Genome assembly variation and its implications for gene discovery in nematode species

Genome assemblers are a critical component of genome science, but the
choice of assembly software and protocols can be daunting. Here, we
investigate genome assembly variation and its implications for gene
discovery across three nematode species—Caenorhabditis bovis, Haemonchus
contortus, and Heligmosomoides bakeri—highlighting the critical interplay
between assembly choice and downstream genomic analysis. Selecting
commonly used genome assemblers, we generated multiple assemblies for each
species, analyzing their structure, completeness, and effect on gene
family analysis. Our findings demonstrate that assembly variations can
significantly affect gene family composition, with notable differences in
gene families important in anthelmintic discovery and immunomodulation.
Despite broadly similar performance using various assembly metrics,
comparisons of assemblies with a single species revealed underlying
structural rearrangements and inconsistencies in gene content, which would
affect downstream analyses. This emphasizes the need for continuous
refinement of genome assemblies and their annotations.