DOI: 10.5061/dryad.5q1h4
title: Data from: The making of a pest: insights from the evolution of chemosensory receptor families in a pestiferous and invasive fly, Drosophila suzukii

description: Background: Drosophila suzukii differs from other melanogaster group
 members in their proclivity for laying eggs in fresh fruit rather than in
 fermenting fruits. Olfaction and gustation play a critical role during
 insect niche formation, and these senses are largely mediated by two
 important receptor families: olfactory and gustatory receptors (Ors and
 Grs). Earlier work from our laboratory has revealed how the olfactory
 landscape of D. suzukii is dominated by volatiles derived from its unique
 niche. Signaling and reception evolve in synchrony, since the interaction
 of ligands and receptors together mediate the chemosensory behavior. Here,
 we manually annotated the Ors and Grs in D. suzukii and two close
 relatives, D. biarmipes and D. takahashii, and compared these repertoires
 to those in other melanogaster group drosophilids to identify candidate
 chemoreceptors associated with D. suzukii’s unusual niche utilization.
 Results: Our comprehensive annotations of the chemosensory genomes in
 three species, and comparative analysis with other melanogaster group
 members provide insights into the evolution of chemosensation in the
 pestiferous D. suzukii. We annotated a total of 71 Or genes in D. suzukii,
 with nine of those being pseudogenes (12.7 %). Alternative splicing of two
 genes brings the total to 62 genes encoding 66 Ors. Duplications of Or23a
 and Or67a expanded D. suzukii’s Or repertoire, while pseudogenization of
 Or74a, Or85a, and Or98b reduced the number of functional Ors to roughly
 the same as other annotated species in the melanogaster group. Seventy-one
 intact Gr genes and three pseudogenes were annotated in D. suzukii.
 Alternative splicing in three genes brings the total number of Grs to 81.
 We identified signatures of positive selection in two Ors and three Grs at
 nodes leading to D. suzukii, while three copies in the largest expanded Or
 lineage, Or67a, also showed signs of positive selection at the external
 nodes. Conclusion: Our analysis of D. suzukii’s chemoreceptor repertoires
 in the context of nine melanogaster group drosophilids, including two of
 its closest relatives (D. biarmipes and D. takahashii), revealed several
 candidate receptors associated with the adaptation of D. suzukii to its
 unique ecological niche.
description: Fig. 2 Olfactory
 receptor phylogeny estimation (RAxML)Phylogenetic analysis of
 Ors in Drosophila suzukii (Dsuz), D. biarmipes (Dbia), D. takahashii
 (Dtak) and D. melanogaster (Dmel) using a Maximum Likelihood method.
 Evolutionary history was inferred using a Maximum Likelihood method based
 on the JTT matrix-based model (Jones et al. 1992). The tree was
 constructed using RAxML under the JTT model of substitution with NNI
 topology search (Stamatikis 2014), based on an amino acid alignment by
 MUSCLE (Edgar 2004). Branch support was estimated using 500 bootstrap
 replications. The tree is rooted with Orco.Ors.treefile.nexFig. 3 Gustatory receptor phylogeny estimation (RAxML)Phylogenetic analysis of Grs in Drosophila suzukii (Dsuz), D. biarmipes (Dbia), D. takahashii (Dtak) and D. melanogaster (Dmel) using a Maximum Likelihood method. Evolutionary history was inferred using a Maximum Likelihood method based on the JTT matrix-based model (Jones et al. 1992). The tree was constructed using RAxML under the JTT model of substitution with NNI topology search (Stamatikis 2014), based on an amino acid alignment by MUSCLE (Edgar 2004). Branch support was estimated using 500 bootstrap replications. The tree is rooted with Gr21a.Grs.treefile.nexOrs_alignment file (Muscle)Olfactory receptor peptide sequences of D. suzukii (Dsuz), D. biarmipes (Dbia), D. takahashii (Dtak) and D. melanogaster (Dmel) ≥ 360 aa in length were multiply aligned using MUSCLE v3.8.31 (Edgar 2004).Ors_alignment.phyGrs_aligment file (Muscle)Gustatory receptor peptide sequences of D. suzukii (Dsuz), D. biarmipes (Dbia), D. takahashii (Dtak) and D. melanogaster (Dmel) ≥ 340 aa in length were multiply aligned using MUSCLE v3.8.31 (Edgar 2004).Grs_aligment.phy