The Yeast Genomics* lab @ NOVA

(*evolutionary, functional, comparative and more)

More lab news…

December 2014

New publication:

Gomes F, et al. The diversity and extracellular enzymatic activities of yeasts isolated from water tanks of Vriesea minarum, an endangered bromeliad species in Brazil, and the description of Occultifur brasiliensis f.a., sp. nov. Antonie Van Leeuwenhoek 107:597-611

DOI: 10.1007/s10482-014-0356-4.

October 2014

Lab members present their work in international conferences

Pedro Almeida

(Poster presentation in the EMBO conference dedicated to Experimental Approaches to Evolution and Ecology using Yeast & other Model Systems, Germany)

Carla Gonçalves

(Oral presentation in the 31st International Specialised Symposium on Yeast - ISSY31, Slovenia)

September 2014

New publication:

Francesca N, et al. 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.

A new yeast species, Phaffomyces usticensis isolated from migratory birds in the Mediterranean island of Ustica was recently described by Nicola Francesca.

April 2014

New publication:

Peris D, et al. Population structure and reticulate evolution of Saccharomyces eubayanus and its lager-brewing hybrids. Mol Ecol. 23:2031-45.

DOI: 10.1111/mec.12702.

An international collaborative research into Saccharomyces eubayanus diversity appears on the April cover of Molecular Ecology.

October 2014

Lab members present their work at the 12th European Conference on Fungal Genetics, Seville, March 23-27.

Marco A. Coelho

(Genetic and genomic insights into the sexual reproductive systems in red yeasts)

Márcia David-Palma

(Molecular determinants of the homothallic sexual behavior of the basidiomycete yeast Phaffia Rhodozyma)

June 2014

New publication:

Almeida P, Gonçalves C, et al. A Gondwanan imprint on global diversity and domestication of wine and cider yeast Saccharomyces uvarum. Nat Commun. 5:4044.

DOI: 10.1038/ncomms5044.

The yeast Saccharomyces uvarum is commonly used in cider and wine fermentation but its natural history has been poorly studied. In a recent work published in Nature Communications, we revealed that the Northern Hemisphere population of S. uvarum has likely derived from a highly diverse South American population. Interestingly, most of the Holarctic strains associated with human-driven fermentations display multiple introgressions from other Saccharomyces species and over-representation of genes relevant for wine fermentation. Such findings constitute a first indication of domestication in S. uvarum.

August 2014

Lab members present talks at the International Mycological Congress (IMC10) in Bangkok, Thailand

José P. Sampaio

(Population genomics reveals new domestication patterns in Saccharomyces yeasts)

Paula Gonçalves

(Horizontal gene transfer of sugar transporters in the Ascomycota)

July 2014

Lab members present talks at the XX Jornadas de Leveduras Prof. Nicolau van Uden at IST, Lisboa

Raquel Barbosa

(Population genomics of Saccharomyces cerevisiae in Brazil)

Carla Gonçalves

(Global diversity and domestication in the wine and cider yeast Saccharomyces uvarum)

January 2014

New publication:

David-Palma M, et al. Global distribution, diversity hotspots and niche transitions of an astaxanthin-producing eukaryotic microbe. Molecular Ecology 23: 921-932.

DOI: 10.1111/mec.12642.

A phylogeographic study of the astaxanthin-producing yeast Phaffia rhodozyma reveals Australasia as a diversity hotspot for the genus Phaffia and highlights that population structure is driven by niche adaptation.

December 2013

New publication:

Leducq J-B, et al. Local climatic adaptation in a widespread microorganism. Proceedings of the Royal Society B 281: 20132472

DOI: 10.1098/rspb.2013.2472.

An international collaborative study investigated the role of climate changes on adaptation of North American populations of the wild yeast Saccharomyces paradoxus. Results suggest that global climatic changes may lead to adaptation to new conditions within groups, or changes in their geographical distributions.

Lab members attended the Portuguese congress of Microbiology and Biotechnology, Microbiotec'13, in Aveiro.

Marco A. Coelho

was awarded the Best Poster Presentation Prize (Genomics and System Biology) attributed by SPM.

New lab members

Oliver Röhl and Renata Santos join the lab.

Lab members present their work at the EMBO Conference: Comparative Genomics of Eukaryotic Microorganisms, in Sant Feliu de Guixols, Spain.

Marco A. Coelho

(Evolution and comparative genomics of the pseudo-bipolar sexual reproduction system in red yeasts)

Márcia David-Palma

(Understanding the molecular determinants of unisexual behavior in the yeast Phaffia rhodozyma)

Carla Gonçalves

(Multiple horizontal gene transfer events involving a fungal transporter gene)

Márcia David-Palma was awarded an ASM "Eukaryotic Cell Outstanding Young Investigator Award" at the conferece".

August 2013

Pedro Almeida presents a talk at the XIV Congress of the European Society for Evolutionary Biology.

Pedro Almeida

(Tracing the origins of domestication in the wine yeast Saccharomyces cerevisiae)

June 2013

Lab members present talks in international conferences

José P. Sampaio

(Invited presentation in the 5th Conference on Physiology of Yeast and Filamentous fungi, Montpellier, France,

entitled "Surveying wild lineages of Saccharomyces to understand patterns of domestication")

Carla Gonçalves

(Oral presentation in the 30th International Specialised Symposium on Yeast - ISSY30, Slovakia, entitled: Fructophily in yeasts: a special role for specific fructose transporters)

May 2013

New publication:

Coelho MA, et al. Extensive Intra-Kingdom Horizontal Gene Transfer Converging on a Fungal Fructose Transporter Gene. PLoS Genet. 9:e1003587.

DOI: 10.1371/journal.pgen.1003587.

In this work we describe our findings concerning a single fungal gene that seems to have been transferred between fungi very often. We believe this may be related to the fact that the gene can be both very useful and detrimental for the host, depending on genetic background and environment. Our results suggest that exchange of genes between fungi may happen much more frequently than assumed so far.

March 2013

New publication:

Coelho MA, et al. Living and Thriving on the Skin: Malassezia Genomes Tell the Story. mBio 4:e00117-13.

DOI: 10.1128/mBio.00117-13

Marco A. Coelho is the leading author of a commentary in mBio entitled "Living and Thriving on the Skin: Malassezia Genomes Tell the Story".

October 2013

New publication:

Francesca N, et al. Wickerhamomyces sylviae f.a., sp. nov., an ascomycetous yeast species isolated from migratory birds in Sicily, Italy. Int J Syst Evol Microbiol. 63:4824-30.

DOI: 10.1099/ijs.0.056382-0.

A new yeast species, Wickerhamomyces sylviae isolated from migratory birds in Sicily was recently described by Nicola Francesca.

May 2015

New publication:

Coelho M.A., et al. Draft genome sequence of Sporidiobolus salmonicolor CBS 6832, a red-pigmented basidiomycetous yeast.

DOI:10.1128/genomeA.00444-15.

We have sequenced and annotated the genome of the red yeast Sporidiobolus salmonicolor strain CBS 6832. This species is recognized mainly as a phyllosphere yeast and is free-living and distributed worldwide. This is the first genome to be sequenced for members of this species. This genome will foster comparative genomics studies to elucidate the evolution of sexual reproduction in fungi, while enabling the direct access to a repertoire of genes encoding enzymes with potential biotechnological applications.

José P. Sampaio is an invited speaker at the 42nd Annual Conference on Yeasts, Smolenice, Slovakia.

José P. Sampaio

(Invited lecuture to the memory of Dr. A. Kochová-Kratochvílová entitled "Taxonomy and diversity: Saccharomyces in the XXI century")

April 2015

New publication and Editor’s Choice:

de Garcia, et al. Sex in the cold: taxonomic reorganization of psychrotolerant yeasts in the order Leucosporidiales.

DOI: 10.1093/femsyr/fov019

Species of Leucosporidiales are a group of psychrotolerant yeasts with biotechnological potential. In this collaborative work, we clarified the evolutionary relationship among the three recognized species of this lineage and proposed a new genus Pseudoleucosporidium gen. nov. and the new combination P. fasciculatum comb. nov. to resolve the polyphyly of Leucosporidium genus.

March 2015

Marco A. Coelho presents a talk at the 28th Fungal Genetics conference, Pacific Grove, CA, USA.

Marco A. Coelho

(Evolution of mating systems in basidiomyceteous yeasts)

July 2015

New publication:

Highlighted Article

Maia TM, et al. Evolution of Mating Systems in Basidiomycetes and the Genetic Architecture Underlying Mating-Type Determination in the Yeast Leucosporidium scottii.

DOI: 10.1534/genetics.115.177717

The tetrapolar system, in which mating is dictated by two alternate sets of MAT genes at genetically unlinked regions, has been proposed to be the ancestral state in basidiomycete fungi. Support for this model has however been gathered only from two more recently derived lineages. In this paper, we used whole-genome sequencing, chromoblot analysis and mating tests to show that Leucosporidium scottii, a basidiomycete yeast belonging to the earliest-branching lineage, has a tetrapolar system governed by two physically unlinked gene clusters: a multiallelic homeodomain (HD) locus and pheromone/receptor (P/R) locus that is only biallelic. These findings strongly reinforces tetrapolarity as the ancestral state of all basidiomycetes.

August 2015

New publication:

Almeida P, et al. A population genomics insight into the Mediterranean origins of wine yeast domestication.

DOI: 10.1111/mec.13341

In this paper, we analyze whole-genome sequences of 145 strains of S. cerevisiae to understand the population genomic structure and the ancestral demography of domesticated wine strains and newly identified oak-associated lineages from Europe and Asia. By analysing the relationship between the wine group a heretofore uncovered oak-associated Mediterranean S. cerevisiae population we found that this new population contains the wild genetic stock that gave rise to the domesticated wine yeasts. Remarkably, the divergence time estimates between these two populations agree with historical evidence for winemaking.

October 2015

New publication:

Gonçalves C, et al. Stepwise functional evolution in a fungal sugar transporter family.

DOI:10.1093/molbev/msv219

In this paper, we examined the evolutionary history of a unique family of fungal sugar facilitators (Ffz-like), which seem to have emerged recently from a larger family of drug antiporters, and are required for fructophilic metabolism in yeasts. A combination of phylogenetic and in vivo functional analyses allowed us to retrace important changes in function, while highlighting HGT as a key evolutionary mechanism for the onset of fructophily in about 100 yeast species that thrive in sugar rich environments.

September 2015

New publication:

Freitas LF, Barbosa R, Sampaio JP, etal. Starmera pilosocereana sp. nov., a yeast isolated from necrotic tissue of cacti in a sandy coastal dune ecosystem.

DOI: 10.1099/ijsem.0.000596

José P. Sampaio is an invited speaker at the 32nd international Specialized Symposium on Yeasts, 13-17 September 2015, Perugia, Italy.

José P. Sampaio

(Plenary lecture entitled "A population genomics view of Saccharomyces natural history and domesticaltion")

November 2015

A commentary on our paper concerning the origins of wine yeast domestication. appears in the News and Views section of Molecular Ecology:

Eberlein C, Leducq JB, Landry CR. 2015.The genomics of wild yeast populations sheds new light on the domestication of Man’s best (micro) friend. Molecular Ecology 24:5309-11.

Also check press coverage about this research published in the daily journal Público (in Portuguese)

New publication:

Yurkov AM, et al. Local climatic conditions constrain soil yeast diversity patterns in Mediterranean forests, woodlands and scrub biome

DOI:10.1093/femsyr/fov103

New publication:

Francesca N, et al. Jaminaea phylloscopi sp. nov. (Microstromatales), a basidiomycetous yeast isolated from migratory birds in the Mediterranean basin.

DOI:10.1099/ijsem.0.000801

New publication:

Pontes A, Röhl O, et al. Cystofilobasidium intermedium sp. nov. and Cystofilobasidium alribaticum f.a. sp. nov., isolated from Mediterranean forest soils.

DOI:doi: 10.1099/ijsem.0.000835

In this paper, multiple isolates belonging to the basidiomycetous genus Cystofilobasidium were obtained from forest soils in Serra da Arrábida Natural Park in Portugal. Phylogenetic analyses support the recognition of two novel species: Cystofilobasidium alribaticum f.a., sp. nov., which does not form hyphae even when different strains are crossed; and Cystofilobasidium intermedium which is self-fertile and forms mycelium with teliospores that upon germination give rise to slender basidia. The most remarkable physiological trait of the two novel species is their ability to grow at 35 ºC, a property not observed for remaining species of the genus.

January 2016

New publication:

Barbosa, et al. Evidence of Natural Hybridization in Brazilian Wild Lineages of Saccharomyces cerevisiae.

DOI:10.1093/gbe/evv263

In this paper, we report a candidate natural habitat of S. cerevisiae in South America (Brazil). Using whole-genome data, we uncover new lineages that appear to have as closest relatives the wild populations found in North America and Japan. We reveal the penetration of the wine genotype into the wild Brazilian population, which represents the first clear observation of the the impact of domesticated microbe lineages on the genetic structure of wild populations. Widespread introgression from the American S. paradoxus population into the newly uncovered Brazilian population is also evident, and this may have facilitated habitat transition and colonization of the tropical ecosystem.

June 2016

New publication:

Burgaud G, et al. Yamadazyma barbieri f.a. sp. nov., a novel ascomycetous anamorphic yeast isolated from a Mid-Atlantic Ridge hydrothermal site (-2300 m) and marine coastal waters

DOI:10.1099/ijsem.0.001239

June 2016

New publication:

David-Palma M, et al. Genetic Dissection of Sexual Reproduction in a Primary Homothallic Basidiomycete.

DOI:10.1371/journal.pgen.1006110

Some fungi are capable of sexual reproduction without the need for a sexually compatible partner, a behavior called homothallism. In this paper, we examined in detail the homothallic sexual cycle of the yeast Phaffia rhodozyma that belongs to the Basidiomycota, a lineage that is best known for containing mushroom-forming species. Here we harnessed available genetic tools to dissect the homothallic life cycle of this yeast and found that all genes normally involved in two-partner sexual reproduction are also required for self-fertility in P. rhodozyma. Based on the analysis of various deletion mutants, we were able to propose a model describing molecular interactions required to trigger sexual development. We also generated preferably outcrossing strains, which are potentially useful for further improvement of P. rhodozyma as a major producer of astaxanthin, an important pigment with industrial and pharmaceutical application.

October 2016

New publication:

Gonçalves M, et al. Distinct domestication trajectories in top-fermenting beer yeasts and wine yeasts.

DOI: 10.1016/j.cub.2016.08.040

How different are S. cerevisiae strains used to produce top-fermented (ale-type) beer and wine? In our study we show that on a genome-wide scale, they are clearly discernible, beer strains being more diverse and clustering according to beer type. Moreover, domestication signatures related to brewing were found to distinguish beer and wine strains.

December 2016

Well defended!

Congratulations to Pedro Almeida who defended his Ph.D. Thesis “Microbe Domestication and the Identification of the Wild Genetic Stock of Wine Yeasts” (see photos in the Gallery)

New publication:

Sampaio JP, etal. Taxonomy, diversity, and typing of brewing yeasts. In Brewing Microbiology: Current Research, Omics and Microbial Ecology (Edited by: Charles W. Bamforth and Nicholas A. Bokulich). Caister Academic Press, U.K. pp. 88-117.

DOI: 10.21775/9781910190616.04

New lab member:

Welcome to Ph.D. student Parichat Into, from Dr. Savitree Limtong lab, who also visited the lab.

February 2017

New publication:

Almeida P, et al. Adaptive divergence in wine yeasts and their wild relatives suggests a prominent role for introgressions and rapid evolution at non coding sites. Molecular Ecology 26:2167-2182.

DOI: 10.1111/mec.14071

New publication:

Gibson B, et al. New yeasts - new brews: modern approaches to brewing yeast design and development. FEMS Yeast Res. [Epub ahead of print]

DOI: 10.1093/femsyr/fox038

April 2017

José P. Sampaio was an invited speaker at the Taller Internacional de Levaduras Cerveceras, Buenos Aires, Argentina and at the II Jornadas Nacionales de Ciencia y Tecnología Cervecera, Bariloche, Argentina.

(Lecture entitled "Domesticación de levaduras cerveceras”)

June 2017

New publication:

Branco S, et al. Evolutionary strata on young mating-type chromosomes despite the lack of sexual antagonism. Proc Natl Acad Sci U S A [Epub ahead of print]

DOI: 10.1073/pnas.1701658114

New publication:

Coelho MA et al. Fungal Sex: The Basidiomycota. Microbiol Spectr. 5

DOI: 10.1128/microbiolspec.FUNK-0046-2016

Well defended!

Congratulations to Márcia Palma who defended hes Ph.D. Thesis “Elucidating the mating system of Phaffia rhodozyma, an astaxanthin-producing yeast with biotechnological potential” (see photos in the Gallery)

March 2017

New publication:

Peris D, et al. Hybridization and adaptive evolution of diverse Saccharomyces species for cellulosic biofuel production. Biotechnol Biofuels. 10:78.

DOI: 10.1186/s13068-017-0763-7

November 2016

New publication:

Mašínová T, Pontes A, et al. Libkindia masarykiana gen. nov. et sp. nov., Yurkovia mendeliana gen. nov. et sp. nov., and Leucosporidium krtinense f.a. sp. nov., isolated from temperate forest soils.

DOI: 10.1099/ijsem.0.001707

New publication:

Bellora N, et al. Comparative genomics provides new insights into the diversity, physiology, and sexuality of the only industrially exploited tremellomycete: Phaffia rhodozyma

DOI:10.1186/s12864-016-3244-7

February 2018

Accepted:

Gonçalves et al. Evidence for loss and reacquisition of alcoholic fermentation in a fructophilic yeast lineage.

April 2018

New students in the lab:

We are happy to host these enthusiastic students that are doing their undergraduate project in the Yeast Genomics Lab! From left to right: Francisco, José, Joana, Andreia, João, Francisca, Céline and André.

May 2018

PhD concluded - 10 May 2018:

Carla Gonçalves got her PhD after a brilliant defense of her thesis entitled “Unravelling the molecular basis of the evolution of fructophily in yeasts: a comparative genomics approach”