Genomics of Ecological Adaptation in Cactophilic Drosophila Guillén, Yolanda Rius, Nuria Delprat, Alejandra Williford, Anna Muyas, Francesc Puig, Marta Casillas, Sonia Ramia, Miquel Egea, Raquel Negre, Barbara Mir, Gisela Camps, Jordi Moncunill, Valentí Ruiz-Ruano, Francisco J. Cabrero, Josefa Lima, Leonardo G. de Dias, Guilherme B. Ruiz, Jeronimo C. Kapusta, Aurélie García-Mas, Jordi Gut, Marta Gut, Ivo G. Torrents, David Camacho Martínez, Juan Pedro Kuhn, Gustavo C.S. Feschotte, Cédric Clark, Andrew G. Betrán, Esther Barbadilla, Antonio Ruiz, Alfredo Cactophilic Drosophila Genome sequence Ecological adaptation Positive selection Orphan genes Gene duplication Cactophilic Drosophila species provide a valuable model to study gene–environment interactions and ecological adaptation. Drosophila buzzatii and Drosophila mojavensis are two cactophilic species that belong to the repleta group, but have very different geographical distributions and primary host plants. To investigate the genomic basis of ecological adaptation, we sequenced the genome and developmental transcriptome of D. buzzatii and compared its gene content with that of D. mojavensis and two other noncactophilic Drosophila species in the same subgenus. The newly sequenced D. buzzatii genome (161.5 Mb) comprises 826 scaffolds (>3 kb) and contains 13,657 annotated protein-coding genes. Using RNA sequencing data of five life-stages we found expression of 15,026 genes, 80% protein-coding genes, and 20% noncoding RNA genes. In total, we detected 1,294 genes putatively under positive selection. Interestingly, among genes under positive selection in the D. mojavensis lineage, there is an excess of genes involved in metabolism of heterocyclic compounds that are abundant in Stenocereus cacti and toxic to nonresident Drosophila species. We found 117 orphan genes in the shared D. buzzatii–D. mojavensis lineage. In addition, gene duplication analysis identified lineage-specific expanded families with functional annotations associated with proteolysis, zinc ion binding, chitin binding, sensory perception, ethanol tolerance, immunity, physiology, and reproduction. In summary, we identified genetic signatures of adaptation in the shared D. buzzatii–D. mojavensis lineage, and in the two separate D. buzzatii and D. mojavensis lineages. Many of the novel lineage-specific genomic features are promising candidates for explaining the adaptation of these species to their distinct ecological niches. 2015-04-07T09:17:08Z 2015-04-07T09:17:08Z 2015 journal article Guillén, N.; et al. Genomics of Ecological Adaptation in Cactophilic Drosophila. Genome Biology and Evolution, 7(1): 349-366 (2015). [http://hdl.handle.net/10481/35440] 1759-6653 http://hdl.handle.net/10481/35440 10.1093/gbe/evu291 eng http://creativecommons.org/licenses/by-nc-nd/3.0/ open access Creative Commons Attribution-NonCommercial-NoDerivs 3.0 License Oxford University Press; Society for Molecular Biology and Evolution