Bioinformatics
and Comparative Genomics
1. Development of Bioinformatic Tools for Molecular Evolution
The large volume of available DNA sequences requires new and powerful computational tools for their analysis. Indeed, the comparative analysis of genes and genomes can provide useful information on their origin and on the mechanisms involved in their evolution. With this goal we are developing bioinformatic tools for the analysis of DNA sequence variation in genes and genomes. We are currently developing coalescent-based statistical tests, algorithms and software for:
1) the analysis of SNPs (Single Nucleotide Polymorphisms)
2) the extensive analysis of nucleotide variation at small DNA coding and noncoding regions (level and pattern of variation, linkage disequilibria, recombination, codon bias, etc.)
3) the analysis of the pattern of variation in whole genomes or chromosomes
4) displaying the pattern of polymorphism (linkage disequilibria, nucleotide diversity, etc.) along large DNA regions of the genome.Relevant Publications
Librado, P. and Rozas, J. 2009. DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25: 1451-1452.
Hutter, S., A. J. Vilella and J. Rozas. 2006. Genome-Wide DNA Polymorphism Analyses using VariScan. BMC Bioinformatics 7: 409.
Rozas, J. 2009. DNA Sequence Polymorphism Analysis using DnaSP. Pp. 337-350. In Posada, D. (ed.) Bioinformatics for DNA Sequence Analysis; Methods in Molecular Biology Series Vol. 537. Humana Press, NJ, USA.
Vilella, A. J., Blanco-García, A., Hutter, S. and Rozas, J. 2005. VariScan: Analysis of evolutionary patterns from large-scale DNA sequence polymorphism data. Bioinformatics 21: 2791-2793
Software
2. Comparative Genomics
Chemoreception is a crucial biological process, essential for the survival of animals. In insects, olfaction allows the recognition of volatile cues that confer the organism the capacity to detect food, predators and mates, while the sense of taste commonly allows the discrimination of soluble stimulants that elicit feeding behaviours, although it can also initiate innate sexual and reproductive responses. The most important protein components underlying the recognition of chemical cues comprise moderate-size multigene families. These families include odorant-binding (OBPs) and chemosensory (CSPs) proteins, involved in peripheral olfactory processing, the chemoreceptor superfamily formed by the olfactory (OR) and gustatory (GR) receptors, and the Ionotropic receptor (IR) gene family.
The availability of whole genome sequence data for several arthropod species offers the possibility of conducting a fine-scale comparative genomic analysis on this gene family. Currently, we are conducting the following research:
1) Identification and annotation of functional and non-functional members of the chemosensory gene families in complete genomes
2) Estimation of the birth-and-death rates (gene duplication and gene loss rates)
3) Study of the impact of the positive and negative selection across gene members
Relevant Publications
Alvarez-Ponce, D., Aguadé, M. and Rozas, J. 2011. Comparative genomics of the vertebrate insulin/TOR signal transduction pathway: A network-level analysis of selective pressures. Genome Biol. Evol. 3: 87-101.
Vieira, F. G. and Rozas, J. 2011. Comparative genomics of the Odorant-Binding and Chemosensory Protein gene families across the Arthropoda: Origin and evolutionary history of the chemosensory system. Genome Biol. Evol. 3: 476-490.
Kirkness, E. F. et al. 2010. Genome sequences of the human body louse and its primary endosymbiont provides insights into the permanent parasitic lifestyle. Proc. Natl. Acad. Sci. USA. 107: 12168-12173.
Richards, S. et al. The International Aphid Genomics Consortium. 2010. Genome Sequence of the Pea Aphid Acyrthosiphon pisum. PLoS Biol. 8: e1000313.
Alvarez-Ponce, D., Aguadé, M. and Rozas, J. 2009. Network-level molecular evolutionary analysis of the insulin/TOR signal transduction pathway across 12 Drosophila genomes. Genome Res. 19: 234-242.
Sánchez-Gracia, A., Vieira, F. G. and Rozas, J. 2009. Molecular evolution of the major chemosensory gene families in insects. Heredity 103: 208-216.
Clark, A. G. et al. 2007. Evolution of genes and genomes on the Drosophila phylogeny. Nature 450: 203-218.
Vieira, F. G., Sánchez-Gracia, A. and Rozas, J. 2007. Comparative genomic analysis of the Odorant-Binding Protein family in 12 Drosophila genomes: Purifying selection and birth-and-death evolution. Genome Biol. 8: R235.
Software
Selected Publications