Genetic diversity of Anadara tuberculosa in two localities of the Colombian Pacific Coast

Abstract

Piangua, Anadara tuberculosa, is an economically important mollusk for the human population living on the Colombian Pacific Coast. In the last years, the demand and exploitation of this mollusk have increased, putting it at risk to the point of being endangered. This research aimed to identify the genetic diversity and population structure of piangua in two localities on the Pacific Coast of Colombia. We assembled a chromosome-level genome using PacBio-Hifi and Arima sequencing. We obtained 274 scaffolds with an N50 of 45.42 Mbp, a total size of 953 Mbp, and a completeness of 91% based on BUSCO scores. The transposable elements accounted for 30.29% of the genome, and 24,317 genes were annotated. Genome-guided variant calling for 89 samples using DArT sequencing data delivered 4,825 bi-allelic SNPs, which supported genetic diversity and population structure analyses. Data showed that the piangua populations in the two localities were under expansion events more than 100k years ago. However, results also showed a reduction in genetic diversity, as evidenced by the loss of heterozygosity, which may be caused by high levels of inbreeding, probably due to a recent overexploitation. Furthermore, although we evidenced gene flow between the two localities, there is also a subtle geographical population structure between the two localities and among mangroves in one of the localities. This is the first study in Colombia that provides relevant genetic information on piangua to lay the foundations for conservation strategies.