The complete mitogenome, phylogenetic placement and cox1 variation of Cape sea urchins (Parechinus angulosus) in southern Africa

Abstract

Background The Cape sea urchin, Parechinus angulosus , is a widely distributed keystone species that inhabits intertidal and subtidal ecosystems along the South African coastline. Despite its importance as an ecosystem engineer, its phylogenetic placement and mitochondrial genomic (hereafter mitogenome) variation remain poorly understood. In the current study, we present the first complete mitogenome for this species, assembled from long-read sequences generated on the Oxford Nanopore sequencing platform, and investigate its phylogenetic placement among other sea urchin species using a combination of Bayesian Inference and Maximum-Likelihood methods. Methods and results A circular genome of 15 722 bp, with an average coverage of 159, comprising 13 protein-coding genes, two rRNAs and 22 tRNAs, was assembled de novo . Phylogenetic reconstructions based on 13 protein-coding genes recovered Paracentrotus lividus as the sister taxon of P. angulosus , and these two species formed a monophyletic clade with Loxechinus albus and Sterechinus neumayeri within Camaradont sea urchins. Using the mitogenome assembly as a template, an additional set of 29 cox1 sequences was mined from publicly available genomic sequences. These revealed that Cape sea urchins maintain substantial mitogenomic variation across their distribution range, expressed predominantly as low-frequency haplotypes. Conclusion This study demonstrates that the Cape sea urchin is genetically distinct within the order Camarodonta and exhibits considerable variation in the cox1 gene across coastal habitats of southern Africa. Furthermore, the identification of a large number of low-frequency haplotypes may indicate population expansion or ongoing purifying selection.

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