Download to read offline
![HyPr: frequent mating
Alexander, Peris et al 2016
HyPr (Hybrid Production) plasmid
doxycycline
shock
Vegetative yeast
mitochondrial genome
chromosome
diploid
a/ a/
[pHMK34-HygMX]
[pHCT2-NatMX]
x
a/a /
a/a//
a/a//
Selection in media
with NAT+HYG
Remove selection for HYG
Check loss of NAT plasmid
>4G
Pre-culture
with NAT
Pre-culture
with HYG](https://image.slidesharecdn.com/embocompgenomicsdpv2-220831142846-401857a5/85/Reticulate-evolution-in-yeasts-and-its-industrial-applications-42-320.jpg)
![iHyPr: iterative Hybrid Production method
Peris et al 2019 BioRxiv
HyPr (Hybrid Production) plasmid
doxycycline
shock
Vegetative yeast
mitochondrial genome
chromosome
diploid
a/ a/
[pHMK34-HygMX]
[pHCT2-NatMX]
x
a/a /
a/a//
Selection in media
with NAT+HYG
Pre-culture
with HYG
Pre-culture
with NAT](https://image.slidesharecdn.com/embocompgenomicsdpv2-220831142846-401857a5/85/Reticulate-evolution-in-yeasts-and-its-industrial-applications-55-320.jpg)
![iHyPr: iterative Hybrid Production method
Peris et al 2019 BioRxiv
HyPr (Hybrid Production) plasmid
doxycycline
shock
Vegetative yeast
mitochondrial genome
chromosome
diploid
Pre-culture
with ZEO
Pre-culture
with HYG
a/ a/
[pHMK34-HygMX]
[pHCT2-NatMX]
x
a/a /
a/a//
a/a/a/a
Selection in media
with NAT+HYG
>4G
a/
/
[pHRW32-ZeoMX]
x
Pre-culture
with HYG
Pre-culture
with NAT](https://image.slidesharecdn.com/embocompgenomicsdpv2-220831142846-401857a5/85/Reticulate-evolution-in-yeasts-and-its-industrial-applications-56-320.jpg)
![iHyPr: iterative Hybrid Production method
Peris et al 2019 BioRxiv
HyPr (Hybrid Production) plasmid
doxycycline
shock
Vegetative yeast
mitochondrial genome
chromosome
diploid
>4G
Pre-culture
with ZEO
Pre-culture
with HYG
a/ a/
[pHMK34-HygMX]
[pHCT2-NatMX]
x
a/a /
a/a//
a/a/a/a
Selection in media
with NAT+HYG
>4G
a/
/
[pHRW32-ZeoMX]
x
a/a/a/a//
Selection in media
with HYG+ZEO
Pre-culture
with HYG
Pre-culture
with NAT
Pre-culture
with ZEO
a/a/a/a/a/a](https://image.slidesharecdn.com/embocompgenomicsdpv2-220831142846-401857a5/85/Reticulate-evolution-in-yeasts-and-its-industrial-applications-57-320.jpg)
![iHyPr: iterative Hybrid Production method
Peris et al 2019 BioRxiv
HyPr (Hybrid Production) plasmid
doxycycline
shock
Vegetative yeast
mitochondrial genome
chromosome
diploid
Pre-culture
with G418
>4G >4G
Pre-culture
with ZEO
Pre-culture
with HYG
a/ a/
[pHMK34-HygMX]
[pHCT2-NatMX]
x
a/a /
a/a//
a/a/a/a
Selection in media
with NAT+HYG
>4G
a/
/
[pHRW32-ZeoMX]
x
a/a/a/a//
Selection in media
with HYG+ZEO
Pre-culture
with HYG
Pre-culture
with NAT
x
a/a////
Reutilization of
NAT plasmid
Selection in media
with NAT+G418
Pre-culture
with ZEO
a/a/a/a/a/a
/////](https://image.slidesharecdn.com/embocompgenomicsdpv2-220831142846-401857a5/85/Reticulate-evolution-in-yeasts-and-its-industrial-applications-58-320.jpg)
Uploaded byDavid Peris Navarro
Reticulate evolution in yeasts and its industrial applications
This document summarizes research on reticulate evolution in yeasts and its industrial applications. Reticulate evolution refers to evolution occurring through hybridization and introgression rather than strictly vertical descent. The document discusses how hybridization has contributed to the diversification and domestication of yeasts like Saccharomyces cerevisiae. It also explores how mining genomic diversity through hybridization could enable new industrial applications, such as developing yeast strains capable of growth at lower temperatures or utilizing additional carbon sources.
More Related Content
Similar to Reticulate evolution in yeasts and its industrial applications
Reticulate evolution in yeasts and its industrial applications
- 1. Reticulate evolution inyeasts and its industrial applications David Peris, Postdoctoral Researcher Biotechnology Department, SBYBI (IATA-CSIC) 18th October 2019 @djperis
- 2. Overview Source of incongruencein the Saccharomyces genus Hybridization as mechanism of domestication Mining genomic diversity for industrial applications
- 3. Yeast life cycle MATMATa MAT/MATa Haploid (n) Haploid (n) Diploid (2n) 2 Sexual types (MAT locus)
- 4. Mating competent cellscan mate MAT MATa Haploid (n) Haploid (n) MAT MATa X MAT/MATa schmoo MATa MAT
- 5. A diploid getssexual competent by sporulation MAT/MATa Diploid (2n) MAT MATa X MAT/MATa a a
- 6.
- 7. Uniparental inheritance ofthe mitochondrial genome MAT MATa X rhoA Birky et al 2001 Ann Rev Gen
- 8. Uniparental inheritance ofthe mitochondrial genome MAT MATa X rhoA rhoB
- 9. Homoplasmic state isquickly reached MAT MATa X rhoA rhoAxB rhoB
- 10.
- 11. MAT X MAT/MATa MATa a a x x xx 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% Biological species concept MAT/MATa a MAT/MATa a a a
- 12. Saccharomyces genomes 1.0 S.paradoxus S. mikatae S. kudriavzevii S. uvarum S. cerevisiae Scannell et al 2011
- 13. Signals of phylogeneticincongruence S. paradoxus S. mikatae S. kudriavzevii S. uvarum S. cerevisiae Rokas et al 2003 Nature
- 14. New strains andspecies Libkind et al 2011 Liti et al 2013 Leducq et al 2016 Naseeb et al 2018 Peter et al 2018 Duan et al 2018 Peris et al In preparation
- 15. Aims Peris et alIn preparation Complete the phylogenetic relationship among Saccharomyces strains What is the source of phylogenetic incongruence
- 16. Saccharomyces Genomes 2.0 Periset al In preparation
- 17. Saccharomyces Genomes 2.0 Periset al In preparation
- 18. What is thesource of phylogenetic incongruence?
- 19. Most of theincongruence is due to ILS Peris et al In preparation
- 20. Nuclear gene flowmostly limited within species: mosaics/admixed Gene flow Peris et al In preparation
- 21. Kuang et al2016 eLife Legras et al 2018 MBE Peris et al In preparation How does introgression impact on the phenotypes?
- 22. The Saccharomyces kudriavzeviipopulations Hittinger et al 2010 Nature Peris et al In preparation
- 23. Genome scans andphylogenetic networks show gene flow Hittinger et al 2010 Nature Peris et al In preparation 11.93%
- 24. Most European S.kudriavzevii can grow in galactose EU1 Hittinger et al 2010 Nature MM + 2% Galactose S. cerevisiae S. paradoxus S. mikatae S. kudriavzevii S. arboricola S. uvarum S. eubayanus
- 25. Balancing selection ofa complete network Asia A Asia B EU1 Hittinger et al 2010 Nature MM + 2% Galactose S. cerevisiae S. paradoxus S. mikatae S. kudriavzevii S. arboricola S. uvarum S. eubayanus
- 26. EU1 MM + 2%Galactose Gene flow promotes loss or gain of a trait EU2 Asia A Asia B Peris et al In preparation S. cerevisiae S. paradoxus S. mikatae S. kudriavzevii S. arboricola S. uvarum S. eubayanus
- 27. Transgressive phenotypes byhybridization Stelkens et al 2014 JEB
- 28. Low frequency ofwild hybrids Barbosa et al 2016 GBE S. cerevisiae S. paradoxus S. mikatae S. jurei S. kudriavzevii S. arboricola S. uvarum S. eubayanus Species
- 29. 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 Pontes et al 2019 Front Gen Peris et al 2018 Yeast Almeida et al 2014 Erny et al 2012 AEM Peris et al 2012 Yeast Peris et al 2012 BMC Genomics Peris et al 2012 PloS One
- 30. S. cerevisiae S. paradoxus S.mikatae S. jurei S. kudriavzevii S. arboricola S. uvarum S. eubayanus Species Alpechin/olive hybrids Pontes et al 2019 Front Gen
- 31. S. cerevisiae S. paradoxus S.mikatae S. jurei S. kudriavzevii S. arboricola S. uvarum S. eubayanus Species Lager brewing hybrids: S. pastorianus Langdon, Peris et al Accepted Nat Ecol & Evol Peris et al 2016 PloS Gen Saaz/Group I Frohberg/Group II
- 32. S. cerevisiae S. paradoxus S.mikatae S. jurei S. kudriavzevii S. arboricola S. uvarum S. eubayanus Species Belgium beers and wine performed by hybrids Langdon, Peris et al Accepted Nat Ecol & Evol Peris et al 2018 Yeast Peris et al 2012 PloS One
- 33. S. cerevisiae S. paradoxus S.mikatae S. jurei S. kudriavzevii S. arboricola S. uvarum S. eubayanus Species Hybrid contaminants, some S. bayanus Langdon, Peris et al Accepted Nat Ecol & Evol
- 34. Phenotypic differentiation basedon 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 Gonçalves et al 2011 PloS ONE Salvadó et al 2011 AEM Peris et al In preparation
- 35. Phenotypic differentiation basedon 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 Gonçalves et al 2011 PloS ONE Salvadó et al 2011 AEM Peris et al In preparation
- 36. 94% of interspecieshybrids inherited the mitochondrial genome of non-cerevisiae species Group 1 Group 2 Group 3 Group 4 Group 5 S. cerevisiae S. paradoxus S. mikatae S. kudriavzevii S. arboricola S. uvarum S. eubayanus Gonçalves et al 2011 PloS ONE Salvadó et al 2011 AEM Peris et al In preparation
- 37. Aim Infer the contributionof each parent to the hybrid phenotype
- 38. Tests in synthetichybrids Peris et al 2018 Yeast
- 39. Rare mating: whendiploids become mating competent Hanson and Wolfe 2017 Ortiz-Merino et al 2017 Braun-Galleani et al 2018 Homing endonuclease (HO) MATa MAT HO MATa MATa 1) MATa/MATa or MAT/MATa Inactivation/Loss of one idiomorph MATa MAT MATa 2) MATa/- 1:106
- 40. Rare mating: whendiploids become mating competent Hanson and Wolfe 2017 Ortiz-Merino et al 2017 Braun-Galleani et al 2018 Homing endonuclease (HO) MATa MAT HO MATa MATa 1) MATa/MATa or MAT/MATa Inactivation/Loss of one idiomorph MATa MAT MATa 2) MATa/- 1:106 MAT MAT/MAT X
- 41. Peris et al2019 BioRxiv HyPr (Hybrid Production) plasmid doxycycline shock HyPr: Hybrid Production method
- 42. HyPr: frequent mating Alexander,Peris et al 2016 HyPr (Hybrid Production) plasmid doxycycline shock Vegetative yeast mitochondrial genome chromosome diploid a/ a/ [pHMK34-HygMX] [pHCT2-NatMX] x a/a / a/a// a/a// Selection in media with NAT+HYG Remove selection for HYG Check loss of NAT plasmid >4G Pre-culture with NAT Pre-culture with HYG
- 43. S. eubayanus cangrow at low temperature Baker, Peris et al 2019 Sci Adv Li, Peris et al 2019 Sci Adv 10C + Glycerol Hybrid Scer-mtDNA Hybrid Seub-mtDNA Seub-with mtDNA Seub-no mtDNA Scer-with mtDNA Scer-no mtDNA
- 44. S. cerevisiae cannot grow at low temperature Baker, Peris et al 2019 Sci Adv Li, Peris et al 2019 Sci Adv 10C + Glycerol Hybrid Scer-mtDNA Hybrid Seub-mtDNA Seub-with mtDNA Seub-no mtDNA Scer-with mtDNA Scer-no mtDNA
- 45. Mitochondrial inheritance directlyrelated with temperature tolerance Baker, Peris et al 2019 Sci Adv Li, Peris et al 2019 Sci Adv 10C + Glycerol Hybrid Scer-mtDNA Hybrid Seub-mtDNA Seub-with mtDNA Seub-no mtDNA Scer-with mtDNA Scer-no mtDNA
- 46. Mitochondrial inheritance directlyrelated with temperature tolerance Baker, Peris et al 2019 Sci Adv Li, Peris et al 2019 Sci Adv 10C + Glycerol Hybrid Scer- mtDNA Hybrid Seub- mtDNA Seub-with mtDNA Seub-no mtDNA Scer-with mtDNA Scer-no mtDNA 37C + Glycerol Hybrid Scer-mtDNA Hybrid Seub-mtDNA Seub-with mtDNA Seub-no mtDNA Scer-with mtDNA Scer-no mtDNA
- 47. Could be applyhybrids to other industrial processes? Piotrowski et al 2014 Front Microbiol
- 48. Redomestication of S.cerevisiae for biofuels Wohlbach et al. 2009 PNAS Sato et al. 2013 AEM Xylose Hydrolysate toxins Y73 2n ACSH D-glucose Glucose -6P Fructose -6P Glyceraldehyde -3P Dihydroxy acetone P Glycerol NADH Phosphoenolpyruvate Acetaldehyde Pyruvate NADH ATP ATP CO2 Ethanol Acetate NADH D-xylose D-Xylulose Xylulose 5P NAD(P)+ NADH ATP NAD(P)H Xylitol Acetyl -CoA ATP Pathway engineered in GLBRCY73 Succinate TCA ATP CO2 CO2 NADH NADH ATP Pyruvate Acetyl-CoA Mitochondrion Cytosol Ssti-XYL1 Ssti-XYL2 Ssti-XYL3
- 49. Redomestication of S.cerevisiae for biofuels Xylose Hydrolysate toxins Y101 n n S.mikatae S.kudriavzevii X R1 R9 … 50 Generation:ACSH 30ºC 14days Y73 2n or MAT MATa/MAT MATa MATa Peris et al 2017 Biotech Biofuels
- 50. Hybrids might improvechassis strains Peris et al 2017 Biotech Biofuels Y101 n n S.mikatae S.kudriavzevii X R1 R9 … 30ºC 14days or CHASSIS ANCESTOR EVOLVED ANCESTOR EVOLVED D-xylose Ethanol CHASSIS ANCESTOR EVOLVED ANCESTOR EVOLVED 50 Generation:ACSH T2 (166.5 h)
- 51. Genotypic diversity Peris etal In preparation
- 52. Genotypic diversity (human-birds) Periset al In preparation
- 53. Genotypic diversity istranslated in different phenotypes Peris et al In preparation
- 54. Aim Expand the numberof species genomes introduced in a single cell
- 55. iHyPr: iterative HybridProduction method Peris et al 2019 BioRxiv HyPr (Hybrid Production) plasmid doxycycline shock Vegetative yeast mitochondrial genome chromosome diploid a/ a/ [pHMK34-HygMX] [pHCT2-NatMX] x a/a / a/a// Selection in media with NAT+HYG Pre-culture with HYG Pre-culture with NAT
- 56. iHyPr: iterative HybridProduction method Peris et al 2019 BioRxiv HyPr (Hybrid Production) plasmid doxycycline shock Vegetative yeast mitochondrial genome chromosome diploid Pre-culture with ZEO Pre-culture with HYG a/ a/ [pHMK34-HygMX] [pHCT2-NatMX] x a/a / a/a// a/a/a/a Selection in media with NAT+HYG >4G a/ / [pHRW32-ZeoMX] x Pre-culture with HYG Pre-culture with NAT
- 57. iHyPr: iterative HybridProduction method Peris et al 2019 BioRxiv HyPr (Hybrid Production) plasmid doxycycline shock Vegetative yeast mitochondrial genome chromosome diploid >4G Pre-culture with ZEO Pre-culture with HYG a/ a/ [pHMK34-HygMX] [pHCT2-NatMX] x a/a / a/a// a/a/a/a Selection in media with NAT+HYG >4G a/ / [pHRW32-ZeoMX] x a/a/a/a// Selection in media with HYG+ZEO Pre-culture with HYG Pre-culture with NAT Pre-culture with ZEO a/a/a/a/a/a
- 58. iHyPr: iterative HybridProduction method Peris et al 2019 BioRxiv HyPr (Hybrid Production) plasmid doxycycline shock Vegetative yeast mitochondrial genome chromosome diploid Pre-culture with G418 >4G >4G Pre-culture with ZEO Pre-culture with HYG a/ a/ [pHMK34-HygMX] [pHCT2-NatMX] x a/a / a/a// a/a/a/a Selection in media with NAT+HYG >4G a/ / [pHRW32-ZeoMX] x a/a/a/a// Selection in media with HYG+ZEO Pre-culture with HYG Pre-culture with NAT x a/a//// Reutilization of NAT plasmid Selection in media with NAT+G418 Pre-culture with ZEO a/a/a/a/a/a /////
- 59. Three different hybridizationschemes Peris et al 2019 BioRxiv
- 60. sppIDer: quick genomecharacterization using NGS Langdon et al 2019 MBE
- 61. sppIDer: quick genomecharacterization using NGS Langdon et al 2019 MBE
- 62. sppIDer: a quickmethod to characterize hybrid genomes Peris et al 2019 BioRxiv
- 63. Six-species hybrid genomesare highly unstable Peris et al 2019 BioRxiv
- 64. Six-species hybrid genomesare highly unstable Peris et al 2019 BioRxiv
- 65. Six-species hybrid genomesare highly unstable Peris et al 2019 BioRxiv
- 66. Alloctoploid (8n) six-specieshybrid was constructed Peris et al 2019 BioRxiv
- 67. Aim The influence ofmitochondrial inheritance in the genome retention Improve the six-species hybrids through ALE
- 68. iHyPr is amethod to generate diversity 80 Generation Peris et al 2019 BioRxiv
- 69. iHyPr is amethod to generate diversity 80 Generation Peris et al 2019 BioRxiv
- 70. Mitochondrial inheritance influencesin the genotypic outcome mtDNA S. cerevisiae Other species Step of hybridization 100 75 50 25 % of S. cerevisiae nuclear genome Peris et al 2019 BioRxiv
- 71. iHyPr combined withALE for the improvement of chassis strains Peris et al 2019 BioRxiv GLBRCY101
- 72. iHyPr is amethod to combine phenotypic traits Peris et al 2019 BioRxiv
- 73. iHyPr is amethod to combine phenotypic traits Peris et al 2019 BioRxiv
- 74. Take-home messages Nuclear geneflow is limited between species
- 75. Take-home messages Nuclear geneflow is limited between species Gene flow can have an impact in the phenotype
- 76. Take-home messages Nuclear geneflow is limited between species Gene flow can have an impact in the phenotype Mitochondrial inheritance is important for temperature tolerance
- 77. Take-home messages Nuclear geneflow is limited between species Gene flow can have an impact in the phenotype Mitochondrial inheritance is important for temperature tolerance Mitochondrial inheritance influences in the genome retention
- 78. Take-home messages Nuclear geneflow is limited between species Gene flow can have an impact in the phenotype Mitochondrial inheritance is important for temperature tolerance Mitochondrial inheritance influences in the genome retention iHyPr is an efficient method to generate polyploids and complex hybrids
- 79. Take-home messages Nuclear geneflow is limited between species Gene flow can have an impact in the phenotype Mitochondrial inheritance is important for temperature tolerance Mitochondrial inheritance influences in the genome retention iHyPr is an efficient method to generate polyploids and complex hybrids iHyPr is an efficient method to generate diversity and combine the phenotypic traits of wild strains
- 80. Lainy Ramírez Aroca AmparoQuerol David Lázaro Laura Pérez-Través Querol Lab Members Eladio Barrio Laura Gutierrez Miguel Morard Barrio Lab Members José Guillamón Guillamón Lab Members Sergi Puig Sergi Lab Members William G Alexander Mira G Basuino Emily J Ubbelohde Diego Libkind Jose Paulo Sampaio Paula Gonçalves Christian Landry Jean-Baptiste Leducq Guillaume Charron Justin Fay Katie Hyma Li Xueying Fengyan Bai Qi Ming Wang Ursula Bond Chris T. Hittinger’s lab Quinn Langdon EmilyClaire Baker Rusell Wrobel Ryan Moriarty Kaitlin Fisher Mehua Kuang Jacek Kominek Dana Opulente Amanda Hulfachor UW & GLBRC Collaboration SBYBI@IATA-CSIC Thank you