Mitogenomic profiling of Marcia recens (Holten, 1802): a step towards taxonomic resolution of India's Ashtamudi short-neck clam

ABSTRACT

The Ashtamudi short-neck clam forms a significant fishery resource holding India’s first Marine Stewardship Council Certification. The taxonomic classification of this particular clam has engendered debate regarding its proper nomenclature. The present study aims to provide its first comprehensive mitogenome profile from the type locality to address the existing taxonomic ambiguity. The mitogenome assembled using the genome skimming method had 17,991 base-pair length with 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs and control region. Phylogenetic analysis based on the concatenated data set of PCGs and rRNAs from 47 representative species of Veneridae grouped all species including short-neck clams from the subfamily Tapetinae into a single clade. This analysis also revealed the polyphyly of the genus Marcia. Nevertheless, the short-neck clam co-clustered with Marcia recens from Chinese waters. Subsequent mitochondrial gene order, genetic distance and morphological analyses substantiated the closer relationship of this clam to the genus Marcia, analogous to the phylogenetic output. The genomic data from the type locality provides additional molecular and phylogenetic evidence for the classification of short-neck clam in the genus Marcia. This will also help to address long-standing taxonomic uncertainties surrounding this species, offering valuable information critical for management and conservation of the resource.

KEYWORDS:

• Genome skimming
• Marine Stewardship Council
• mitochondrial genome
• nomenclature
• phylogeny
• topotype

Acknowledgements

The authors express sincere gratitude to Dr. P. Vijayagopal, Former Head of the Marine Biotechnology Division and Dr. A. Gopalakrishnan, Director, CMFRI for their support and facilities provided for the research. This work is a part of the Ph.D. thesis of S.R and the author acknowledges the Council of Scientific and Industrial Research (CSIR), India for the fellowship received to carry out this research. We extend our sincere thanks to the associate editor for the time and effort invested in our article. We also express our gratitude towards the anonymous expert reviewers for their time and critical assessments.

Authors contributions

S.R conceptualised the experiment, collected and processed the specimens. S.R and J.N.S analysed data, and wrote the paper. W.S and S.K.A curated the data and carried out parts of data analysis. All the authors have reviewed and approved the manuscript.

Data availability statement

All the sequencing reads were submitted to NCBI-GenBank

Disclosure statement

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