognathus crassus, JX313665 (Timmermans et al. 2015); Metrius contractus, MF497817 (López-López and Vogler 2017); Damaster mirabilissimus, GQ344500 (Wan et al. 2012); Calosoma sp., GU176340 (Song et al. 2010); Nebria sp., KT876906 (Linard et al. 2016); Acilius sp., KT876878 (Linard et al. 2016); Colymbetes sp., KT876885 (Linard et al. 2016); Liopterus sp., KT876902 (Linard et al. 2016); and Hygrotus sp., KM244659 (Timmermans et al. 2015).

Disclosure statement

No potential conflict of interest was reported by the authors.

Additional information

Funding

This study was supported by a grant from the National Institute of Biological Resources (NIBR), funded by the Ministry of Environment (MOE) of the Republic of Korea [NIBR201703102].