A foundation for comparative genomics and evolutionary studies in Nucella lapillus based on complete mitogenome assembly

Abstract

The Atlantic dog whelk, Nucella lapillus, is a marine snail that exhibits divergent evolution in response to habitat adaptation, resulting in distinct populations at the phenotypic, genotypic, and karyotypic levels. In this study, we utilized short- and long-read NGS data to perform a de novo assembly of the entire mitochondrial genome of N. lapillus and developed a multiplex PCR protocol to sequence most of its length using ONT sequencing. Our analysis revealed a typical circular configuration of 16,474 bp in length with 13 protein-coding genes, 22 different tRNA genes, 2 of them showing two copies, 2 rRNA genes, and a control region. Long-read sequencing enabled us to identify a 1826 bp perfect inverted repeat within the control region. Comparative analysis of the mitogenomes of related species in the Muricidae family revealed a conserved gene configuration for N. lapillus. We found a low genetic diversity, as well as a moderate genetic differentiation among the studied populations. Interestingly, there was no observed differentiation between the two chromosomal races, suggesting either introgression and permanent incorporation of the mitochondrial DNA haplotype from one of the chromosomal races into the other or a slower evolutionary rate of the mtDNAs with respect to that of the karyotypes. Our study serves as a foundation for comparative genomics and evolutionary investigations in this species.