Intraspecific de novo gene birth revealed by presence–absence variant genes in Caenorhabditis elegans

Genes embed their evolutionary history in the form of various alleles. Presence–absence variants (PAVs) are extreme cases of such alleles, where a gene present in one haplotype does not exist in another. Because PAVs may result from either birth or death of a gene, PAV genes and their alternative alleles, if available, can represent a basis for rapid intraspecific gene evolution. Using long-read sequencing technologies, this study traced the possible evolution of PAV genes in the PD1074 and CB4856 C. elegans strains as well as their alternative alleles in 14 other wild strains. We updated the CB4856 genome by filling 18 gaps and identified 46 genes and 7,460 isoforms from both strains not annotated previously. We verified 328 PAV genes, out of which 46 were C. elegans-specific. Among these possible newly born genes, 12 had alternative alleles in other wild strains; in particular, the alternative alleles of three genes showed signatures of active transposons. Alternative alleles of three other genes showed another type of signature reflected in accumulation of small insertions or deletions. Research on gene evolution using both species-specific PAV genes and their alternative alleles may provide new insights into the process of gene evolution.