The Yeast Genomics* lab @ NOVA

(*evolutionary, functional, comparative and more)

People

Pedro Almeida

PhD Student

Lab: (+351) 21 294 85 30 (ext. 11108)

Email: pmca@campus.fct.unl.pt

BSc in Biology, Universidade de Lisboa, 2009

MSc in Applied Microbiology, Universidade de Lisboa, 2011

Research interests

My scientific interests cover a range of fundamental topics related with microbial ecology and evolution. The systematic isolation of Saccharomyces yeast species from natural habitats, as the bark and surrounding soil of oak and beech trees, provides a unique opportunity to investigate both natural diversity and domestication in microorganisms. Focusing on wine yeasts (S. cerevisiae and S. uvarum) and using a diverse array of evolutionary genomic methods I am trying to understand the geography and genomic transformations associated with wine yeast domestication. I am also interested in studying the biogeography of natural populations of Saccharomyces yeasts: How is the genetic diversity distributed over a global and continental scale? Is there a parallel in the patterns of geographic diversity between micro- and macroorganisms? What was the importance of past climatic events in shaping this diversity?

Publications

Almeida P, Barbosa R, Bensasson D, Gonçalves P, Sampaio JP. Adaptive divergence in wine yeasts and their wild relatives suggests a prominent role for introgressions and rapid evolution at non coding sites. Molecular Ecology (in press).

DOI: 10.1111/mec.14071

Gonçalves M, Pontes A, Almeida P, Barbosa R, Serra M, Libkind D, Hutzler M, Gonçalves P, Sampaio JP. 2016. Distinct domestication trajectories in top-fermenting beer yeasts and wine yeasts. Curr Biol. 26:1-12.

DOI: 10.1016/j.cub.2016.08.040

Barbosa R, Almeida P, Safar SV, Santos RO, Morais PB, Nielly-Thibault L, Leducq JB, Landry CR, Gonçalves P, Rosa CA, Sampaio JP. Evidence of Natural Hybridization in Brazilian Wild Lineages of Saccharomyces cerevisiae. Genome Biol Evol. 2016. 8:317-29.

DOI:10.1093/gbe/evv263

Almeida P, Barbosa R, Zalar P, Imanishi Y, Shimizu K, Turchetti B, Legras JL, Serra M, Dequin S, Couloux A, Guy J, Bensasson D, Gonçalves P, Sampaio JP. A Population Genomics Insight into the Mediterranean Origins of Wine Yeast Domestication. Mol Ecol. 24:5412-27.

DOI: 10.1111/mec.13341.

Francesca N, Carvalho C, Sannino C, Guerreiro MA, Almeida PM, Settanni L, Massa B, Sampaio JP, Moschetti G. 2014. Yeasts vectored by migratory birds collected in the Mediterranean island of Ustica and description of Phaffomyces usticensis f.a. sp. nov., a new species related to the cactus ecoclade. FEMS Yeast Research 14: 910-921.

DOI: 10.1111/1567-1364.12179

Almeida P&, Gonçalves C&, Teixeira S, Libkind D, Bontrager M, Masneuf-Pomarède I, Albertin W, Durrens P, Sherman DJ, Marullo P, Hittinger CT, Gonçalves P, Sampaio JP. 2014. A Gondwanan imprint on global diversity and domestication of wine and cider yeast Saccharomyces uvarum. Nature Communications 5:4044.

DOI:10.1038/ncomms5044

Leducq J-B, Guillaume C, Samani P, Dubé AK, Sylvester K, James B, Almeida P, Sampaio JP, Hittinger CT, Bell G, Landry CR. 2014. Local climatic adaptation in a widespread microorganism. Proceedings of the Royal Society B 281: 20132472.

DOI:10.1098/rspb.2013.2472

Francesca N, Carvalho C, Almeida PM, Sannino C, Settanni L, Sampaio JP, Moschetti G. 2013. Wicherhamomyces sylviae f.a., sp. nov., an ascomycetous yeast species isolated from migratory birds in Sicily, Italy. International Journal of Systematic and Evolutionary Microbiology 63: 4824–4830.

DOI:10.1099/ijs.0.056382-0

(& equally contributing)