Comprehensive detection of structural variation and transposable element differences between wild type laboratory lineages ofC. elegans

Abstract

High quality reference genomes are vital to study the impact of sequence variation on genome structure and function. Recent advancements in long-read sequencing have greatly improved the quality of de novo genome assemblies and enhanced the detection of sequence variants at the scale of hundreds or thousands of bases. The nematode Caenorhabditis elegans is a powerful model system for both genetic and evolutionary studies. Comparisons between two diverged wild isolates, the Bristol and Hawaiian strains, have been widely utilized in the analysis of small genetic structural variations in C. elegans. The reference genomes most widely used for these isolates were assembled using short read sequencing, which makes the detection of large structural variations challenging. To comprehensively detect both large and small structural variations as well as sequence divergence in the Hawaiian and Bristol C. elegans isolates, we generated de novo genome assemblies for each strain using both long- and short-read sequencing. With these assemblies, we annotate over 3.1Mb of sequence divergence between the Bristol and Hawaiian isolates: 337,584 SNPs, 94,503 small insertion-deletions (<50bp), and 4,334 structural variations (>50bp). By comparing our de novo genome assembly of the Bristol isolate to the VC2010 Bristol assembly, we also reveal that lab lineages display 1,162 SNPs, 1,528 indels, as well as 897 structural variations- over 2Mb of total variation. Our work highlights both the importance of using long-read sequencing in de novo genome assembly to identify the total genetic variation between strains and the underappreciated impact of long-term laboratory cultivation on genome structure.