The Computational Evolutionary Genomics group at CBGP develops comparative (meta-)genomic methods to decipher what makes each organism and microbial ecosystem unique. In particular, we use phylogenomic techniques to study processes such as gene sub/neo-functionalization, duplication, horizontal transfer, domain conservation or orthology detection. At the metagenomic scale, we are interested in the functional characterization of microbial communities as a whole, aiming at the the identification of functional modules associated with environmental or host conditions. For this, we combine theoretical knowledge in evolutionary biology, sequencing data, and high performance computational resources. Our current research lines are:
We analyze shotgun metagenomics data (soil, ocean, gut, etc.) to identify functional modules within microbial communities that might differentiate sample or environmental conditions. We are particularly interested in exploring the unknown fraction of the those data (i.e. sequences with no homologs), currently accounting for 20-50% of the sequenced genes and transcripts. Our ultimate goals are i) understanding the interactions of microbial communities with their environments, ii) identifying functional modules that can function as predictors for specific environmental conditions (Fig.1) , and iii) discovering novel gene functions with potential applications in biotechnology (i.e. novel enzymes).
Phylogenetic diversity within microbial communities
Metagenomics data are incomplete, noisy and quite challenging for classic evolutionary analysis. We pursue a better insight on microbial (prok- and eukaryotic) biodiversity, as well as the implementation of bioinformatic methods to identify pathogenic organisms in both agricultural environments and human health. To do so we work on the implementation and further application of phylogenetic methods for taxonomic identification of metagenomic species (Fig. 2), integration of pan-genomic data, and strain resolution.
Evolution at the gene family level
We are interested in different aspects of gene family evolution, such as dating the emergence of specific functions, studying gene duplication, identifying horizontal gene transfers, or characterizing gene fusion events. We are specialized in large scale phylogenomic analysis, where hundreds of genomes can be compared at once. We apply those techniques to gain insights about the evolution of gene function and its practical application in establishing genotype-phenotype associations in plant breeding programs.
Phylogenomic methods and tools
We develop functional prediction methods, metagenomic frameworks, orthology resources and genomic databases. Many of those tools are the result of our own needs, but we also work on providing open source implementations that are useful to other researchers in the field.