The mitochondrial genome of common whelk Buccinum undatum (Neogastropoda: Buccinidae)

Abstract

The complete mitogenome of Buccinum undatum obtained from transcriptome analysis is presented here. The mitogenome is 15,265 bp in length and comprises 13 protein-coding genes, 2 ribosomal subunit genes, and 22 transfer RNAs. The complete genome was used to perform a phylogenetic analysis together with other Buccinoidea representatives with mitogenome data from GenBank.

Keywords:

• mtDNA
• genome
• transcriptome
• phylogeny
• marine snail

The common whelk (Buccinum undatum Linnaeus, 1758, (Gastropoda: Buccinidae)) is a common gastropod found in the subtidal zone mainly from 15 m down to 200 m in the North Atlantic and has been harvested for commercial fisheries. In this study, we determined the complete mitogenome sequence of B. undatum, contributing to further studies in population biology, species identification, evolutionary and phylogenetic analysis (e.g. Pálsson et al. 2014; Magnúsdóttir et al. 2018).

A single specimen of B. undatum was collected from the Bay of Breidafjördur, West Iceland (65.50°N, 23.14°W) on 25^th June 2015 and stored in liquid nitrogen, RNA was extracted from mantle tissue using an Omega Biotek EZNA Mollusc RNA kit (http://omegabiotek.com/store/product/e-z-n-a-mollusc-rna-kit/), as per manufacturer’s instructions. Transcriptome libraries were prepared using the Illumina TruSeq RNA library prep kit v2 and sequenced using an Illumina HiSeq2500 (DeCODE Genetics, Iceland). Sequenced transcripts were quality trimmed to an average of 132,735,808 reads, using BBDuk (http://jgi.doe.gov/data-and-tools/bb-tools).

The complete mitochondrial genome of B. undatum was assembled based on mapping of the transcripts to the mitochondrion genome of Buccinum pemphigum Dall, 1907 (Xu et al. 2016) using BBMap (Bushnell 2014). The coverage of sequences per nucleotide ranged from 60 to 434,056, with an average of 51,528. The genome was found to be circular and 15,265 bp in length with relative frequencies of A, G, C and T to be 0.295, 0.156, 0.163, 0.386, respectively. Protein-coding genes, rRNA, and tRNA genes were annotated by MITOS (Bernt et al. 2013), see Appendix 1. Gene content and order is identical to B. pemphigum (Xu et al. 2016), and is composed of 13 protein-coding genes, two rRNA genes, and 22 tRNA genes. The potential origin of replication was located in a 50-bp noncoding region between COX3 and tRNA-Ile.

The complete mitogenome sequence of B. undatum has been deposited to GenBank database with the accession number MK035573.

The sequence was aligned with complete mitogenome sequences of nine species from two families of true whelks (Buccinidae) and dog whelks (Nassariidae) of the superfamily Buccinoidea as well as Rapana venosa (Gastropoda: Muricidae), using Muscle version 3.8.31 (Edgar 2004). A phylogenetic tree of the whole genome was reconstructed based on maximum-likelihood analyses applying phyml (Guindon et al. 2010) in seaview (Gouy et al. 2010), with R. venosa KM213962.1 as an outgroup. The tree was redrawn using the R-package ape (Paradis et al. 2004). The tree was well resolved with highly supported nodes (Figure 1).

Figure 1. Phylogeny of Buccinum undatum based on the complete mitochondrion. The tree is reconstructed using maximum likelihood. The tree was rooted with Rapana venosa KM213962, (not shown). Numbers at nodes present support with the aLRT values obtained with the GTR model in seaview (Gouy et al. 2010).

Disclosure statement

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

Additional information

Funding

This work is supported by the Icelandic Research Council, under grant number 141302051.

Appendix

Appendix 1. Visual representation of the complete mitochondrial genome of the common whelk Buccinum undatum (Gastropoda: Buccinidae), obtained with MITOS (Bernt et al.2013)