Cubillos Riffo Francisco Alberto
Dr. Francisco A Cubillos obtained his PhD in 2010 at the University of Nottingham, UK, under the supervision of Prof. Edward J Louis and Dr. Gianni Liti. The research carried out by Cubillos during his PhD studies were focused in understanding the genetic architecture of complex traits in a model organism, like yeast (Saccharomyces cerevisiae). The major finding was that in most cases the genetic background interaction together with the environment specifically determined the variants underlying differences between individuals. Moreover, it was seen that genotypes differentially respond to growth conditions due to independent genomic regions responsible for the phenotypic differences. This study represents the first one in demonstrating the complex G x E interactions in yeast and is being highly cited nowadays. In paralalell, an active collaboration with Dr. Warringer from University of Gothenburg lead to a series of higly cited papers describing the phenotypic landscape in yeast, were Dr Cubillos had a crucial role in identifying the genes responsible for those phenotypic differences and its subsequent validation. Since then, Dr Cubillos has been involved in several research projects in yeast with collaborators around the world aiming to decipher the genetics behind phenotypic variation
After completing his PhD, Dr Cubillos moved to the INRA-Versailles Research Centre in Paris, France to carry out his Post-Doctoral studies in the model organism Arabidosis Thaliana in the laboratory of Dr. Olivier Loudet. Was during this time, that Dr Cubillos began to work in natural variation in expression traits to understand the role of non-coding regions in plant adaptation to extreme environments, particularly, drought stress. In this context, several ‘Omics’ approeaches were used, like RNA-Seq, DNA-seq and the sequencing of epigenomes in order to dissect the molecular bases behind expression differences between natural accessions. During this time, Dr Cubillos obtained a returning grant awarded by CONICYT to return to Chile and establish his own research group.
The current research line lead by Dr. Cubillos is focused in natural genetic and phenotypic variation in S. eubayanus, one of the lager yeast parents. For this, Dr Cubillos has obtained several research and international collaboration grants. The current grants by Dr Cubillos aim to isolate and characterise strains at the molecular level for biotechnological applications.
1. 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
2. Thompson DA & Cubillos FA. 2016. Natural gene expression variation studies in yeast. Yeast. 2017 Jan;34(1):3-17
3. Cubillos F.A. Exploiting budding yeast natural variation for industrial processes. 2016. Current Genetics. Nov;62(4):745-75.
4. Kessi-Pérez EI, Araos S, García V, Salinas F, Abarca V, Larrondo LF, Martínez C & Cubillos FA. 2016. RIM15 antagonistic pleiotropy is responsible for differences in fermentation and stress response kinetics in budding yeast. FEMS Yeast Research. pii: fow021. Epub 2016 Mar 4.
5. 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.
6. 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
7. 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 letters 361(2): 104-106.
8. 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 ONE 9(1): e86533.
9. 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 ONE 9 (1), e84687
10. 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.
11. 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 arboricolus genome. BMC Genomics. 14 (1), 69.
12. Salinas F, Cubillos FA, Soto D, García V, Bergström A, Warringer J, Ganga A, Louis EJ, Liti G* & Martinez C*. 2012. The Genetic Basis of Natural Variation in Oenological Traits in Saccharomyces cerevisiae. PLoS ONE. 7 (11), e49640.
13. 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 thaliana highlights distinct transcriptome architectures. BMC Genomics. Mar 27;13:117.
14. 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.
15. 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.
16. 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 Genetics. Jun;7(6):e1002111.
17. 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 Research, Jul;21(7):1131-8.
18. 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.
19. Cubillos FA, Louis EJ, Liti G*. 2009. Generation of a Large Set of Genetically Tractable Haploid and Diploid Saccharomyces Strains. FEMS Yeast Research. 9, 1217-1225.
20. Liti G*, Haricharan S, Cubillos FA, Tierney AL, Sharp S, Bertuch AA, Parts L, Bailes E, Louis EJ. 2009. Segregating YKU80 and TLC1 Alleles Underlying Natural Variation in Telomere Properties in Wild Yeast. PLoS Genetics. 5 (9); e1000659.
21. 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
2016. Beca Santander Iberoamericana para estancia en España en laboratorio de José Manuel Guillamón, IATA-CSIC, Valencia.
2010. Premio ‘University Endowed Postgraduate Prize 2009/2010’ para los 10 alumnos más sobresalientes del programa PhD, University of Nottingham.
2010. Beca completa para asistir al Congreso ‘ECFG, 10th International European Conference on Fungal Genetics’, Amsterdam, Holanda.
2009. Beca Heredity Fieldwork de la Sociedad de Genética, Reino Unido para realizar pasantía en ‘High throughput phenotyping’ en el laboratorio de Anders Blomberg, Gotemburgo, Suecia
2007. Beca Chile para estudios de doctorado en el extranjero (Universidad de Nottingham, Reino Unido) otorgada por el Gobierno de Chile.
April 2017 – to date: Proyecto Basal USA 1555 - Vridei O21771CR_CONT Universidad de Santiago de Chile. Principal Investigator.
January 2017 – to date: Grant INACH Regular RT_09_16 (2017-2020). ‘Biochemical and molecular responses disclose mechanisms of Antarctic macroalgae to thrive under Climate Change’. Co-PI.
May 2016 to date: Networking Grant REDES 150077 for International Scientific Cooperation Universidad de Santiago de Chile – INRA Montpellier, France with Prof Sylvie Dequin. ‘Applied yeast genetics for high quality food products’. Principal Investigator.
January 2016 to date: Research Grant Millennium Nucleus in Synthetic Fungi Biology. Associate Researcher.
May 2015 to date: Research Grant FONDECYT Regular ‘Identification of natural genetic variants underlying nitrogen assimilation diversity in yeast’, Co-Principal Investigator.
October 2014 to date: Research Grant FONDECYT de Iniciación ‘Quantitative genetic analysis of the response to mycotoxins in yeast’, Principal Investigator.
January 2014 to December 2016: Research Grant for International Scientific Cooperation ECOS/CONICYT –2013 ‘Identification of allelic variants underlying Nitrogen Metabolism in yeast through an integrative BS-RNA seq approach’. Principal Investigator.
September 2013 to September 2015: Research Grant Gobierno Regional de Atacama ‘Establecimiento de sistemas sustentables para el control del proceso de producción de Vino Pajarete de la Provincia del Huasco, para fortalecer su identidad local’. Co-Principal Investigator.
May 2013 to May 2015: Research Grant ‘Study of the regulatory variants underlying natural diversity in Saccharomyces cerevisiae’ CONICYT-PAI Program ‘Apoyo al Retorno de Investigadores/as desde el Extranjero – Convocatoria 2012’. Principal Investigator.
Director de tesis:
5 tesis de pregrado y 1 tesis de post-grado