Discovery and evolutionary analysis of novel genes and translated ORFs

This thesis analyzes the generation of new genes created de novo and evaluates their evolution mainly in yeast but also in flies. First of all, we used next generation sequencing technology to analyze both new sequences that had not been described and new isoforms that could give rise to new peptide...

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Detalles Bibliográficos
Autor: Montañés Domínguez, José Carlos
Tipo de recurso: tesis doctoral
Estado:Versión publicada
Fecha de publicación:2024
País:España
Institución:CBUC, CESCA
Repositorio:TDR. Tesis Doctorales en Red
OAI Identifier:oai:www.tdx.cat:10803/691842
Acceso en línea:http://hdl.handle.net/10803/691842
Access Level:acceso abierto
Palabra clave:De novo genes
Evolution
Gene duplication
Long read sequencing
Ribo-seq
Gens duplicats
Gens de novo
Evolució
Seqüenciació de lectura llarga
Empremta ribosomal
575
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spelling Discovery and evolutionary analysis of novel genes and translated ORFsMontañés Domínguez, José CarlosDe novo genesEvolutionGene duplicationLong read sequencingRibo-seqGens duplicatsGens de novoEvolucióSeqüenciació de lectura llargaEmpremta ribosomal575This thesis analyzes the generation of new genes created de novo and evaluates their evolution mainly in yeast but also in flies. First of all, we used next generation sequencing technology to analyze both new sequences that had not been described and new isoforms that could give rise to new peptides with functions not yet described in the species Schizosaccharomyces pombe. In addition, using specific methodologies such as Ribo-seq we have been able to detect open reading frames that are translated. Secondly, we used the same methodology to compare the evolution of de novo genes with the most well-known mechanism to generate new genes: gene duplication. In this analysis we have been able to see that there is an enrichment of both de novo and duplicated genes at the species level but their conservation over time is limited. In addition, we have seen how de novo genes tend to exhibit a high rate of change in their amino acids sequences favoring the loss of positively charged amino acids. Finally, we also analyzed the untranslated regions of mRNAs which we found to have translational activity and possibly encode novel proteins. As a whole, the thesis shows us methods for the identification of de novo genes, their properties and their evolution.Aquesta tesi analitza la generació de nous gens creats de novo i avalua la seva evolució principalment en llevats però també en mosques. En primer lloc, hem utilitzat la tecnologia de seqüenciació de nova generació per analitzar tant noves seqüències que no havien estat descrites com noves isoformes que podrien donar lloc a nous pèptids amb funcions encara no descrites a l'espècie Schizosaccharomyces pombe. A més, utilitzant metodologies específiques com Ribo-seq hem pogut detectar marcs de lectura oberts que són traduïts. En segon lloc, hem utilitzat la mateixa metodologia per comparar l'evolució de gens de novo amb el mecanisme més conegut per generar nous gens: la duplicació gènica. En aquesta anàlisi hem pogut veure que existeix un enriquiment tant de gens de novo com de gens duplicats a nivell d'espècie però la seva conservació al llarg del temps és limitada. A més, hem vist com els gens de novo tendeixen a tenir una alta taxa de canvi en les seves seqüències d'aminoàcids afavorint la pèrdua d'aminoàcids carregats positivament. Finalment, també hem analitzat les regions no traduïdes dels ARNm que, segons hem comprovat, tenen activitat traduccional i possiblement codifiquen noves proteïnes. En conjunt, la tesi ens mostra mètodes per a la identificació de gens de novo, les seves propietats i la seva evolució.Programa de Doctorat en BiomedicinaUniversitat Pompeu FabraAlbà Soler, MarUniversitat Pompeu Fabra. Departament de Medicina i Ciències de la Vida202420242024info:eu-repo/semantics/doctoralThesisinfo:eu-repo/semantics/publishedVersion225 p.application/pdfhttp://hdl.handle.net/10803/691842TDX (Tesis Doctorals en Xarxa)reponame:TDR. Tesis Doctorales en Redinstname:CBUC, CESCAInglésL'accés als continguts d'aquesta tesi queda condicionat a l'acceptació de les condicions d'ús establertes per la següent llicència Creative Commons: http://creativecommons.org/licenses/by/4.0/http://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccessoai:www.tdx.cat:10803/6918422026-06-14T12:46:07Z
dc.title.none.fl_str_mv Discovery and evolutionary analysis of novel genes and translated ORFs
title Discovery and evolutionary analysis of novel genes and translated ORFs
spellingShingle Discovery and evolutionary analysis of novel genes and translated ORFs
Montañés Domínguez, José Carlos
De novo genes
Evolution
Gene duplication
Long read sequencing
Ribo-seq
Gens duplicats
Gens de novo
Evolució
Seqüenciació de lectura llarga
Empremta ribosomal
575
title_short Discovery and evolutionary analysis of novel genes and translated ORFs
title_full Discovery and evolutionary analysis of novel genes and translated ORFs
title_fullStr Discovery and evolutionary analysis of novel genes and translated ORFs
title_full_unstemmed Discovery and evolutionary analysis of novel genes and translated ORFs
title_sort Discovery and evolutionary analysis of novel genes and translated ORFs
dc.creator.none.fl_str_mv Montañés Domínguez, José Carlos
author Montañés Domínguez, José Carlos
author_facet Montañés Domínguez, José Carlos
author_role author
dc.contributor.none.fl_str_mv Albà Soler, Mar
Universitat Pompeu Fabra. Departament de Medicina i Ciències de la Vida
dc.subject.none.fl_str_mv De novo genes
Evolution
Gene duplication
Long read sequencing
Ribo-seq
Gens duplicats
Gens de novo
Evolució
Seqüenciació de lectura llarga
Empremta ribosomal
575
topic De novo genes
Evolution
Gene duplication
Long read sequencing
Ribo-seq
Gens duplicats
Gens de novo
Evolució
Seqüenciació de lectura llarga
Empremta ribosomal
575
description This thesis analyzes the generation of new genes created de novo and evaluates their evolution mainly in yeast but also in flies. First of all, we used next generation sequencing technology to analyze both new sequences that had not been described and new isoforms that could give rise to new peptides with functions not yet described in the species Schizosaccharomyces pombe. In addition, using specific methodologies such as Ribo-seq we have been able to detect open reading frames that are translated. Secondly, we used the same methodology to compare the evolution of de novo genes with the most well-known mechanism to generate new genes: gene duplication. In this analysis we have been able to see that there is an enrichment of both de novo and duplicated genes at the species level but their conservation over time is limited. In addition, we have seen how de novo genes tend to exhibit a high rate of change in their amino acids sequences favoring the loss of positively charged amino acids. Finally, we also analyzed the untranslated regions of mRNAs which we found to have translational activity and possibly encode novel proteins. As a whole, the thesis shows us methods for the identification of de novo genes, their properties and their evolution.
publishDate 2024
dc.date.none.fl_str_mv 2024
2024
2024
dc.type.none.fl_str_mv info:eu-repo/semantics/doctoralThesis
info:eu-repo/semantics/publishedVersion
format doctoralThesis
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10803/691842
url http://hdl.handle.net/10803/691842
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.rights.none.fl_str_mv http://creativecommons.org/licenses/by/4.0/
info:eu-repo/semantics/openAccess
rights_invalid_str_mv http://creativecommons.org/licenses/by/4.0/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv 225 p.
application/pdf
dc.publisher.none.fl_str_mv Universitat Pompeu Fabra
publisher.none.fl_str_mv Universitat Pompeu Fabra
dc.source.none.fl_str_mv TDX (Tesis Doctorals en Xarxa)
reponame:TDR. Tesis Doctorales en Red
instname:CBUC, CESCA
instname_str CBUC, CESCA
reponame_str TDR. Tesis Doctorales en Red
collection TDR. Tesis Doctorales en Red
repository.name.fl_str_mv
repository.mail.fl_str_mv
_version_ 1869418225690738688
score 15,811543

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