Abstract
<jats:p> The black bean aphid, <jats:italic>Aphis fabae</jats:italic> is a crop pest and vector of insect-transmitted pathogens, comprising closely related sub-species with overlapping host ranges. In other <jats:italic>Aphis</jats:italic> species, over-expression of specific detoxification genes has been linked to insecticide tolerance. We present two chromosome-scale assemblies for a clonal <jats:italic>A.</jats:italic> <jats:italic>fabae</jats:italic> line, representing two phased haplotypes, generated using HiFi and Hi-C sequencing technologies. A comprehensive genome annotation, built with PacBio Iso- Seq data, was used to investigate genes underlying insecticide tolerance. Both genomes are comprised of four chromosomal blocks (haplotype 1: 427 Mb; haplotype 2: 396 Mb) with high BUSCO completeness (98.7%). Comparative genomics revealed an expansion of UDP-glycosyltransferases, whose expression is linked to insecticide detoxification in other <jats:italic>Aphis</jats:italic> species. These high-quality references provide a foundation for studying <jats:italic>A. fabae</jats:italic> sub-species and a genomic resource for investigating insecticide tolerance across the <jats:italic>Aphis</jats:italic> genus. </jats:p>