The genomics of microbe domestication - Testing the hypothesis of secondary domestication events in Saccharomyces cerevisiae
Autor(a) principal: | |
---|---|
Data de Publicação: | 2022 |
Tipo de documento: | Dissertação |
Idioma: | eng |
Título da fonte: | Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
Texto Completo: | http://hdl.handle.net/10362/142851 |
Resumo: | For thousands of years microbes have been used, typically inadvertently, for the fermentation of a wide diversity of beverages and foods, which has led to the selection of relevant characteristics, thus promoting the domestication process. The yeast Saccharomyces cerevisiae is probably the most well-studied microbe with respect to domestication. However, most studies have been focused on a few industrially important lineages such as that of wine yeasts. Thus, this work aimed at deepening and extending the study of domestication trajectories in S. cerevisiae employing a broad perspective and using an integrated approach. For this, bioinformatic and experimental analyses were combined for a balanced perspective of genetic and phenotypic diversity of S. cerevisiae. In chapter 2, the emergence of a domesticated lineage associated with cachaça, and its relationship with wine yeasts was investigated. Our findings lead us to propose different domestication trajectories. We identified initial transitions from wild to domesticate, that gave rise to primary domesticated populations with specific traits related to the fermentation in which they were selected. We also identified secondarily domesticated populations that originate from primary domesticates that have been subjected to new and distinctive selective pressures. In chapter 3 we studied a population linked to wine yeasts but that arose after an inter-species hybridization. We analyzed in detail the consequences of an ancient hybridization between S. cerevisiae and S. paradoxus for adaptation to an anthropic environment. This study further highlighted the different layers of genomic and phenotypic transitions related to domestication and lead to the proposal of the concept of quasi-domesticate. Chapter 4 provided a comprehensive view of wild and domesticated populations of S. cerevisiae, integrating results from several recent publications. In that study, the distribution and ecology of wild populations was evaluated, and the evolution of certain genes that code for relevant phenotypic traits was investigated. The detailed study of domestication trajectories in S. cerevisiae carried out in this work revealed unanticipated levels of complexity, with cases of secondary domestication and of quasi-domestication. The results gathered in this project contribute to a better understanding of the mechanisms underpinning S. cerevisiae domestication. This will not only enable a better understanding the biology of this model organism from a fundamental perspective but will also be relevant for applied domains like the rational improvement of industrial fermentations. |
id |
RCAP_e459d227dd45e5a2b006821767fc92cc |
---|---|
oai_identifier_str |
oai:run.unl.pt:10362/142851 |
network_acronym_str |
RCAP |
network_name_str |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
repository_id_str |
7160 |
spelling |
The genomics of microbe domestication - Testing the hypothesis of secondary domestication events in Saccharomyces cerevisiaeMicrobe domesticationSaccharomyces cerevisiaeevolutionpopulation genomicsmicrobial ecologyDomínio/Área Científica::Engenharia e Tecnologia::Outras Engenharias e TecnologiasFor thousands of years microbes have been used, typically inadvertently, for the fermentation of a wide diversity of beverages and foods, which has led to the selection of relevant characteristics, thus promoting the domestication process. The yeast Saccharomyces cerevisiae is probably the most well-studied microbe with respect to domestication. However, most studies have been focused on a few industrially important lineages such as that of wine yeasts. Thus, this work aimed at deepening and extending the study of domestication trajectories in S. cerevisiae employing a broad perspective and using an integrated approach. For this, bioinformatic and experimental analyses were combined for a balanced perspective of genetic and phenotypic diversity of S. cerevisiae. In chapter 2, the emergence of a domesticated lineage associated with cachaça, and its relationship with wine yeasts was investigated. Our findings lead us to propose different domestication trajectories. We identified initial transitions from wild to domesticate, that gave rise to primary domesticated populations with specific traits related to the fermentation in which they were selected. We also identified secondarily domesticated populations that originate from primary domesticates that have been subjected to new and distinctive selective pressures. In chapter 3 we studied a population linked to wine yeasts but that arose after an inter-species hybridization. We analyzed in detail the consequences of an ancient hybridization between S. cerevisiae and S. paradoxus for adaptation to an anthropic environment. This study further highlighted the different layers of genomic and phenotypic transitions related to domestication and lead to the proposal of the concept of quasi-domesticate. Chapter 4 provided a comprehensive view of wild and domesticated populations of S. cerevisiae, integrating results from several recent publications. In that study, the distribution and ecology of wild populations was evaluated, and the evolution of certain genes that code for relevant phenotypic traits was investigated. The detailed study of domestication trajectories in S. cerevisiae carried out in this work revealed unanticipated levels of complexity, with cases of secondary domestication and of quasi-domestication. The results gathered in this project contribute to a better understanding of the mechanisms underpinning S. cerevisiae domestication. This will not only enable a better understanding the biology of this model organism from a fundamental perspective but will also be relevant for applied domains like the rational improvement of industrial fermentations.Os microrganismos são utilizados desde há milhares de anos, normalmente inadvertidamente, na fermentação de inúmeras bebidas e alimentos, o que promoveu o processo de domesticação. A levedura Saccharomyces cerevisiae, é provavelmente o microrganismo mais bem estudado no que diz respeito à domesticação. No entanto, a maioria dos estudos têm-se focado em linhagens industrialmente relevantes, tais como as leveduras do vinho. Neste trabalho procurou-se aprofundar e alargar o estudo das trajectórias de domesticação em S. cerevisiae, usando uma abordagem abrangente e integrada. Foram combinadas análises bioinformáticas e experimentais de modo a obter uma perspetiva equilibrada da diversidade genética e fenotípica em S. cerevisiae, dando relevo tanto a populações domesticadas como a populações selvagens. No capítulo 2, foi investigada uma linhagem domesticada associada com a cachaça e a sua relação com as leveduras do vinho. Os nossos resultados apoiam a tese de que ocorreram múltiplas trajectórias de domesticação nesta espécie. Identificámos transições iniciais de selvagens para domesticados, que deram origem a populações domesticadas primárias com traços específicos relacionados com as fermentações em que ocorreu a selecção. Identificámos ainda populações domesticadas secundárias que têm origem em domesticados primários sujeitos a novas e distintas pressões selectivas. No capítulo 3 foi estudada uma população ligada às leveduras do vinho, mas que se originou após hibridação inter-específica. Analisámos em pormenor as consequências desta hibridação ente S. cerevisiae e S. paradoxus na adaptação ao ambiente antrópico. Este estudo destacou ainda mais a complexidade das transições genómicas e fenotípicas relacionadas com a domesticação, levando à proposta do conceito de "quasi-domesticate". O capítulo 4 focou-se numa visão abrangente tanto de populações selvagens como domesticadas. Nesse estudo, foi avaliada a distribuição e ecologia das populações selvagens, e investigada a evolução de certos genes que codificam traços fenotípicos relevantes. O estudo detalhado das trajectórias de domesticação em S. cerevisiae realizado neste projecto contribuiu para suportar a tese de que este processo é complexo e multidimensional, envolvendo vários tipos de transições. Salienta-se que uma melhor compreensão dos mecanismos subjacentes à domesticação de S. cerevisiae permitirá não só compreender melhor a biologia deste organismo numa perspetiva fundamental, como também a sua aplicação mais racional em processos fermentativos industriais.Sampaio, JoséGonçalves, PaulaRUNPontes, Ana Patrícia Teixeira2022-08-04T14:50:16Z2022-07-072022-07-07T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/masterThesisapplication/pdfhttp://hdl.handle.net/10362/142851enginfo:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2024-03-11T05:20:49Zoai:run.unl.pt:10362/142851Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-20T03:50:33.868954Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse |
dc.title.none.fl_str_mv |
The genomics of microbe domestication - Testing the hypothesis of secondary domestication events in Saccharomyces cerevisiae |
title |
The genomics of microbe domestication - Testing the hypothesis of secondary domestication events in Saccharomyces cerevisiae |
spellingShingle |
The genomics of microbe domestication - Testing the hypothesis of secondary domestication events in Saccharomyces cerevisiae Pontes, Ana Patrícia Teixeira Microbe domestication Saccharomyces cerevisiae evolution population genomics microbial ecology Domínio/Área Científica::Engenharia e Tecnologia::Outras Engenharias e Tecnologias |
title_short |
The genomics of microbe domestication - Testing the hypothesis of secondary domestication events in Saccharomyces cerevisiae |
title_full |
The genomics of microbe domestication - Testing the hypothesis of secondary domestication events in Saccharomyces cerevisiae |
title_fullStr |
The genomics of microbe domestication - Testing the hypothesis of secondary domestication events in Saccharomyces cerevisiae |
title_full_unstemmed |
The genomics of microbe domestication - Testing the hypothesis of secondary domestication events in Saccharomyces cerevisiae |
title_sort |
The genomics of microbe domestication - Testing the hypothesis of secondary domestication events in Saccharomyces cerevisiae |
author |
Pontes, Ana Patrícia Teixeira |
author_facet |
Pontes, Ana Patrícia Teixeira |
author_role |
author |
dc.contributor.none.fl_str_mv |
Sampaio, José Gonçalves, Paula RUN |
dc.contributor.author.fl_str_mv |
Pontes, Ana Patrícia Teixeira |
dc.subject.por.fl_str_mv |
Microbe domestication Saccharomyces cerevisiae evolution population genomics microbial ecology Domínio/Área Científica::Engenharia e Tecnologia::Outras Engenharias e Tecnologias |
topic |
Microbe domestication Saccharomyces cerevisiae evolution population genomics microbial ecology Domínio/Área Científica::Engenharia e Tecnologia::Outras Engenharias e Tecnologias |
description |
For thousands of years microbes have been used, typically inadvertently, for the fermentation of a wide diversity of beverages and foods, which has led to the selection of relevant characteristics, thus promoting the domestication process. The yeast Saccharomyces cerevisiae is probably the most well-studied microbe with respect to domestication. However, most studies have been focused on a few industrially important lineages such as that of wine yeasts. Thus, this work aimed at deepening and extending the study of domestication trajectories in S. cerevisiae employing a broad perspective and using an integrated approach. For this, bioinformatic and experimental analyses were combined for a balanced perspective of genetic and phenotypic diversity of S. cerevisiae. In chapter 2, the emergence of a domesticated lineage associated with cachaça, and its relationship with wine yeasts was investigated. Our findings lead us to propose different domestication trajectories. We identified initial transitions from wild to domesticate, that gave rise to primary domesticated populations with specific traits related to the fermentation in which they were selected. We also identified secondarily domesticated populations that originate from primary domesticates that have been subjected to new and distinctive selective pressures. In chapter 3 we studied a population linked to wine yeasts but that arose after an inter-species hybridization. We analyzed in detail the consequences of an ancient hybridization between S. cerevisiae and S. paradoxus for adaptation to an anthropic environment. This study further highlighted the different layers of genomic and phenotypic transitions related to domestication and lead to the proposal of the concept of quasi-domesticate. Chapter 4 provided a comprehensive view of wild and domesticated populations of S. cerevisiae, integrating results from several recent publications. In that study, the distribution and ecology of wild populations was evaluated, and the evolution of certain genes that code for relevant phenotypic traits was investigated. The detailed study of domestication trajectories in S. cerevisiae carried out in this work revealed unanticipated levels of complexity, with cases of secondary domestication and of quasi-domestication. The results gathered in this project contribute to a better understanding of the mechanisms underpinning S. cerevisiae domestication. This will not only enable a better understanding the biology of this model organism from a fundamental perspective but will also be relevant for applied domains like the rational improvement of industrial fermentations. |
publishDate |
2022 |
dc.date.none.fl_str_mv |
2022-08-04T14:50:16Z 2022-07-07 2022-07-07T00:00:00Z |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/masterThesis |
format |
masterThesis |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://hdl.handle.net/10362/142851 |
url |
http://hdl.handle.net/10362/142851 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
application/pdf |
dc.source.none.fl_str_mv |
reponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação instacron:RCAAP |
instname_str |
Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
instacron_str |
RCAAP |
institution |
RCAAP |
reponame_str |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
collection |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
repository.name.fl_str_mv |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
repository.mail.fl_str_mv |
|
_version_ |
1799138102038495232 |