Genome structural variation in natural Caenorhabditis elegans populations

Abstract

Structural variation, involving large alterations in chromosome structure, drives genetic diversification and the emergence of new phenotypes. These changes are widespread in natural populations and play an important role in adaptation and speciation. For many species, research has been limited to laboratory adapted strains and experimental evolution, which may not reflect the diversity of structural variants in the wild. Furthermore, technological limitations have proved to be a major barrier to accurate and comprehensive variant calling. In this study, we used PacBio sequencing data from 14 wild Caenorhabditis elegans strains to characterize structural variants in a natural population. With long-reads, we overcame limitations associated with short-read approaches and leveraged population-level data to further refine the accuracy of variant calls. We found that large, rapidly evolving gene families, such as GPCR, F-Box, and C-Type lectin, were prominent among the variants predicted to have phenotypic consequences. These results shed light on the significant role of structural variants in the evolution of Caenorhabditis elegans in its wild habitats and the limitations of treating N2 as the reference wild-type.