Population genomics and complex traits

Gianni LITI, Research Director, DR1 CNRS
  • Domestication reprogrammed the budding yeast life cycle

    De Chiara M, Barré BP, Persson K, Irizar A, Vischioni C, Khaiwal S, Stenberg S, Amadi OC, Žun G, Doberšek K, Taccioli C, Schacherer J, Petrovič U, Warringer J, Liti G.
    Nature Ecology & Evolution. doi: 10.1038/s41559-022-01671-9.
    PMID: 35210580

  • Aborting meiosis allows recombination in sterile diploid yeast hybrids

    Mozzachiodi S, Tattini L, Llored A, Irizar A, Škofljanc N, D'Angiolo M, De Chiara M, Barré BP, Yue JX, Lutazi A, Loeillet S, Laureau R, Marsit S, Stenberg S, Albaud B, Persson K, Legras JL, Dequin S, Warringer J, Nicolas A, Liti G.
    Nature Communications. 2021 Nov 12;12(1):6564. doi: 10.1038/s41467-021-26883-8.
    PMID: 34772931

  • A yeast living ancestor reveals the origin of genomic introgressions

    D'Angiolo M, De Chiara M, Yue JX, Irizar A, Stenberg S, Persson K, Llored A, Barré B, Schacherer J, Marangoni R, Gilson E, Warringer J, Liti G@
    Nature. 2020 Nov;587(7834):420-425.
    PMID: 33177709

  • Discordant Evolution of Mitochondrial and Nuclear Yeast Genomes at Population Level

    De Chiara M, Friedrich A, Barré B, Breitenbach M, Schacherer J@, Liti G@

    BMC Biology. 2020; 18(1):49

    PMID: 32393264

  • Intragenic Repeat Expansion in the Cell Wall Protein Gene HPF1 Controls Yeast Chronological Aging

    Barré BP@, Hallin J, Yue JX, Persson K, Mikhalev E, Irizar A, Thompson D, Molin M, Warringer J, Liti G@

    Genome Research. 2020; 30(5):697-710

    PMID: 32277013

  • Accurate tracking of the mutational landscape of diploid hybrid genomes

    Tattini L, Tellini N, Mozzachiodi S, D'Angiolo M, Loeillet S, Nicolas A, Liti G.

    Mol Biol Evol. 2019. [Epub ahead of print]

    PMID: 31397846
  • simuG: a general-purpose genome simulator

    Yue JX, Liti G.

    Bioinformatics. 2019. [Epub ahead of print]
    PMID: 31116378

  • Shared molecular targets confer resistance over short and long evolutionary timescales

    Li J, Vázquez-García I, Persson K, González A, Yue JX, Barré B, Hall MN, Long A, Warringer J, Mustonen V, Liti G.

    Mol Biol Evol. 2019

    PMID: 30657986

  • Tetrad analysis in plants and fungi finds large differences in gene conversion rates but no GC bias

    Liu H, Huang J, Sun X, Li J, Hu Y, Yu L, Liti G, Tian D, Hurst LD, Yang S.

    Nat Ecol Evol. 2018 2:164-173.

    PMID: 29158556

  • Genome evolution across 1,011 Saccharomyces cerevisiae isolates

    Peter J*, De Chiara M*, Friedrich A, Yue JX, Pflieger D, Bergström A, Sigwalt A, Barre B, Freel K, Llored A, Cruaud C, Labadie K, Aury JM, Istace B, Lebrigand K, Barbry P, Engelen S, Lemainque A, Wincker P, Liti G@, Schacherer J@.

    Nature. 2018 556:339-344.
    PMID: 29643504

    *co-first authors, @co-senior authors

  • Long-read sequencing data analysis for yeasts

    Yue JX, Liti G.

    Nat Protoc. 2018 13:1213-1231.

    PMID: 29725120


  • Yeast chromosome numbers minimized using genome editing

    Liti G

    Nature. 2018; 560:317-318.

    PMID: 30097656


  • de novo assembly and population genomic survey of natural yeast isolates with the Oxford Nanopore MinION sequencer

    Istace B, Friedrich A, d'Agata L, Faye S, Payen E, Beluche O, Caradec C, Davidas S, Cruaud C, Liti G, Lemainque A, Engelen S, Wincker P, Schacherer J, Aury JM.

    Gigascience. 2017 Feb 1;6(2):1-13. doi: 10.1093/gigascience/giw018.
    PMID: 28369459

  • Identification of Nitrogen Consumption Genetic Variants in Yeast Through QTL Mapping and Bulk Segregant RNA-Seq Analyses

    Cubillos FA, Brice C, Molinet J, Tisné S, Abarca V, Tapia SM, Oporto C, García V, Liti G, Martínez C.

    G3 (Bethesda). 2017 Jun 7;7(6):1693-1705. doi: 10.1534/g3.117.042127.

    PMID: 28592651

  • The genetic architecture of low-temperature adaptation in the wine yeast Saccharomyces cerevisiae

    García-Ríos E, Morard M, Parts L, Liti G, Guillamón JM.

    BMC Genomics. 2017 Feb 14;18(1):159. doi: 10.1186/s12864-017-3572-2.

    PMID: 28196526

  • Mismatch Repair Incompatibilities in Diverse Yeast Populations

    Bui DT, Friedrich A, Al-Sweel N, Liti G, Schacherer J, Aquadro CF, Alani E.

    Genetics. 2017 Apr;205(4):1459-1471. doi: 10.1534/genetics.116.199513. Epub 2017 Feb 13.

    PMID: 28193730

  • Contrasting evolutionary genome dynamics between domesticated and wild yeasts

    Yue JX, Li J, Aigrain L, Hallin J, Persson K, Oliver K, Bergström A, Coupland P, Warringer J, Lagomarsino MC, Fischer G, Durbin R, Liti G.

    Nat Genet. 2017 Jun;49(6):913-924. doi: 10.1038/ng.3847. Epub 2017 Apr 17.

    PMID: 28416820

  • Clonal Heterogeneity Influences the Fate of New Adaptive Mutations

    Vázquez-García I@, Salinas F, Li J, Fischer A, Barré B, Hallin J, Bergström A, Alonso-Perez E, Warringer J, Mustonen V@, Liti G@.

    Cell Rep. 2017 ;21(3):732-744.

    PMID: 29045840

    @co-corresponding authors


  • Powerful decomposition of complex traits in a diploid model

    Hallin J, Märtens K, Young AI, Zackrisson M, Salinas F, Parts L, Warringer J, Liti G.

    Nat Commun. 2016 Nov 2;7:13311. doi: 10.1038/ncomms13311.

    PMID: 27804950

  • ISSY32 Highlights

    Liti G, Buzzini P.

    Yeast. 2016 Jul;33(7):241-2. doi: 10.1002/yea.3176.

    PMID: 27383392

  • Ploidy influences the functional attributes of de novo lager yeast hybrids

    Krogerus K, Arvas M, De Chiara M, Magalhães F, Mattinen L, Oja M, Vidgren V, Yue JX, Liti G, Gibson B.

    Appl Microbiol Biotechnol. 2016 Aug;100(16):7203-22. doi: 10.1007/s00253-016-7588-3.

    PMID: 27183995

  • Predicting quantitative traits from genome and phenome with near perfect accuracy

    Märtens K, Hallin J, Warringer J, Liti G, Parts L.

    Nat Commun. 2016 May 10;7:11512. doi: 10.1038/ncomms11512.

    PMID: 27160605

  • Extensive Recombination of a Yeast Diploid Hybrid through Meiotic Reversion

    Laureau R, Loeillet S, Salinas F, Bergström A, Legoix-Né P, Liti G, Nicolas A.

    PLoS Genet. 2016 Feb 1;12(2):e1005781. doi: 10.1371/journal.pgen.1005781.

    PMID: 26828862

  • Yeast 2.0: a new chapter

    Liti G.

    Yeast. 2016 Jan;33(1):3-4. doi: 10.1002/yea.3143.

    PMID: 26756884


  • Concerted evolution of life stage performances signals recent selection on yeast nitrogen use

    Ibstedt S, Stenberg S, Bagés S, Gjuvsland AB, Salinas F, Kourtchenko O, Samy JK, Blomberg A, Omholt SW, Liti G, Beltran G, Warringer J.

    Mol Biol Evol. 2015 Jan;32(1):153-61. doi: 10.1093/molbev/msu285.

    PMID: 25349282

  • Deletion of the Saccharomyces cerevisiae ARO8 gene, encoding an aromatic amino acid transaminase, enhances phenylethanol production from glucose

    Romagnoli G, Knijnenburg TA, Liti G, Louis EJ, Pronk JT, Daran JM.

    Yeast. 2015 Jan;32(1):29-45. doi: 10.1002/yea.3015.

    PMID: 24733517

  • Elucidating the molecular architecture of adaptation via evolve and resequence experiments

    Long A, Liti G, Luptak A, Tenaillon O.

    Nat Rev Genet. 2015 Oct;16(10):567-82. doi: 10.1038/nrg3937.

    PMID: 26347030

  • The fascinating and secret wild life of the budding yeast S. cerevisiae

    Liti G.

    Elife. 2015 Mar 25;4. doi: 10.7554/eLife.05835.

    PMID: 25807086

  • ATG18 and FAB1 are involved in dehydration stress tolerance in Saccharomyces cerevisiae

    López-Martínez G, Margalef-Català M, Salinas F, Liti G, Cordero-Otero R.

    PLoS One. 2015 Mar 24;10(3):e0119606. doi: 10.1371/journal.pone.0119606.

    PMID: 25803831

  • Saccharomyces pastorianus: genomic insights inspiring innovation for industry

    Gibson B, Liti G.

    Yeast. 2015 Jan;32(1):17-27. doi: 10.1002/yea.3033.

    PMID: 25088523

  • A high-definition view of functional genetic variation from natural yeast genomes

    Bergström A, Simpson JT, Salinas F, Barré B, Parts L, Zia A, Nguyen Ba AN, Moses AM, Louis EJ, Mustonen V, Warringer J, Durbin R, Liti G.

    Mol Biol Evol. 2014 Apr;31(4):872-88. doi: 10.1093/molbev/msu037

    PMID: 24425782

  • Phenotypic characterisation of Saccharomyces spp. yeast for tolerance to stresses encountered during fermentation of lignocellulosic residues to produce bioethanol

    Wimalasena TT, Greetham D, Marvin ME, Liti G, Chandelia Y, Hart A, Louis EJ, Phister TG, Tucker GA, Smart KA.

    Microb Cell Fact. 2014 Mar 27;13(1):47. doi: 10.1186/1475-2859-13-47.

    PMID: 24670111

  • Filling annotation gaps in yeast genomes using genome-wide contact maps

    Marie-Nelly H, Marbouty M, Cournac A, Liti G, Fischer G, Zimmer C, Koszul R.

    Bioinformatics. 2014 Aug 1;30(15):2105-13. doi: 10.1093/bioinformatics/btu162.

    PMID: 24711652

  • A set of genetically diverged Saccharomyces cerevisiae strains with markerless deletions of multiple auxotrophic genes

    Louvel H, Gillet-Markowska A, Liti G, Fischer G.

    Yeast. 2014 Mar;31(3):91-101. doi: 10.1002/yea.2991.

    PMID: 24288298

  • Standing genetic variation drives repeatable experimental evolution in outcrossing populations of Saccharomyces cerevisiae

    Burke MK, Liti G, Long AD.

    Mol Biol Evol. 2014 Dec;31(12):3228-39. doi: 10.1093/molbev/msu256.

    PMID: 25172959

  • Mapping genetic variants underlying differences in the central nitrogen metabolism in fermenter yeasts

    Jara M, Cubillos FA, García V, Salinas F, Aguilera O, Liti G, Martínez C.

    PLoS One. 2014 Jan 21;9(1):e86533. doi: 10.1371/journal.pone.0086533.

    PMID: 24466135

  • High-quality genome (re)assembly using chromosomal contact data

    Marie-Nelly H, Marbouty M, Cournac A, Flot JF, Liti G, Parodi DP, Syan S, Guillén N, Margeot A, Zimmer C, Koszul R.

    Nat Commun. 2014 Dec 17;5:5695. doi: 10.1038/ncomms6695.

    PMID: 25517223

  • Kinetochore assembly and heterochromatin formation occur autonomously in Schizosaccharomyces pombe

    Brown WR, Thomas G, Lee NC, Blythe M, Liti G, Warringer J, Loose MW.

    Proc Natl Acad Sci U S A. 2014 Feb 4;111(5):1903-8. doi: 10.1073/pnas.1216934111.

    PMID: 2444988

  • High quality de novo sequencing and assembly of the Saccharomyces arboricolus genome

    Liti G, Nguyen Ba AN, Blythe M, Müller CA, Bergström A, Cubillos FA, Dafhnis-Calas F, Khoshraftar S, Malla S, Mehta N, Siow CC, Warringer J, Moses AM, Louis EJ, Nieduszynski CA.

    BMC Genomics. 2013 Jan 31;14:69. doi: 10.1186/1471-2164-14-69.

    PMID: 23368932

  • Recurrent rearrangement during adaptive evolution in an interspecific yeast hybrid suggests a model for rapid introgression

    Dunn B, Paulish T, Stanbery A, Piotrowski J, Koniges G, Kroll E, Louis EJ, Liti G, Sherlock G, Rosenzweig F.

    PLoS Genet. 2013 Mar;9(3):e1003366. doi: 10.1371/journal.pgen.1003366.

    PMID: 23555283

  • Ancient evolutionary trade-offs between yeast ploidy states

    Zörgö E, Chwialkowska K, Gjuvsland AB, Garré E, Sunnerhagen P, Liti G, Blomberg A, Omholt SW, Warringer J.

    PLoS Genet. 2013 Mar;9(3):e1003388. doi: 10.1371/journal.pgen.1003388.

    PMID: 23555297

  • Inferring genome-wide recombination landscapes from advanced intercross lines: application to yeast crosses

    Illingworth CJ, Parts L, Bergström A, Liti G, Mustonen V.

    PLoS One. 2013 May 2;8(5):e62266. doi: 10.1371/journal.pone.0062266.

    PMID: 23658715

  • ICY 2012 highlights

    Abbas C, Kurtzman C, Liti G.

    Yeast. 2013 Aug;30(8):293-4. doi: 10.1002/yea.2966.

    PMID: 23922150

  • High-resolution mapping of complex traits with a four-parent advanced intercross yeast population

    Cubillos FA, Parts L, Salinas F, Bergström A, Scovacricchi E, Zia A, Illingworth CJ, Mustonen V, Ibstedt S, Warringer J, Louis EJ, Durbin R, Liti G.

    Genetics. 2013 Nov;195(3):1141-55. doi: 10.1534/genetics.113.155515.

    PMID: 24037264

  • 'New' yeasts for a new Yeast

    Armstrong J, Davis D, Liti G, Oliver S.

    Yeast. 2012 Oct;29(10):407. doi: 10.1002/yea.2923.

    PMID: 23065797

  • Advances in quantitative trait analysis in yeast

    Liti G, Louis EJ.

    PLoS Genet. 2012;8(8):e1002912. doi: 10.1371/journal.pgen.1002912.

    PMID: 22916041

  • Surprisingly diverged populations of Saccharomyces cerevisiae in natural environments remote from human activity

    Wang QM, Liu WQ, Liti G, Wang SA, Bai FY.

    Mol Ecol. 2012 Nov;21(22):5404-17. doi: 10.1111/j.1365-294X.2012.05732.x.

    PMID: 22913817

  • Apparent ploidy effects on silencing are post-transcriptional at HML and telomeres in Saccharomyces cerevisiae

    McLaughlan JM, Liti G, Sharp S, Maslowska A, Louis EJ.

    PLoS One. 2012;7(7):e39044. doi: 10.1371/journal.pone.0039044.

    PMID: 22792162

  • Life history shapes trait heredity by accumulation of loss-of-function alleles in yeast

    Zörgö E, Gjuvsland A, Cubillos FA, Louis EJ, Liti G, Blomberg A, Omholt SW, Warringer J.

    Mol Biol Evol. 2012 Jul;29(7):1781-9. doi: 10.1093/molbev/mss019.

    PMID: 22319169

  • Quantifying selection acting on a complex trait using allele frequency time series data

    Illingworth CJ, Parts L, Schiffels S, Liti G, Mustonen V.

    Mol Biol Evol. 2012 Apr;29(4):1187-97. doi: 10.1093/molbev/msr289.

    PMID: 22114362

  • The genetic basis of natural variation in oenological traits in Saccharomyces cerevisiae

    Salinas F, Cubillos FA, Soto D, Garcia V, Bergström A, Warringer J, Ganga MA, Louis EJ, Liti G, Martinez C.

    PLoS One. 2012;7(11):e49640. doi: 10.1371/journal.pone.0049640.

    PMID: 23185390

  • Trait variation in yeast is defined by population history

    Warringer J, Zörgö E, Cubillos FA, Zia A, Gjuvsland A, Simpson JT, Forsmark A, Durbin R, Omholt SW, Louis EJ, Liti G, Moses A, Blomberg A.

    PLoS Genet. 2011 Jun;7(6):e1002111. doi: 10.1371/journal.pgen.1002111.

    PMID: 21698134

  • A Geographically Diverse Collection of Schizosaccharomyces pombe Isolates Shows Limited Phenotypic Variation but Extensive Karyotypic Diversity

    Brown WR, Liti G, Rosa C, James S, Roberts I, Robert V, Jolly N, Tang W, Baumann P, Green C, Schlegel K, Young J, Hirchaud F, Leek S, Thomas G, Blomberg A, Warringer J.

    G3 (Bethesda). 2011 Dec;1(7):615-26. doi: 10.1534/g3.111.001123.

    PMID: 22384373

  • The rise of yeast population genomics

    Liti G, Schacherer J.

    C R Biol. 2011 Aug-Sep;334(8-9):612-9. doi: 10.1016/j.crvi.2011.05.009.

    PMID: 21819942

  • Revealing the genetic structure of a trait by sequencing a population under selection

    Parts L, Cubillos FA, Warringer J, Jain K, Salinas F, Bumpstead SJ, Molin M, Zia A, Simpson JT, Quail MA, Moses A, Louis EJ, Durbin R, Liti G.

    Genome Res. 2011 Jul;21(7):1131-8. doi: 10.1101/gr.116731.110.

    PMID: 21422276

  • From sequence to function: Insights from natural variation in budding yeasts

    Nieduszynski CA, Liti G.

    Biochim Biophys Acta. 2011 Oct;1810(10):959-66. doi: 10.1016/j.bbagen.2011.02.004.

    PMID: 21320572

  • Assessing the complex architecture of polygenic traits in diverged yeast populations

    Cubillos FA, Billi E, Zörgö E, Parts L, Fargier P, Omholt S, Blomberg A, Warringer J, Louis EJ, Liti G.

    Mol Ecol. 2011 Apr;20(7):1401-13. doi: 10.1111/j.1365-294X.2011.05005.x.

    PMID: 21261765

  • Segregating YKU80 and TLC1 alleles underlying natural variation in telomere properties in wild yeast

    Liti G, Haricharan S, Cubillos FA, Tierney AL, Sharp S, Bertuch AA, Parts L, Bailes E, Louis EJ.

    PLoS Genet. 2009 Sep;5(9):e1000659. doi: 10.1371/journal.pgen.1000659.

    PMID: 19763176

  • Population genomics of domestic and wild yeasts

    Liti G, Carter DM, Moses AM, Warringer J, Parts L, James SA, Davey RP, Roberts IN, Burt A, Koufopanou V, Tsai IJ, Bergman CM, Bensasson D, O'Kelly MJ, van Oudenaarden A, Barton DB, Bailes E, Nguyen AN, Jones M, Quail MA, Goodhead I, Sims S, Smith F, Blomberg A, Durbin R, Louis EJ.

    Nature. 2009 Mar 19;458(7236):337-41. doi: 10.1038/nature07743.

    PMID: 19212322

  • Generation of a large set of genetically tractable haploid and diploid Saccharomyces strains

    Cubillos FA, Louis EJ, Liti G.

    FEMS Yeast Res. 2009 Dec;9(8):1217-25. doi: 10.1111/j.1567-1364.2009.00583.x.

    PMID: 19840116

  • Sequence diversity, reproductive isolation and species concepts in Saccharomyces

    Liti G, Barton DB, Louis EJ.

    Genetics. 2006 Oct;174(2):839-50. Epub 2006 Sep 1.

    PMID: 16951060

  • Inferences of evolutionary relationships from a population survey of LTR-retrotransposons and telomeric-associated sequences in the Saccharomyces sensu stricto complex

    Liti G, Peruffo A, James SA, Roberts IN, Louis EJ.

    Yeast. 2005 Feb;22(3):177-92.

    PMID: 15704235

  • Yeast evolution and comparative genomics

    Liti G, Louis EJ.

    Annu Rev Microbiol. 2005;59:135-53.

    PMID: 15877535

  • Analysis of a Ty1-less variant of Saccharomyces paradoxus: the gain and loss of Ty1 elements

    Moore SP, Liti G, Stefanisko KM, Nyswaner KM, Chang C, Louis EJ, Garfinkel DJ.

    Yeast. 2004 Jun;21(8):649-60.

    PMID: 15197730

  • NEJ1 prevents NHEJ-dependent telomere fusions in yeast without telomerase

    Liti G, Louis EJ.

    Mol Cell. 2003 May;11(5):1373-8.

    PMID: 12769859

  • Non-radioactive dot-blot DNA reassociation for unequivocal yeast identification

    Cardinali G, Liti G, Martini A.

    Int J Syst Evol Microbiol. 2000 Mar;50 Pt 2:931-6.

    PMID: 10758906

Les équipes de recherche