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Please use this identifier to cite or link to this item: http://hdl.handle.net/10481/35440

Title: Genomics of Ecological Adaptation in Cactophilic Drosophila
Authors: 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, Juan P.
Kuhn, Gustavo C.S.
Feschotte, Cédric
Clark, Andrew G.
Betrán, Esther
Barbadilla, Antonio
Ruiz, Alfredo
Issue Date: 2015
Abstract: 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.
Sponsorship: This work was supported by grants BFU2008-04988 and BFU2011-30476 from Ministerio de Ciencia e Innovación (Spain) to A.R., by an FPI fellowship to Y.G. and a PIF-UAB fellowship to N.R, and by the National Institute of General Medical Sciences of the National Institute of Health under award number R01GM071813 to E.B.
Publisher: Oxford University Press; Society for Molecular Biology and Evolution
Keywords: Cactophilic Drosophila
Genome sequence
Ecological adaptation
Positive selection
Orphan genes
Gene duplication
URI: http://hdl.handle.net/10481/35440
ISSN: 1759-6653
Rights : Creative Commons Attribution-NonCommercial-NoDerivs 3.0 License
Citation: 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]
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