The rise of the yeast genus Saccharomyces: biodiversity and evolution
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The rise of the yeast genus Saccharomyces: biodiversity and evolution
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The rise of the yeast genus Saccharomyces: biodiversity and evolution
- 1. The rise of the yeast genus Saccharomyces: biodiversity and evolution David Peris, Postdoctoral Marie Curie Fellow Biotechnology Department, SBYBI Group (IATA-CSIC) 23th September 2019 @djperis
- 2. Saccharomyces cerevisiae as a species model Image provided by: http://faculty.ccbcmd.edu/courses/bio141/lecguide/unit4/fungi/u1fig35.html Well characterize eukaryotic cell
- 3. Saccharomyces cerevisiae as a species model Image provided by: http://faculty.ccbcmd.edu/courses/bio141/lecguide/unit4/fungi/u1fig35.html Small genome Well characterize eukaryotic cell
- 4. Saccharomyces cerevisiae as a species model Image provided by: http://faculty.ccbcmd.edu/courses/bio141/lecguide/unit4/fungi/u1fig35.html Easy to manipulate Small genome Well characterize eukaryotic cell
- 5. Saccharomyces cerevisiae as a species model Image provided by: http://faculty.ccbcmd.edu/courses/bio141/lecguide/unit4/fungi/u1fig35.html Easy to manipulate Small genome Similarities to other eukaryotes Well characterize eukaryotic cell
- 6. S. cerevisiae is important for their multiple applications! Ales Traditional beverages Wine Cider Sake
- 7. In rich conditions, yeast divides by mitosis Haploid (n) Haploid (n) Diploid (2n) Clonal divisions (mitosis)
- 8. How do we define a species? Life cycle MAT MATa MAT/MATa Haploid (n) Haploid (n) Diploid (2n) 2 Sexual types (MAT locus)
- 9. Sexual competent cells can mate MAT MATa MAT/MATa Haploid (n) Haploid (n) Diploid (2n) MAT MATa X MAT/MATa schmoo MATa MAT MATa MAT
- 10. Sporulation is promoted under starvation or stressful conditions MAT/MATa Diploid (2n) a a Tetrad Spore Sporulation
- 11. A diploid gets sexual competent by sporulating MAT/MATa Diploid (2n) MAT MATa X MAT/MATa a a
- 12. MAT X MAT/MATa MATa a a x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x: No growth 4/128 = 3.1% If spore viability below 5% suggests different species (postzygotic barrier) MAT/MATa a MAT/MATa a a a
- 13. Saccharomyces genomes 1.0 S. paradoxus S. mikatae S. kudriavzevii S. uvarum S. cerevisiae Scannell et al 2011
- 14. The genus Saccharomyces Libkind et al 2011 Liti et al 2013 Naseeb et al 2018 S. paradoxus S. mikatae S. arboricola S. kudriavzevii S. uvarum S. cerevisiae S. eubayanus S. jureii
- 15. Two stories Population genomics of Saccharomyces eubayanus The Saccharomyces genus as a model S. cerevisiae S. paradoxus S. jurei S. mikatae S. arboricola S. kudriavzevii S. eubayanus S. uvarum
- 16. Population genomics of Saccharomyces eubayanus
- 17. Two of the three big beer families: Skål! Pale Ale IPA Kölsch Juleøl Kornøl Vossaøl Pilsner Bayer Bokkøl
- 18. Two of the three big beer families: Skål! Pale Ale IPA Kölsch Juleøl Kornøl Vossaøl Pilsner Bayer Bokkøl
- 19. Two of the three big beer families: Skål! 15-25°C Pale Ale IPA Kölsch Juleøl Kornøl Vossaøl Pilsner Bayer Bokkøl
- 20. Two of the three big beer families: Skål! 15-25°C S. cerevisiae Beer 1 Beer 2 Kveik Pale Ale IPA Kölsch Juleøl Kornøl Vossaøl Pilsner Bayer Bokkøl Gallone et al 2016 Preiss et al 2018
- 21. Two of the three big beer families: Skål! 15-25°C 12-18°C Stored <7°C S. cerevisiae Beer 1 Beer 2 Kveik Pale Ale IPA Kölsch Juleøl Kornøl Vossaøl Pilsner Bayer Bokkøl Gallone et al 2016 Preiss et al 2018
- 22. Two of the three big beer families: Skål! 15-25°C 12-18°C Stored <7°C S. cerevisiae Beer 1 Beer 2 Kveik Hybrid Pale Ale IPA Kölsch Juleøl Kornøl Vossaøl Pilsner Bayer Bokkøl Gallone et al 2016 Preiss et al 2018 Libkind et al 2011
- 23. Two types of yeasts for two types of Lager Saaz/Group I Frohberg/Group II S. pastorianus x S. eubayanus S. cerevisiae Libkind et al 2011
- 24. Two types of yeasts for two types of Lager Saaz/Group I Frohberg/Group II Hybrid (4n) Hybrid (3n) S. carlsbergensis x Wendland 2015 Euk Cell S. eubayanus S. cerevisiae S. pastorianus 10°C Maltotriose- ↓Banana flavor 22°C Maltotriose+ ↑Banana flavor
- 25. S. eubayanus is distributed worldwide A. saccharum F. grandifolia Nothofagus trees Pinus taeda Cedrus spp. Ilex aquifolium Araucaria araucana Libkind et al 2011 Bing et al 2014 Peris et al 2014, 2016 Gayevskiy et al 2015 Langdon, Peris et al 2019 Nespolo et al 2019 Cyttaria harioti
- 26. Structured populations in S. eubayanus Peris et al 2014 Mol Ecol Peris et al 2016 PloS Genetics
- 27. Structured populations in S. eubayanus Peris et al 2014 Mol Ecol Peris et al 2016 PloS Genetics Langdon, Peris et al 2019 BioRxiv Nespolo et al 2019 BioRxiv yHCT69 yHCT107 yHCT105 yHCT99 yHAB94 CDFM21.L1 yHRVM108 yHKS210 yHAB578
- 28. Persistent gene flow Peris et al 2016 PloS Gen
- 29. Persistent gene flow Peris et al 2016 PloS Gen
- 30. Persistent gene flow Peris et al 2016 PloS Gen
- 31. Persistent gene flow Peris et al 2016 PloS Gen Langdon, Peris et al 2019 BioRxiv Nespolo et al 2019 BioRxiv 0.42% 0.58% 0.45% 0.55%
- 33. Geographically structured Eizaguirre, Peris et al 2019 Env Microbiol
- 34. Geographically structured, but also mtDNA haplotypes Eizaguirre, Peris et al 2019 Env Microbiol
- 35. Are Saaz and Frohberg genomes identical? Peris et al 2016 PloS Gen
- 36. None of the S. eubayanus strains is the direct parental donor of lager strains Peris et al 2016 PloS Gen
- 37. Who is the parental S. eubayanus donor? Langdon, Peris et al 2019 BioRxiv
- 38. The Saccharomyces genus model S. cerevisiae S. paradoxus S. jurei S. mikatae S. arboricola S. kudriavzevii S. eubayanus S. uvarum
- 39. Population and species range by genetic divergence Peris et al In preparation
- 40. Species range differs between yeasts and multicellular organisms Peris et al In preparation
- 41. The least diverse Saccharomyces species (humans-macaque) Peris et al In preparation
- 42. The most diverse Saccharomyces species (human-birds) Peris et al In preparation
- 43. Saccharomyces strains are phenotypically diverse Peris et al In preparation
- 44. Saccharomyces Genomes 2.0 Peris et al In preparation Sichuan & West China lineages
- 45. What is the source of phylogenetic incongruence?
- 46. Most of the incongruence is due to ILS Peris et al In preparation Sichuan & West China lineages
- 47. Nuclear gene flow mostly limited within species Gene flow Peris et al In preparation
- 48. How does introgression impact to carbon metabolism? Kuang et al 2016 eLife Legras et al 2018 MBE Peris et al In preparation
- 49. Complex ancestries to the GAL/MEL regulon Peris et al In preparation
- 50. Diversity in the galactose metabolism Peris et al In preparation Group 1 Group 2 Group 3 Group 4 Group 5 S. cerevisiae S. paradoxus S. mikatae S. kudriavzevii S. arboricola S. uvarum S. eubayanus Galactose
- 51. S. kudriavzevii a special case for galactose study Peris et al In preparation Group 1 Group 2 Group 3 Group 4 Group 5 S. cerevisiae S. paradoxus S. mikatae S. kudriavzevii S. arboricola S. uvarum S. eubayanus Galactose EU1
- 52. Balancing selection of a complete network Peris et al In preparation Group 1 Group 2 Group 3 Group 4 Group 5 S. cerevisiae S. paradoxus S. mikatae S. kudriavzevii S. arboricola S. uvarum S. eubayanus Galactose Asia A Asia B
- 53. Gene flow promotes loss or gain of a trait Peris et al In preparation Group 1 Group 2 Group 3 Group 4 Group 5 S. cerevisiae S. paradoxus S. mikatae S. kudriavzevii S. arboricola S. uvarum S. eubayanus Galactose EU2
- 54. Two more DNAs
- 55. Mitochondrial and 2µm gene flow between species Gene flow Mitochondrial 2µm plasmid Peris et al In preparation
- 56. Phenotypic differentiation based on temperature tolerance Termotolerant Cryotolerant Peris et al In preparation
- 57. Phenotypic differentiation based on temperature tolerance Group 1 Group 2 Group 3 Group 4 Group 5 S. cerevisiae S. paradoxus S. mikatae S. kudriavzevii S. arboricola S. uvarum S. eubayanus Peris et al In preparation
- 58. S. cerevisiae S. paradoxus S. mikatae S. jurei S. kudriavzevii S. arboricola S. uvarum S. eubayanus Species Hybridization as a domestication mechanism Langdon, Peris et al Accepted Nat Ecol & Evol Peris et al 2018 Yeast Peris et al 2012a Yeast Peris et al 2012 BMC Genomics Peris et al 2012 PloS One
- 59. S. cerevisiae S. paradoxus S. mikatae S. jurei S. kudriavzevii S. arboricola S. uvarum S. eubayanus Species 94% of interspecies hybrids inherited the non-cerevisiae mtDNA Langdon, Peris et al Accepted Nat Ecol & Evol Peris et al 2018 Yeast Peris et al 2012a Yeast Peris et al 2012 BMC Genomics Peris et al 2012 PloS One
- 60. 60 Mitochondrial inheritance directly related with temperature tolerance Baker, Peris et al 2019 Sci Adv Li, Peris et al 2019 Sci Adv
- 61. 61 Take-home messages Saccharomyces yeasts are geographically well structured
- 62. 62 Take-home messages Saccharomyces yeasts are geographically well structured Saccharomyces yeasts are diverse
- 63. 63 Take-home messages Saccharomyces yeasts are geographically well structured Saccharomyces yeasts are diverse Nuclear gene flow is limited between species, but frequent at the mtDNA and 2µm plasmid
- 64. 64 Take-home messages Saccharomyces yeasts are geographically well structured Saccharomyces yeasts are diverse Nuclear gene flow is limited between species, but frequent at the mtDNA and 2µm plasmid Gene flow can have an impact in the phenotype
- 65. 65 Take-home messages Saccharomyces yeasts are geographically well structured Saccharomyces yeasts are diverse Nuclear gene flow is limited between species, but frequent at the mtDNA and 2µm plasmid Gene flow can have an impact in the phenotype Mitochondrial inheritance is important to temperature tolerance
- 66. 66 Take-home messages Saccharomyces yeasts are geographically well structured Saccharomyces yeasts are diverse Nuclear gene flow is limited between species, but frequent at the mtDNA and 2µm plasmid Gene flow can have an impact in the phenotype Mitochondrial inheritance is important to temperature tolerance The origin of S. eubayanus parental donor of Lager strains is still unknown
- 69. Thank you