Genomic insights into clonal diversity in UK populations of the potato aphid, Macrosiphum euphorbiae

The potato aphid Macrosiphum euphorbiae is one of many polyphagous crop pests involved in the transmission of insect-vectored pathogens. While their North American counterparts reproduce via cyclical parthenogenesis, UK populations of M. euphorbiae appear to persist asexually, resulting in the maintenance of several genotypes, with some demonstrating genotype-specific traits; this includes innate resistance to parasitism from the hymenopterous parasitoid wasp Aphidius ervi. The genetic and molecular basis for genotype-specific traits is often unknown. Here we present a chromosome scale assembly for a parasitoid-resistant clonal line of M. euphorbiae and provide insights into the genotypic composition and distribution of UK potato aphid populations using microsatellite and whole-genome sequencing (WGS) techniques, focusing on geographically separated potato crops within two distinct areas of the UK (Merseyside and Tayside). We show that the genome consists of five chromosomal blocks, has a total size of 560 Mbp and a highly complete BUSCO score (C: 98.0%). The sampled potato aphid populations were dominated by two genotypes, one of which is absent from commercial farm settings. While the genetic and molecular basis for genotype-specific traits is unknown, the M. euphorbiae genotype distribution suggests either an intolerance to farming practices, such as insecticide use, or a broader host range in some populations. WGS data highlighted the asexual clonal lifestyle of M. euphorbiae genotypes in the UK, resolving individuals to a higher resolution than using microsatellite data. WGS data also indicates that M. euphorbiae UK populations are the result of a previous hybridization event. The work presented here will provide useful information for integrated pest management of potato aphids, elaborating on the relationship between genotype diversity and functional traits such as parasitism and insecticide resistance, and host plant use, as well as providing more resources for further comparative genomics studies within the Aphididae.