MGL

Our group is interested in studying Natural variation in yeast, particularly in ethanol-tolerant species and for this, we are isolating hundreds of new S. cerevisiaeS. uvarum, S. eubayanus, Lachancea and Hanseniespora isolates from Central and South Forests in Chile. With this, we aim to identify the genetic variants underlying phenotypic differences across isolates for beer (wine, mead, cider and any kind of) fermentation and obtain new isolates suitable for the fermentation industry (with genetics knowledge!)

Our Team

Francisco Cubillos

Francisco Cubillos

Principal Investigator
Antonio Molina

Antonio Molina

Technician
Valentina Abarca

Valentina Abarca

Research Assistant
Claudia Villegas

Claudia Villegas

Research Assistant
Jose Ruiz

Jose Ruiz

Research assistant
Carlos Villarroel

Carlos Villarroel

Postdoc - Bioinformatics
Wladimir Mardones

Wladimir Mardones

Postdoc - Experimental Evolution
Pablo Villarreal

Pablo Villarreal

Postdoc - Non-conventional yeast
Jennifer Molinet

Jennifer Molinet

Postdoc - Yeast Hybrids
Franco Vega

Franco Vega

PhD student - Biotechnology PhD Program, Universidad de Santiago de Chile
Tomás Peña

Tomás Peña

PhD student - Biotechnology PhD Program, Universidad de Santiago de Chile
Vasni Zavaleta

Vasni Zavaleta

PhD student - Biotechnology PhD Program, Universidad de Santiago de Chile
Pablo Quintrel

Pablo Quintrel

PhD student - Microbiology PhD Program, Universidad de Santiago de Chile
Macarena las Heras

Macarena las Heras

PhD student - Doctorado en Ciencias e Innovación en Medicina, UDD
Constanza Acuña

Constanza Acuña

Undergraduate student - Biochemistry, Universidad de Santiago de Chile
Sebastian Flores

Sebastian Flores

Undergraduate student - Biotechnology Engineering, Universidad de Santiago de Chile
Sebastian Olivares

Sebastian Olivares

Undergraduate student - Chemical Enginnering, Universidad de Santiago de Chile
Alonso Marquez

Alonso Marquez

Undergraduate student -

Would you like to be part of our team? We have PhD and Post-doc funding opportunities

Research Lines

Our interest can be dissected into:

–      Quantitative genetics to identify G x E interactions

–      Experimental evolution in native yeasts

–      Study the genetic diversity of Chilean Saccharomyces isolates

–      Produce new isolates and hybrids for the beer industry

Molecular Genetics Lab Manuscripts

2020

Urbina K*, Villarreal P*, Nespolo RF, Salazar R, Santander R, Cubillos FA. Volatile compound screening using HS-SPME-GC/MS on Saccharomyces eubayanus strains under low-temperature pilsner wort fermentation. Microorganisms 2020, 8(5), 755; https://doi.org/10.3390/microorganisms8050755 [Article]

Nespolo RF*, Villarroel CA*, Oporto CI, Tapia SM, Vega F, Urbina K, De Chiara M, Mozzachiodi S, Mikhalev E, Thompson D, Saenz-Agudelo P, Larrondo LF, Liti G, Cubillos FA. An Out-of-Patagonia migration explains the worldwide diversity and distribution of Saccharomyces eubayanus lineages. PLoS Genetics. 2020. 10.1371/journal.pgen.1008777 [Article].

Devia J., Bastias C., Kessi-Perez EI., Villarroel CA, Cubillos FA, Liti G., Martínez C & Salinas F. Transcriptional activity and protein levels for horizontally acquired genes in yeast reveal hallmarks of adaptation to fermentative environments. Frontiers in Genetics 2020. doi: 10.3389/fgene.2020.00293 [Article].       

Roberto F. Nespolo, Jaiber J. Solano-Iguaran, Rocío Paleo-López, Julian F. Quintero-Galvis, Francisco A. Cubillos, Francisco Bozinovic. Performance, genomic rearrangements and signatures of adaptive evolution: lessons from fermentative yeasts. Ecology and Evolution. 2020. Doi: 10.1002/ece3.6208.

Mardones W, Villarroel CA, Krogerus K, Tapia SM, Urbina K, Oporto CI, O’Donnell S, Minebois R, Nespolo R, Fischer G, Querol A, Gibson B, Cubillos FA*. Molecular profiling of beer wort fermentation diversity across natural Saccharomyces eubayanus isolates. Microb Biotechnol. 2020 Feb 25. doi: 10.1111/1751-7915.13545 [Article]

Libkind D, Peris D, Cubillos FA, Steenwyk JL, Opulente DA, Langdon QK, Rokas A, Hittinger CT. Into the wild: new yeast genomes from natural environments and new tools for their analysis. FEMS Yeast Res. 2020 Feb 3. pii: foaa008. doi: 10.1093/femsyr/foaa008 [Article]

​​2019

Oporto, C. I., Villarroel, C. A., Tapia, S. M., Garcia, V., and Cubillos, F. A. 2019. Distinct Transcriptional Changes in Response to Patulin Underlie Toxin Biosorption Differences in Saccharomyces Cerevisiae. Toxins (Basel). 11 [Article]​

Molinet, J., Cubillos, F. A., Salinas, F., Liti, G., and Martinez, C. 2019. Genetic variants of TORC1 signaling pathway affect nitrogen consumption in Saccharomyces cerevisiae during alcoholic fermentation. PLoS One. 14:e0220515 [Article]​

Cubillos, F. A., Gibson, B., Grijalva-Vallejos, N., Krogerus, K., and Nikulin, J. 2019. Bioprospecting for brewers: Exploiting natural diversity for naturally diverse beers. Yeast. [Article]​​​

2018

Brice C, Cubillos FA, Dequin S, Camarasa C, Martínez C 2018. Adaptability of the Saccharomyces cerevisiaeyeasts to wine fermentation conditions relies on their strong ability to consume nitrogen. PLoS 2018 Feb 12;13(2):e0192383. doi: 10.1371/journal.pone.0192383. eCollection 2018.[Pubmed]

Tapia, S. M., Cuevas, M., Abarca, V., Delgado, V., Rojas, V., García, V., Brice, C., Martínez, C., Salinas, F., Larrondo, L. F., and Cubillos, F. A. 2018. GPD1 and ADH3 natural variants underlie glycerol yield differences in wine fermentation. Front. Microbiol. 9:1–13 [Article]​

2017

​Quispe X, Tapia SM, Villarroel C, Oporto C, Abarca V, García V, Martínez C, Cubillos FA. 2017. Genetic basis of mycotoxin susceptibility differences between budding yeast isolates. Scientific Reports. 2017 Aug 23;7(1):9173. doi: 10.1038/s41598-017-09471-z.
[Pubmed]

Godoy L, Silva-Moreno E, Mardones W, Guzman D, Cubillos FA, Ganga A. 2017. Genomics Perspectives on Metabolism, Survival Strategies, and Biotechnological Applications of Brettanomyces bruxellensisLAMAP2480. J Mol Microbiol Biotechnol. 2017 Jun 9;27(3):147-158.
[Pubmed]

Cubillos FA, Brice C, Molinet J, Tisné S, Abarca V, Tapia SM, Oporto C, García V, Liti G & Martínez C. 2017. Identification of nitrogen consumption genetic variants in yeast through QTL mapping and Bulk segregant RNA-seq analyses. G3(Bethesda). 2017 Jun 7;7(6):1693-1705.
[Pubmed]

Thompson DA & Cubillos FA. 2017. Natural gene expression variation studies in yeast. Yeast Jan;34(1):3-17.
[Pubmed]

​​2016

Cubillos F.A.Exploiting budding yeast natural variation for industrial processes. 2016. Current Genetics. Nov;62(4):745-75.
[Pubmed]

Kessi-Pérez EI, Araos S, García V, Salinas F, Abarca V, Larrondo LF, Martínez C & Cubillos FA. 2016. RIM15antagonistic pleiotropy is responsible for differences in fermentation and stress response kinetics in budding yeast. FEMS Yeast Research. pii: fow021. Epub 2016 Mar 4.
[Pubmed]

Salinas F, de Boer CG, Abarca V, García V, Cuevas M, Araos S, Larrondo LF, Martínez C, Cubillos FA. 2016. Natural variation in non-coding regions underlying phenotypic diversity in budding yeast. Scientific Reports, srep21849.
[Pubmed]

2014
Cubillos FA*, Stegle O, Grondin C, Canut M, Tisne S, Gy I & Loudet O. 2014. Extensive cis-Regulatory Variation Robust to Environmental Perturbation in Arabidopsis. Plant Cell 26(11):4298-4310.
[Pubmed]

Valdes J, Tapia P, Cepeda P, Varela J, Godoy L, Cubillos FA, Silva E, Martínez C & Ganga A. Draft genome sequence and transcriptome analysis of the wine spoilage yeast Dekkera bruxellensisLAMAP2480 provides insights into genetic diversity, metabolism and survival. FEMS microbiology letters361(2): 104-106.
[Pubmed]

Jara M*, Cubillos FA*, García V, Salinas F, Aguilera O, Liti G & Martínez C. 2014. Natural variation in the central nitrogen metabolism in fermenter yeasts. PLoS ONE9(1): e86533.
[Pubmed]

Coustham V, Vlad D, Deremetz A, Gy I, Cubillos FA, Kerdaffrec E, Loudet O & Bouché N. 2014. SHOOT GROWTH1 Maintains Arabidopsis Epigenomes by Regulating IBM1. PLoS ONE9  (1), e84687.
[Pubmed]

2013
Cubillos FA*, Parts L*, Salinas F, Bergström A, Scovacicricchi E, Zia A, Illingworth CJ, Mustonen V, Ibstedt S, Warringer J, Louis EJ, Durbin R†& Liti G†. 2013. High-Resolution Mapping of Complex Traits with a Four-Parent Advanced Intercross Yeast Population. Genetics.195(3):1141-55
[Pubmed]

Liti G, Nguyen Ba A, Blythe M, Müller C, Bergström A, Cubillos FA, Dafhnis-Calas F, Khoshraftar S, Malla S, Mehta N, Siow C, Warringer J, Moses A, Louis EJ*& Nieduszynski C*. 2013. High Quality de novo Sequencing and Assembly of the Saccharomyces arboricolusgenome. BMC Genomics.14 (1), 69.
[Pubmed].

2012

Salinas F, Cubillos FA, Soto D, García V, Bergström A, Warringer J, GangaA, Louis EJ, Liti G* & Martinez C*. 2012. The Genetic Basis of Natural Variation in Oenological Traits in Saccharomyces cerevisiae. PLoS ONE. 7 (11), e49640.
​[Pubmed]

Cubillos FA*, Yansouni J*, Khalili H, Balzergue S, Elftieh S, Martin-Magniette ML, Serrand Y, Lepiniec L, Baud S, Dubreucq B, Renou JP, Camilleri C§& Loudet O§. 2012. Expression variation in connected recombinant populations of Arabidopsis thalianahighlights distinct transcriptome architectures. BMC Genomics. Mar 27;13:117.
[Pubmed]

Zörgö E, Gjuvsland A, Cubillos FA, Louis EJ, Liti G, Blomberg A, Omholt SW & Warringer J. 2012. Life history shapes trait heredity by promoting accumulation of loss-of-function alleles in yeast.Molecular Biology Evolution.Jul;29(7):1781-9.
[Pubmed]

Cubillos FA, Coustham V & Loudet O. 2012. Lessons from eQTL mapping studies: non-coding regions and their role behind natural phenotypic variation in plants. Current Opinion in Plant Biology. Apr;15(2):192-8.
[Pubmed]

2011

Warringer J, Zörgö E, Cubillos FA, Zia A, Gjuvsland A, Simpson J, Forsmark A, Durbin R, Omholt S, Louis EJ, Liti G, Moses A & Blomberg A. 2011. Trait variation in yeast is defined by population history. PLoS GeneticsJun;7(6):e1002111.
[Pubmed]

Parts L, Cubillos FA, Warringer J, Jain K, Salinas F, Bumpstead S, Molin M, Zia A, Simpson J, Quail M, Moses A, Louis EJ, Durbin R & Liti G. 2011. Revealing the genetic structure of a trait by sequencing a population under selection. Genome ResearchJul;21(7):1131-8. [Pubmed]

Cubillos FA, Billi E, Zörgö E, Parts L, Fargier P, Omholt S, Blomberg A, Warringer J, Louis EJ & Liti G. 2011. Assessing the complex architecture of polygenic traits in diverged yeast populations. Molecular Ecology, Apr;20(7):1401-13.
[Pubmed]

2009

Cubillos FA, Louis EJ, Liti G*. 2009. Generation of a Large Set of Genetically Tractable Haploid and Diploid SaccharomycesStrains. FEMS Yeast Research. 9, 1217-1225.
[Pubmed]

Liti G*, Haricharan S, Cubillos FA, Tierney AL, Sharp S, Bertuch AA, Parts L, Bailes E, Louis EJ. 2009. Segregating YKU80and TLC1Alleles Underlying Natural Variation in Telomere Properties in Wild Yeast. PLoS Genetics.5 (9); e1000659.
[Pubmed]

Cubillos FA, Vásquez C, Faugeron S, Ganga A, Martínez C. 2009. Self-fertilization is the main sexual reproduction mechanism in native wine yeast populations.FEMS Microbiology Ecology. Jan;67(1):162-70.
[Pubmed]

Current Grants

January 2020 – January 2022: Networking Grant CONICYT-PCI REDES for International Scientific Cooperation between iBio – Wisconsin Energy Institute (US) and Delft University Technology (Netherlands). ‘The SynVAR Collaborative Network: Yeast genetics for Synthetic Biology and Natural Variation advances in native Patagonian yeasts’. Principal Investigator.

January 2019 – January 2022: Research Grant for International Scientific Cooperation ECOS/CONICYT C18B03 ‘Genomic and physiological Characterization of ethanol-producing yeast populations from Patagonia’ between Universidad de Santiago de Chile and Sorbonne Université. Principal Researcher. 

May 2018 – May 2020 . FIC Región de los Rios. ‘Hacia la denominación de origen de la cerveza de Los Ríos: descubriendo una levadura nativa’.

April 2018 to date. FONDECYT Regular 1180161 ‘Decoding the genomic and phenomic complexity of the cryotolerant yeast Saccharomyces eubayanus’.

January 2018 – to date: Millennium Institute for Integrative and Synthetic Biology (MIISSB).

Resources

Yeast collections are available upon request. Please contact Valentina Abarca or Francisco A. Cubillos