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https://www.arca.fiocruz.br/handle/icict/12687
GENOMICS OF ECOLOGICAL ADAPTATION IN CACTOPHILIC DROSOPHILA
genome sequence
ecological adaptation
positive selection
orphan genes
gene
Author
Guillen, Yolanda
Rius, Nuria
Delprat, Alejandra
Williford, Anna
Muyas, Francesc
Puig, Marta
Casillas, Sonia
Ramia, Miquel
Egea, Raquel
Negre, Barbara
Mir, Gisela
Camps, Jordi
Moncunill, Valentı
Ruiz-Ruano, Francisco J.
Cabrero, Josefa
Lima, Leonardo G. de
Dias, Guilherme B.
Ruiz, Jeronimo Conceição
Kapusta, Aure lie
Garcia-Mas, Jordi
Gut, Marta
Gut, Ivo G.
Torrents, David
Camacho, Juan P.
Kuhn, Gustavo Campos e Silva
Feschotte, Cedric
Clark, Andrew G
Betran, Esther
Barbadilla, Antonio
Ruiz, Alfredo
Rius, Nuria
Delprat, Alejandra
Williford, Anna
Muyas, Francesc
Puig, Marta
Casillas, Sonia
Ramia, Miquel
Egea, Raquel
Negre, Barbara
Mir, Gisela
Camps, Jordi
Moncunill, Valentı
Ruiz-Ruano, Francisco J.
Cabrero, Josefa
Lima, Leonardo G. de
Dias, Guilherme B.
Ruiz, Jeronimo Conceição
Kapusta, Aure lie
Garcia-Mas, Jordi
Gut, Marta
Gut, Ivo G.
Torrents, David
Camacho, Juan P.
Kuhn, Gustavo Campos e Silva
Feschotte, Cedric
Clark, Andrew G
Betran, Esther
Barbadilla, Antonio
Ruiz, Alfredo
Affilliation
Universitat Autonoma de Barcelona. Departamento de Genetica i de Microbiologia. Barcelona, Spain
Universitat Autonoma de Barcelona. Departamento de Genetica i de Microbiologia. Barcelona, Spain
Universitat Autonoma de Barcelona. Departamento de Genetica i de Microbiologia. Barcelona, Spain
University of Texas at Arlington. Department of Biology.
Universitat Autonoma de Barcelona. Departamento de Genetica i de Microbiologia. Barcelona, Spain
Universitat Autonoma de Barcelona. Departamento de Genetica i de Microbiologia. Barcelona, Spain
Universitat Autonoma de Barcelona. Departamento de Genetica i de Microbiologia. Barcelona, Spain/Universitat Autonoma de Barcelona. Institut de Biotecnologia i de Biomedicina. Spain
Universitat Autonoma de Barcelona. Departamento de Genetica i de Microbiologia. Barcelona, Spain/Universitat Autonoma de Barcelona. Institut de Biotecnologia i de Biomedicina. Spain
Universitat Autonoma de Barcelona. Departamento de Genetica i de Microbiologia. Barcelona, Spain/Universitat Autonoma de Barcelona. Institut de Biotecnologia i de Biomedicina. Spain
Centre for Genomic Regulation. EMBL/CRG Research Unit in Systems Biology. Barcelona, Spain/Universitat Pompeu Fabra. Barcelona, Spain
IRTA. Centre for Research in Agricultural . Barcelona, Spain/The Peter MacCallum Cancer Centre. East Melbourne, Victoria, Australia
Centro Nacional de Analisis Genomico. Parc Cientı´fic de Barcelona. Barcelona, Spain
Barcelona Supercomputing Center. Barcelona, Spain/Institucion Catalana de Recerca i Estudis Avancats. Barcelona, Spain
Universidad de Granada. Facultad de Ciencias. Departamento de Genetica. Spain
Universidad de Granada. Facultad de Ciencias. Departamento de Genetica. Spain
Universidade Federal de Minas Gerais. Instituto de Ciencias Biologicas. Departamento de Biologia Geral. Belo Horizonte, MG, Brasil
Universidade Federal de Minas Gerais. Instituto de Ciencias Biologicas. Departamento de Biologia Geral. Belo Horizonte, MG, Brasil
Fundação Oswaldo Cruz. Centro de Pesquisas Rene´ Rachou. Informatica de Biossistemas. Belo Horizonte, MG, Brasil
University of Utah School of Medicine. Department of Human Genetics.
IRTA. Centre for Research in Agricultural . Barcelona, Spain
Centro Nacional de Analisis Genomico. Parc Cientı´fic de Barcelona. Barcelona, Spain
Centro Nacional de Analisis Genomico. Parc Cientı´fic de Barcelona. Barcelona, Spain
Barcelona Supercomputing Center. Barcelona, Spain/Institucion Catalana de Recerca i Estudis Avancats. Barcelona, Spain
Universidad de Granada. Facultad de Ciencias. Departamento de Genetica. Spain
Universidade Federal de Minas Gerais. Instituto de Ciencias Biologicas. Departamento de Biologia Geral. Belo Horizonte, MG, Brasil
University of Utah School of Medicine. Department of Human Genetics.
Cornell University. Department of Molecular Biology and Genetics.
University of Texas at Arlington. Department of Biology.
Universitat Autonoma de Barcelona. Departamento de Genetica i de Microbiologia. Barcelona, Spain/Universitat Autonoma de Barcelona. Institut de Biotecnologia i de Biomedicina. Spain
Universitat Autonoma de Barcelona. Departamento de Genetica i de Microbiologia. Barcelona, Spain
Universitat Autonoma de Barcelona. Departamento de Genetica i de Microbiologia. Barcelona, Spain
Universitat Autonoma de Barcelona. Departamento de Genetica i de Microbiologia. Barcelona, Spain
University of Texas at Arlington. Department of Biology.
Universitat Autonoma de Barcelona. Departamento de Genetica i de Microbiologia. Barcelona, Spain
Universitat Autonoma de Barcelona. Departamento de Genetica i de Microbiologia. Barcelona, Spain
Universitat Autonoma de Barcelona. Departamento de Genetica i de Microbiologia. Barcelona, Spain/Universitat Autonoma de Barcelona. Institut de Biotecnologia i de Biomedicina. Spain
Universitat Autonoma de Barcelona. Departamento de Genetica i de Microbiologia. Barcelona, Spain/Universitat Autonoma de Barcelona. Institut de Biotecnologia i de Biomedicina. Spain
Universitat Autonoma de Barcelona. Departamento de Genetica i de Microbiologia. Barcelona, Spain/Universitat Autonoma de Barcelona. Institut de Biotecnologia i de Biomedicina. Spain
Centre for Genomic Regulation. EMBL/CRG Research Unit in Systems Biology. Barcelona, Spain/Universitat Pompeu Fabra. Barcelona, Spain
IRTA. Centre for Research in Agricultural . Barcelona, Spain/The Peter MacCallum Cancer Centre. East Melbourne, Victoria, Australia
Centro Nacional de Analisis Genomico. Parc Cientı´fic de Barcelona. Barcelona, Spain
Barcelona Supercomputing Center. Barcelona, Spain/Institucion Catalana de Recerca i Estudis Avancats. Barcelona, Spain
Universidad de Granada. Facultad de Ciencias. Departamento de Genetica. Spain
Universidad de Granada. Facultad de Ciencias. Departamento de Genetica. Spain
Universidade Federal de Minas Gerais. Instituto de Ciencias Biologicas. Departamento de Biologia Geral. Belo Horizonte, MG, Brasil
Universidade Federal de Minas Gerais. Instituto de Ciencias Biologicas. Departamento de Biologia Geral. Belo Horizonte, MG, Brasil
Fundação Oswaldo Cruz. Centro de Pesquisas Rene´ Rachou. Informatica de Biossistemas. Belo Horizonte, MG, Brasil
University of Utah School of Medicine. Department of Human Genetics.
IRTA. Centre for Research in Agricultural . Barcelona, Spain
Centro Nacional de Analisis Genomico. Parc Cientı´fic de Barcelona. Barcelona, Spain
Centro Nacional de Analisis Genomico. Parc Cientı´fic de Barcelona. Barcelona, Spain
Barcelona Supercomputing Center. Barcelona, Spain/Institucion Catalana de Recerca i Estudis Avancats. Barcelona, Spain
Universidad de Granada. Facultad de Ciencias. Departamento de Genetica. Spain
Universidade Federal de Minas Gerais. Instituto de Ciencias Biologicas. Departamento de Biologia Geral. Belo Horizonte, MG, Brasil
University of Utah School of Medicine. Department of Human Genetics.
Cornell University. Department of Molecular Biology and Genetics.
University of Texas at Arlington. Department of Biology.
Universitat Autonoma de Barcelona. Departamento de Genetica i de Microbiologia. Barcelona, Spain/Universitat Autonoma de Barcelona. Institut de Biotecnologia i de Biomedicina. Spain
Universitat Autonoma de Barcelona. Departamento de Genetica i de Microbiologia. Barcelona, Spain
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 replet a 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 (161.5Mb) 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 na excess of genes involved inmetabolism of heterocyclic compounds that are abundant in Stenocereus cacti and toxic to nonresident Drosophila species. We found 117 orphangenes 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 Drosophilagenome sequence
ecological adaptation
positive selection
orphan genes
gene
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