Hidden in the genomic bycatch: insights into genome reorganization and population structure of the parasitic nematode <i>Contortylenchus reversus</i>

<jats:title>ABSTRACT</jats:title> <jats:p> Insect-parasitic nematodes are widespread and often significantly reduce host fitness, yet we know surprisingly little about most species. <jats:italic>Contortylenchus reversus</jats:italic> is a hemocoel-inhabiting parasitic nematode that infects <jats:italic>Dendroctonus</jats:italic> bark beetles, notably impacting host mobility and fecundity. We first detail a chromosome-scale genome assembly of <jats:italic>C. reversus</jats:italic> , recovered serendipitously from a sequencing project targeting a host ( <jats:italic>Dendroctonus ponderosae</jats:italic> ). We assembled the 79.4 Mb genome into nine linkage groups and, through transcriptome-aided annotation, identified 11,244 protein-coding genes. Synteny comparisons with the only relatives for which there are complete assemblies reveal extensive chromosomal rearrangements and extreme loss of gene collinearity suggesting these insect-parasitic nematodes may have exceptionally malleable genomes. Using this genome assembly and repurposed reduced-representation genomic data from 707 <jats:italic>D. ponderosae</jats:italic> individuals, we investigated infection frequencies and population structure, identifying infection rates ranging from 0% to 50% across 18 geographically widespread collection sites. Population structure of <jats:italic>C. reversus</jats:italic> appears broadly concordant with the structure of the host beetle, suggesting a shared evolutionary history, while genetic variation (nucleotide diversity) in the parasitic nematode is highly reduced in comparison to its host. These results offer insights into its population genetics, host associations, and the evolutionary dynamics of a nematode–beetle interaction and highlight how genomic bycatch can reveal previously hidden details about an important species in a complex community. </jats:p>