The genome of Drosophila subpulchrella helps polarising the evolution of pest traits in its sister species Drosophila suzukii

Drosophila suzukii, an invasive fruit fly characterised by temperate habitat and unusual egg laying behaviour, is an excellent model to investigate adaptation to new ecological niches. To increase the resolution power of genome analyses, we produced a draft genomes and transcriptome of D. subuplchrella, the sister species of D.suzukii. Dated phylogenomic trees indicate that they speciated from a common ancestor characterised by reduced generations per year: this is compatible with a long history of adaptation to temperate climates in the subgroup. Uneven sorting of orthologs and of repetitive element is suggestive of some past genetic admixtures between the two species, a hypothesis corroborated by a fertile hybrid obtained in our lab. Comparative genomics indicates that the two species share most of their gustative, but not odorant, gene repertoire confirming a gradual chemosensory specialisation in the subgroup. Overall, our results support a progressive modification scenario toward the peculiar D. suzukii biology and ecology. More generally, our study shows that a sister species can highly increase the precision of comparative genomics when studying novel traits and adaptation.