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 popular 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 critical gene families like cyp , gst , ugt , and nhr . Despite broadly similar performance using various assembly metrics, comparisons of assemblies with a single species revealed underlying structural rearrangements and inconsistencies in gene content. This emphasizes the imperative for continuous refinement of genomic resources. Our findings advocate for a cautious and informed approach to genome assembly and annotation to ensure reliable and insightful genomic interpretations.