Evolutionary
Genomics

Welcome to Evolutionary Genomics Group

The advent of Genomics marks a gear shift in Biology and no biological science has been more affected than Microbiology. Microbial genomes are small and easier to analyze, therefore, the powers of the genomic tools are here at their best. Prokaryotic microbes will be, with all probability, the first living organisms in which a genomic-centered Biology will be developed. And from all the aspects of prokaryotic biology that will benefit from that understanding their evolution will be one of the most deeply affected.


The Evolutionary Genomics Group of Universidad Miguel Hernández was created with the aims of exploiting the vast richness of information that the growing database of microbial genomes is generating to understand how these microbes evolve and adapt to their specific environments. On the other hand, the roots of our group are in Microbiology, and this is our main scope, the biological (holistic) understanding of microbial evolution. To achieve this understanding we are experienced in Bioinformatics , that together with high throughput sequencing and Microbial Ecology  form the methodological framework of the group. The study of microbes in their natural environment by metagenomics and more classical, culture based, approaches represent also one of the axis of the group endeavours. The population genomics (microdiversity) is another important avenue from which we hope to improve our understanding of microbial evolution.


Our laboratory is among the most experienced metagenomics research groups in the world (see below). We have been publishing important papers about microbial diversity since the mid-eighties and have been pioneers in the application of metagenomics to aquatic environments. We have been the masterminds in the study of the genomes of Haloquadratum walsbyi, Salinibacter ruber, Alteromonas macleodii, and Spiribacter salinus. We have been also pioneers in the reconstruction of genomes by assembly from metagenomes or s Ca. Nanosalinarum (single cell genome), Ca. Actinomarina , Ca. Talassoarchaea, marine Acidimicrobiales.


Our studies of population genomics of aquatic bacteria and archaea lead to the proposal of a model of population biology of prokaryotes, the constant diversity model in which large genomic diversity is present in populations of free living aquatic microbes, thanks to the predatory pressure exercised by their accompanying viral populations, providing a highly plastic and efficient resource exploitation.


Some selected and relevant publications


1.Bolhuis H, Palm P, Wende A, Falb M, Rampp M, Rodriguez-Valera F, Pfeiffer F, Oesterhelt D. The genome of the square archaeon Haloquadratum walsbyi : life at the limits of water activity. BMC Genomics. 2006 Jul 4;7:169. PubMed PMID: 16820047; PubMed Central PMCID: PMC1544339.

2.Mongodin EF, Nelson KE, Daugherty S, Deboy RT, Wister J, Khouri H, Weidman J, Walsh DA, Papke RT, Sanchez Perez G, Sharma AK, Nesbø CL, MacLeod D, Bapteste E, Doolittle WF, Charlebois RL, Legault B, Rodriguez-Valera F. The genome of Salinibacter ruber: convergence and gene exchange among hyperhalophilic bacteria and archaea. Proc Natl Acad Sci U S A. 2005 Dec 13;102(50):18147-52. Epub 2005 Dec 5. PubMed PMID: 16330755; PubMed Central PMCID: PMC1312414.

3.Ivars-Martinez E, Martin-Cuadrado AB, D'Auria G, Mira A, Ferriera S, Johnson J, Friedman R, Rodriguez-Valera F. Comparative genomics of two ecotypes of the marine planktonic copiotroph Alteromonas macleodii suggests alternative lifestyles associated with different kinds of particulate organic matter. ISME J. 2008 Dec;2(12):1194-212. doi: 10.1038/ismej.2008.74. Epub 2008 Jul 31. PubMed PMID: 18670397.

4.López-Pérez M, Ghai R, Leon MJ, Rodríguez-Olmos Á, Copa-Patiño JL, Soliveri J, Sanchez-Porro C, Ventosa A, Rodriguez-Valera F. Genomes of "Spiribacter", a streamlined, successful halophilic bacterium. BMC Genomics. 2013 Nov 13;14:787. doi: 10.1186/1471-2164-14-787. PubMed PMID: 24225341; PubMed Central PMCID: PMC3832224.

5.Ghai R, Pašić L, Fernández AB, Martin-Cuadrado AB, Mizuno CM, McMahon KD, Papke RT, Stepanauskas R, Rodriguez-Brito B, Rohwer F, Sánchez-Porro C, Ventosa A, Rodríguez-Valera F. New abundant microbial groups in aquatic hypersaline environments. Sci Rep. 2011;1:135. doi: 10.1038/srep00135. Epub 2011 Oct 31. PubMed PMID: 22355652; PubMed Central PMCID: PMC3216616

6.Ghai R, Mizuno CM, Picazo A, Camacho A, Rodriguez-Valera F. Metagenomics uncovers a new group of low GC and ultra-small marine Actinobacteria. Sci Rep. 2013;3:2471. doi: 10.1038/srep02471. PubMed PMID: 23959135; PubMed Central PMCID: PMC3747508.

7.Martin-Cuadrado AB, Garcia-Heredia I, Moltó AG, López-Úbeda R, Kimes N, López-García P, Moreira D, Rodriguez-Valera F. A new class of marine Euryarchaeota group II from the mediterranean deep chlorophyll maximum. ISME J. 2014 Dec 23. doi: 10.1038/ismej.2014.249. [Epub ahead of print] PubMed PMID: 25535935.

8.Mizuno CM, Rodriguez-Valera F, Ghai R. Genomes of planktonic Acidimicrobiales: widening horizons for marine Actinobacteria by metagenomics. MBio. 2015 Feb 10;6(1). pii: e02083-14. doi: 10.1128/mBio.02083-14. PubMed PMID: 25670777; PubMed Central PMCID: PMC4337565.

9.Rodriguez-Valera F, Martin-Cuadrado AB, Rodriguez-Brito B, Pasić L, Thingstad TF, Rohwer F, Mira A. Explaining microbial population genomics through phage predation. Nat Rev Microbiol. 2009 Nov;7(11):828-36. doi: 10.1038/nrmicro2235. PubMed PMID: 19834481.

10.Mizuno CM, Rodriguez-Valera F, Kimes NE, Ghai R. Expanding the marine virosphere using metagenomics. PLoS Genet. 2013;9(12):e1003987. doi: 10.1371/journal.pgen.1003987. Epub 2013 Dec 12. PubMed PMID: 24348267; PubMed Central PMCID: PMC3861242.

11.Rodriguez-Valera F, Ussery DW. Is the pan-genome also a pan-selectome? F1000Res. 2012 Sep 21;1:16. doi: 10.12688/f1000research.1-16.v1. eCollection 2012. PubMed PMID: 24358823; PubMed Central PMCID: PMC3782348.