The complete mitochondrial genome of Harpovoluta charcoti (Gastropoda: Neogastropoda: Volutidae)

Abstract

We report the complete mitochondrial genome sequence of Harpovoluta charcoti, a circum-Antarctic species of volutid gastropod inhabiting bathyal soft bottom substrates. The mitogenome is 15,487 bp in length, has a base composition of A (28.3%), T (37.3%), C (16.0%) and G (18.4%), and contains 13 protein-coding genes, two ribosomal RNA genes, and 22 transfer RNA genes. Gene order and strand orientation are the same as in other non-toxoglossan neogastropods. Phylogenetic analyses support the monophyly of Volutidae, but not of the subfamilies Amoriinae or Cymbiinae as currently circumscribed.

Keywords:

• Mitochondrial genome
• Neogastropoda
• Volutidae
• Antarctica

The neogastropod family Volutidae is part of a rapid Late Cretaceous radiation of predatory marine gastropods. The majority of species inhabit shallow water soft bottom substrates throughout tropical and temperate regions, but several lineages have expanded into polar regions and the deep sea. To date, few representatives of the Volutidae have been included in detailed molecular phylogenetic studies (e.g. Harasewych et al. 1997, 2019; Cunha et al. 2009; Zou et al. 2011). We report the fourth complete mitochondrial genome sequence for Volutidae based on a species from Antarctica, an incremental contribution toward a better understanding of the evolution and biogeography of this family.

Genomic DNA (gDNA) was extracted from a 40 mg sliver of foot muscle taken from a frozen specimen (maintained at −80 °C) of Harpovoluta charcoti (Lamy, 1910) [United States National Museum, USNM 1123691] dredged off Renaud Island, Antarctica (65°37′25″S, 67°47′04″W) in 217 m. DNA was extracted using the Qiagen DNeasy spin-column using the manufacturer’s protocol. A portion of the cytochrome c oxidase I (COXI) gene was PCR-amplied and Sanger-sequenced using the primers and protocols in Harasewych (2019) to serve as the initial reference sequence for assembly of the mitogenome. DNA libraries were constructed and sequenced on an Illumina MiSeq (Illumina, San Diego, CA, USA) with MiSeq Reagent Kit v3 at the Smithsonian National Museum of Natural History’s Laboratories of Analytical Biology following previously published protocols (Harasewych et al. 2019), producing 3,183,332 reads (length 30–301 bp; mean length 277.9 bp).

The mitogenome was assembled using the ‘map to reference’ feature of Geneious Prime^® 2020.0.5 (http://www.geneious.com) with the barcode region of the COXI gene determined by Sanger Sequencing as the initial reference sequence. A total of 6111 reads mapped to the mitochondrial genome. Coverage ranged from 7× to 853× per site (108.3 ± 35.7). Mitochondrial elements were annotated using MITOS2 (Donath et al. 2019), ARWEN 1.2 (Laslett & Canbäck 2008) and the ORF finder in Geneious Prime^®.

The mitochondrial genome of Harpovoluta charcoti reconstructed from these data (GenBank Acc. no. MT232845) is a double-stranded circular molecule 15,487 bp in length and is within the range reported for other Volutidae (Neptuneopsis gilchristi, 15,312 bp, Harasewych et al. 2019; Melo melo 15,721 bp, Zhong et al. 2019). It is composed of 28.3% A, 37.3% T, 16.0% C and 18.4% G and contains the usual 13 protein-coding genes, 2 ribosomal genes and 22 tRNA genes. Of these, all but 8 tRNA genes are coded on the heavy (+) strand. The tRNA cluster MYCWQGE and tRNA-T are coded on the light strand. Protein-coding genes span 11,134 bp (71.9%), rRNA genes 2223 bp (11.4%), tRNA genes 1499 bp (9.7%) of the mitogenome. Twenty-four intergenic regions 650 bp in total (4.2% of the mitogenome), range in size from 1 to 272 bp, the largest, between tRNA-F and COX3, presumably includes the origin of replication. Ten overlapping regions (18 bp in total) are interspersed throughout the genome. The gene order corresponds to the consensus gene order shared by most caenogastropod (Osca et al. 2015:122) and neogastropod (Cunha et al. 2009; Figure 1) mitogenomes.

Figure 1. Relationships of Harpovoluta charcoti to other members of the Neogastropoda. Nucleotide sequences of all protein-coding genes and ribosomal genes were individually aligned using MAFFT v. 7 (Katoh et al. 2019), ambiguous positions removed using GBlocks v.0.91b (Castresana 2000), then concatenated, leading to alignments with 10,806 nucleotide positions for protein-coding genes and 1838 positions for the rRNA genes. Phylogenetic analyses were run using a partitioned matrix, each with the bestfit model [selected by ModelFinder (Kalyaanamoorthy et al. 2017), option -m TESTONLYMERGE and Bayesian Information Criterion (BIC)]. Maximum likelihood analyses (1000 independent tree searches and ultrafast-bootstrap runs) were performed using IQ-TREE (Nguyen et al. 2015) with the general time reversible (GTR) model of nucleotide evolution. Bayesian inference using MrBayes v3.1.2 (Ronquist and Huelsenbeck 2003) with four MCMC chains for two million generations, sampling every 1000 and discarding the first 25% as burn-in. Branch support shown as maximum-likelihood bootstrap values (when ≥50)/Bayesian posterior probability (when ≥0.8).

Phylogenetic analyses produced trees that are consistent with previous studies (Harasewych et al. 2019). The eight species of Volutidae included in this study, four based on complete and four on partial (each ≥7689 bp) mitogenomes, emerged as a monophyletic clade with high support in both maximum likelihood and Bayesian analyses. However, the relationships among these taxa contradict the monophyly of the subfamilies Amoriinae or Cymbiinae as currently defined (WoRMS 2020).

Acknowledgments

The authors are grateful to Dr K.M. Halanych for depositing this specimen, as well as others collected during the United States Antarctic Research Program Cruise in the collections of the Smithsonian Institution. The authors thank Kathrine Murphy of the National Museum of Natural History’ s Laboratories of Analytical Biology for assistance with Illumina sequencing.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Data availability

The data that support the findings of this study are openly available in GenBank at https://www.ncbi.nlm.nih.gov/nucleotide/, GenBank Acc. No. MT232845.