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Genomics of ecological adaptation in cactophilic Drosophila
- Source :
- Digital.CSIC. Repositorio Institucional del CSIC, instname, Digital.CSIC: Repositorio Institucional del CSIC, Consejo Superior de Investigaciones Científicas (CSIC), Genome Biology and Evolution, Digibug. Repositorio Institucional de la Universidad de Granada, Recercat. Dipósit de la Recerca de Catalunya, Dipòsit Digital de Documents de la UAB, Universitat Autònoma de Barcelona
- Publication Year :
- 2015
- Publisher :
- Oxford University Press, 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.<br />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.
- Subjects :
- Cactaceae
0106 biological sciences
Gene duplication
Lineage (evolution)
Genome, Insect
Genomics
010603 evolutionary biology
01 natural sciences
Genome
Open Reading Frames
03 medical and health sciences
Cactophilic Drosophila
Chitin binding
Ecological adaptation
Genetics
Animals
Drosòfila -- Genètica
Gene
Zinc ion binding
Ecosystem
Ecology, Evolution, Behavior and Systematics
030304 developmental biology
0303 health sciences
biology
Sequence Analysis, RNA
Ecology
Molecular Sequence Annotation
Orphan gene
biology.organism_classification
Adaptation, Physiological
3. Good health
Orphan genes
Drosophila mojavensis
Positive selection
Gene Expression Regulation
Genome sequence
Drosophila
Transcriptome
Research Article
Subjects
Details
- Language :
- English
- Database :
- OpenAIRE
- Journal :
- Digital.CSIC. Repositorio Institucional del CSIC, instname, Digital.CSIC: Repositorio Institucional del CSIC, Consejo Superior de Investigaciones Científicas (CSIC), Genome Biology and Evolution, Digibug. Repositorio Institucional de la Universidad de Granada, Recercat. Dipósit de la Recerca de Catalunya, Dipòsit Digital de Documents de la UAB, Universitat Autònoma de Barcelona
- Accession number :
- edsair.doi.dedup.....b1f4b362dc4aa205e1bd2d38912d8e13