Transposable elements and heterochromatic regions are enriched for structural variation and sequence divergence in the genome of wild-type Caenorhabditis elegans.

Genomic structural variants (SVs) and transposable elements (TEs) can be significant contributors to genome evolution, gene expression alterations, and genetic disease risk. Recent advancements in long-read sequencing have greatly improved the quality of de novo genome assemblies and enhanced the detection of larger and highly repetitive sequence variants at the scale of hundreds or thousands of bases. Comparisons between 2 diverged wild isolates of Caenorhabditis elegans, the Bristol and Hawaiian strains, have been widely utilized in the analysis of small genetic variations. To comprehensively detect SVs and TEs, we generated de novo genome assemblies and annotations for the N2 Bristol and CB4856 Hawaiian C. elegans strains from our lab collection using both long- and short-read sequencing. Within our lab assemblies, we annotate over 3.1 Mb of sequence divergence between the Bristol and Hawaiian isolates: 246,298 homozygous single-nucleotide polymorphisms (SNPs), 73,789 homozygous small insertion-deletions (<50 bp), and 4,334 SVs (>50 bp). We also define the location and movement of specific TEs between N2 Bristol and CB4856 Hawaiian wild-type isolates. Specifically, we find the N2 Bristol genome has 20.6% more TEs from the Tc1/mariner family than the CB4856 Hawaiian genome. Moreover, we identified Zator elements as the most abundant and mobile TE family in the genome. Using specific TE sequences with unique SNPs, we also identified 9 TEs that moved intrachromosomally and 8 TEs that moved to new chromosomes between the N2 Bristol and CB4856 Hawaiian genomes. Further, we show an enrichment of genomic variation in transposon sequences and silenced heterochromatic regions of chromosomes in the germline. Taken together, our studies demonstrate how specific regions of the genome, including large-scale repetitive regions, are more susceptible to accumulation of genetic variation and changes to genome structure.