Genome survey and evolutionary analysis of 8 Lamprotula species: SSR profiling, mitochondrial characterization, and population dynamics inference.

Abstract

Freshwater bivalves are vital to aquatic ecosystems but face severe global threats. Understanding their genomic traits and evolution is crucial for effective conservation. This study conducted whole-genome sequencing on 8 Lamprotula species. These 8 species exhibited high genomic complexity, characterized by large genomes (1.89 to 2.65 Gb), high heterozygosity (>0.8), and high repeat content (>60%), estimated by k-mer analysis. Genome assemblies showed that L. caveata had the largest genome, while L. polysticta had the smallest. Furthermore, the assembled genome sizes of these 8 species exhibited an average increase of 22.58% compared to k-mer analysis estimates, largely due to their high heterozygosity. The mitochondrial genomes of these 8 species ranged in size from 15.69 kb to 17.13 kb, with GC contents varying from 36.36% to 40.77%. Phylogenetic analysis indicated early divergence of L. leai and L. caveata from the other 6 species. Pairwise Sequentially Markovian Coalescent analysis revealed population bottlenecks over the past million years, with L. rochechouarti showing more significant population size fluctuations during the Pleistocene Glacial Epoch. In summary, this study provides comprehensive genomic insights into 8 Lamprotula species, highlighting their high genomic complexity and evolutionary divergence, thereby establishing a crucial foundation for future conservation and genetic research efforts.