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Genome Biol Evol. 2014 Dec 31;7(1):349-66. doi: 10.1093/gbe/evu291.

Genomics of ecological adaptation in cactophilic Drosophila.

Author information

1
Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Spain.
2
Department of Biology, University of Texas at Arlington.
3
Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Spain Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Spain.
4
EMBL/CRG Research Unit in Systems Biology, Centre for Genomic Regulation (CRG), Barcelona, Spain Universitat Pompeu Fabra (UPF), Barcelona, Spain.
5
IRTA, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Barcelona, Spain The Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia.
6
Centro Nacional de Análisis Genómico (CNAG), Parc Científic de Barcelona, Torre I, Barcelona, Spain.
7
Barcelona Supercomputing Center (BSC), Edifici TG (Torre Girona), Barcelona, Spain and Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
8
Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Spain.
9
Instituto de Ciências Biológicas, Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil.
10
Informática de Biossistemas, Centro de Pesquisas René Rachou-Fiocruz Minas, Belo Horizonte, MG, Brazil.
11
Department of Human Genetics, University of Utah School of Medicine.
12
IRTA, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Barcelona, Spain.
13
Department of Molecular Biology and Genetics, Cornell University.
14
Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Spain alfredo.ruiz@uab.cat.

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.

KEYWORDS:

cactophilic Drosophila; ecological adaptation; gene duplication; genome sequence; orphan genes; positive selection

PMID:
25552534
PMCID:
PMC4316639
DOI:
10.1093/gbe/evu291
[Indexed for MEDLINE]
Free PMC Article

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