Regulatory and coding changes underlying development and host detection in vertebrate-parasitizing blowflies

The evolutionary transition to parasitism in the family Calliphoridae serves as a compelling model to study the genetic and molecular basis of ecological adaptations. In this study, we sequenced and annotated the genomes of Chrysomya megacephala, Chrysomya putoria, and Lucilia eximia to provide a foundation to investigate the evolution of coding and non-coding sequences within the family Calliphoridae. Combining these new resources with publicly available genomes from 11 representatives of the family, we focused on two species with distinct parasitic strategies, Cochliomyia hominivorax -a flesh-eating parasite-, and Protophormia azurea -a blood-feeding parasite- to identify unique and shared genomic features associated with the evolution of the parasitic lifestyle. Comparative analyses of conserved non-exonic elements revealed 44 genes inferred to convergently evolve at an accelerated evolutionary rate, 41 % of which associate with development, highlighting their potential role in larval feeding specialization. Analyses of coding regions identified genes, including those linked to olfaction, taste, chitin and cuticle formation, inferred to evolve at accelerated rates in both Co. hominivorax and P. azurea. This study advances our understanding of aspects of the evolution of genomic regions of members of the family under natural selection and their potential contribution to parasitism.