Comparative Genomics

The research interests of the group are focused around the use of comparative genomics and phylogenomics to study the origin, evolution and function of complex biological systems. This includes understanding how specific biochemical pathways, protein complexes or cellular organelles have emerged and evolved as well as using this evolutionary information to gain insight into their function. Through collaborations with experimental groups we apply comparative genomics to discover new mechanisms and genes involved in interesting processes, especially those of clinical relevance (see lines of research). On the technical side, our work often involves the development of new bioinformatics tools and algorithms that we make available to the community.

1. Host-Microbiome interactions in health and disease
We use state of the art metagenomics approaches to understand host-microbiome interactions in health and disease. We have a particular focus on the role of the fungal component of the microbiom

2. Comparative genomic of fungal pathogens
By comparing genomes of different species and strains we want to understand what genomic re-arrangements underlie the emergence of pathogenesis

3. Phylogenomics and genome evolution
We combine the development of original algorithms to treat phylogenomic data with its application to gain knowledge on problems of biological relevance

4. Evolution of the eukaryotic cell
We use large-scale evolutionary analyses to investigate the origin and evolution two most widespread organelles for which an endosymbiotic origin has been proposed: mitochondria and peroxisomes.

Carreté L, Ksiezopolska E, Pegueroles C, Gómez-Molero E, Saus E, Iraola S, Loska D, Bader O. Fairhead. C. Gabaldón T.
“Patterns of genomic variation in the opportunistic pathogen Candida glabrata suggest the existence of mating and a secondary association with humans.”
Current Biology, 28(1):15-27.e7, 2018.

Willis JR, González-Torres P, Pittis AA, Bejarano LA, Cozzuto L, Andreu-Somavilla N, Alloza-Trabado M, Valentín A, Ksiezopolska E, Company C, Onywera H, Montfort M, Hermoso A, Iraola-Guzmán S, Saus E, Labeeuw A, Carolis C, Hecht J, Ponomarenko J, Gabaldón T.
“Citizen science charts two major “stomatotypes” in the oral microbiome of adolescents and reveals links with habits and drinking water composition.”
Microbiome, 6(1):218, doi: 10.1186/s40168-018-0592-3,2018.

Saus E, Willis JR, Pryszcz LP, Hafez A, Llorens C, Himmelbauer H, Gabaldón T.
“nextPARS: parallel probing of RNA structures in Illumina.”
RNA, 24(4):609-619, doi: 10.1261/rna.063073.117, 2018.

Julca I, Marcet-Houben M, Vargas P, Gabaldón T.
“Phylogenomics of the olive tree (Olea europaea) reveals the relative contribution of ancient allo- and autopolyploidization events.”
BMC Biol, 16(1):15, 2018.

Ropars J, Maufrais C, Diogo D, Marcet-Houben M, Perin A, Sertour N, Mosca K, Permal E, Laval G, Bouchier C, Ma L, Schwartz K, Voelz K, May RC, Poulain J, Battail C, Wincker P, Borman AM, Chowdhary A, Fan S, Kim SH, Le Pape P, Romeo O, Shin JH, Gabaldon T, Sherlock G, Bougnoux ME, d’Enfert C.
“Gene flow contributes to diversification of the major fungal pathogen Candida albicans.”
Nat Commun, 9(1):2253, 2018.