Publications by authors named "Miquel Ràmia"

5 Publications

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Genomics of ecological adaptation in cactophilic Drosophila.

Genome Biol Evol 2014 Dec 31;7(1):349-66. Epub 2014 Dec 31.

Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Spain

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.
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http://dx.doi.org/10.1093/gbe/evu291DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4316639PMC
December 2014

Natural variation in genome architecture among 205 Drosophila melanogaster Genetic Reference Panel lines.

Genome Res 2014 Jul 8;24(7):1193-208. Epub 2014 Apr 8.

Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27595, USA;

The Drosophila melanogaster Genetic Reference Panel (DGRP) is a community resource of 205 sequenced inbred lines, derived to improve our understanding of the effects of naturally occurring genetic variation on molecular and organismal phenotypes. We used an integrated genotyping strategy to identify 4,853,802 single nucleotide polymorphisms (SNPs) and 1,296,080 non-SNP variants. Our molecular population genomic analyses show higher deletion than insertion mutation rates and stronger purifying selection on deletions. Weaker selection on insertions than deletions is consistent with our observed distribution of genome size determined by flow cytometry, which is skewed toward larger genomes. Insertion/deletion and single nucleotide polymorphisms are positively correlated with each other and with local recombination, suggesting that their nonrandom distributions are due to hitchhiking and background selection. Our cytogenetic analysis identified 16 polymorphic inversions in the DGRP. Common inverted and standard karyotypes are genetically divergent and account for most of the variation in relatedness among the DGRP lines. Intriguingly, variation in genome size and many quantitative traits are significantly associated with inversions. Approximately 50% of the DGRP lines are infected with Wolbachia, and four lines have germline insertions of Wolbachia sequences, but effects of Wolbachia infection on quantitative traits are rarely significant. The DGRP complements ongoing efforts to functionally annotate the Drosophila genome. Indeed, 15% of all D. melanogaster genes segregate for potentially damaged proteins in the DGRP, and genome-wide analyses of quantitative traits identify novel candidate genes. The DGRP lines, sequence data, genotypes, quality scores, phenotypes, and analysis and visualization tools are publicly available.
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http://dx.doi.org/10.1101/gr.171546.113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4079974PMC
July 2014

InvFEST, a database integrating information of polymorphic inversions in the human genome.

Nucleic Acids Res 2014 Jan 18;42(Database issue):D1027-32. Epub 2013 Nov 18.

Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain, Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain and Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.

The newest genomic advances have uncovered an unprecedented degree of structural variation throughout genomes, with great amounts of data accumulating rapidly. Here we introduce InvFEST (http://invfestdb.uab.cat), a database combining multiple sources of information to generate a complete catalogue of non-redundant human polymorphic inversions. Due to the complexity of this type of changes and the underlying high false-positive discovery rate, it is necessary to integrate all the available data to get a reliable estimate of the real number of inversions. InvFEST automatically merges predictions into different inversions, refines the breakpoint locations, and finds associations with genes and segmental duplications. In addition, it includes data on experimental validation, population frequency, functional effects and evolutionary history. All this information is readily accessible through a complete and user-friendly web report for each inversion. In its current version, InvFEST combines information from 34 different studies and contains 1092 candidate inversions, which are categorized based on internal scores and manual curation. Therefore, InvFEST aims to represent the most reliable set of human inversions and become a central repository to share information, guide future studies and contribute to the analysis of the functional and evolutionary impact of inversions on the human genome.
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http://dx.doi.org/10.1093/nar/gkt1122DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3965118PMC
January 2014

The Drosophila melanogaster Genetic Reference Panel.

Nature 2012 Feb 8;482(7384):173-8. Epub 2012 Feb 8.

Department of Genetics, North Carolina State University, Raleigh, North Carolina 27695, USA.

A major challenge of biology is understanding the relationship between molecular genetic variation and variation in quantitative traits, including fitness. This relationship determines our ability to predict phenotypes from genotypes and to understand how evolutionary forces shape variation within and between species. Previous efforts to dissect the genotype-phenotype map were based on incomplete genotypic information. Here, we describe the Drosophila melanogaster Genetic Reference Panel (DGRP), a community resource for analysis of population genomics and quantitative traits. The DGRP consists of fully sequenced inbred lines derived from a natural population. Population genomic analyses reveal reduced polymorphism in centromeric autosomal regions and the X chromosome, evidence for positive and negative selection, and rapid evolution of the X chromosome. Many variants in novel genes, most at low frequency, are associated with quantitative traits and explain a large fraction of the phenotypic variance. The DGRP facilitates genotype-phenotype mapping using the power of Drosophila genetics.
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http://dx.doi.org/10.1038/nature10811DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3683990PMC
February 2012

PopDrowser: the Population Drosophila Browser.

Bioinformatics 2012 Feb 15;28(4):595-6. Epub 2011 Dec 15.

Institut de Biotecnologia i de Biomedicina and Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain.

Motivation: The completion of 168 genome sequences from a single population of Drosophila melanogaster provides a global view of genomic variation and an understanding of the evolutionary forces shaping the patterns of DNA polymorphism and divergence along the genome.

Results: We present the 'Population Drosophila Browser' (PopDrowser), a new genome browser specially designed for the automatic analysis and representation of genetic variation across the D. melanogaster genome sequence. PopDrowser allows estimating and visualizing the values of a number of DNA polymorphism and divergence summary statistics, linkage disequilibrium parameters and several neutrality tests. PopDrowser also allows performing custom analyses on-the-fly using user-selected parameters.

Availability: PopDrowser is freely available from http://PopDrowser.uab.cat.
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http://dx.doi.org/10.1093/bioinformatics/btr691DOI Listing
February 2012