Population genomics in Drosophila melanogaster: a bioinformatics approach

High-throughput sequencing technologies are allowing the description of genome-wide variation patterns for an ever-growing number of organisms. However, we still lack a thorough comprehension of the relative amount of different types of genetic variation, their phenotypic effects, and the detection...

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Detalles Bibliográficos
Autor: Hervás Fernàndez, Sergi
Tipo de recurso: tesis doctoral
Estado:Versión publicada
Fecha de publicación:2018
País:España
Institución:CBUC, CESCA
Repositorio:TDR. Tesis Doctorales en Red
OAI Identifier:oai:www.tdx.cat:10803/665851
Acceso en línea:http://hdl.handle.net/10803/665851
Access Level:acceso abierto
Palabra clave:Genòmica
Genómica
Genomics
Bioinformàtica
Bioinformática
Bioinformatics
Evolució
Evolución
Evolution
Ciències Experimentals57
575
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spelling Population genomics in Drosophila melanogaster: a bioinformatics approachHervás Fernàndez, SergiGenòmicaGenómicaGenomicsBioinformàticaBioinformáticaBioinformaticsEvolucióEvoluciónEvolutionCiències Experimentals57575High-throughput sequencing technologies are allowing the description of genome-wide variation patterns for an ever-growing number of organisms. However, we still lack a thorough comprehension of the relative amount of different types of genetic variation, their phenotypic effects, and the detection and quantification of distinct selection regimes acting on genomes. The recent compilation of more than one thousand of worldwide wild-derived Drosophila melanogaster genome sequences reassembled using a standardized pipeline (Drosophila Genome Nexus, DGN, Lack et al. 2015, 2016) provides a unique resource to test molecular population genetics hypotheses, and ultimately understand the evolutionary dynamics of genetic variation in the populations. Besides, the increasing amount of genomic data available requires the continuous development and optimization of bioinformatics tools able to handle and analyze such information. Thus, the development and implementation of new biologically-oriented software addressing several steps from data acquisition, filtering, processing, display or analysis to the final reporting step is a constantly growing need, especially in fields dealing with large data sets, such as population genomics. This thesis is conceived as a comprehensive bioinformatics and population genomics project. It is centered in the development and application of bioinformatics tools for the analysis and visualization of nucleotide variation patterns and the detection of selective events in the genome of D. melanogaster, using the DGN data. The main goal is accomplished in three sequential steps: (i) capture the evolutionary properties of the analyzed sequences (i.e., create a catalog of population genetics metrics) and implement a tool for the graphical display of such information; (ii) develop a statistical package for the computation of the diverse selection regimes acting on genomes (positive and purifying selection), and finally (iii) perform an initial population genomics analysis in D. melanogaster using the previously developed tools. The common approach applied to process the data, starting at the assembly of genome sequences and ending up at the estimates of population genetics metrics, allows performing, for the first time, a comprehensive comparison and interpretation of results using samples from five continents. Overall, this work provides a global overview of the nucleotide variation and adaptation patterns along the genome, and a general assessment of the relative impact of the major genomic determinants of genetic variation, in Drosophila meta-populations with different geographical origin.Universitat Autònoma de BarcelonaBarbadilla Prados, AntonioCasillas Viladerrams, SòniaUniversitat Autònoma de Barcelona. Departament de Genètica i de Microbiologia201920192018info:eu-repo/semantics/doctoralThesisinfo:eu-repo/semantics/publishedVersion252 p.application/pdfapplication/pdfhttp://hdl.handle.net/10803/665851TDX (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-nc-nd/4.0/http://creativecommons.org/licenses/by-nc-nd/4.0/info:eu-repo/semantics/openAccessoai:www.tdx.cat:10803/6658512026-06-14T12:46:07Z
dc.title.none.fl_str_mv Population genomics in Drosophila melanogaster: a bioinformatics approach
title Population genomics in Drosophila melanogaster: a bioinformatics approach
spellingShingle Population genomics in Drosophila melanogaster: a bioinformatics approach
Hervás Fernàndez, Sergi
Genòmica
Genómica
Genomics
Bioinformàtica
Bioinformática
Bioinformatics
Evolució
Evolución
Evolution
Ciències Experimentals57
575
title_short Population genomics in Drosophila melanogaster: a bioinformatics approach
title_full Population genomics in Drosophila melanogaster: a bioinformatics approach
title_fullStr Population genomics in Drosophila melanogaster: a bioinformatics approach
title_full_unstemmed Population genomics in Drosophila melanogaster: a bioinformatics approach
title_sort Population genomics in Drosophila melanogaster: a bioinformatics approach
dc.creator.none.fl_str_mv Hervás Fernàndez, Sergi
author Hervás Fernàndez, Sergi
author_facet Hervás Fernàndez, Sergi
author_role author
dc.contributor.none.fl_str_mv Barbadilla Prados, Antonio
Casillas Viladerrams, Sònia
Universitat Autònoma de Barcelona. Departament de Genètica i de Microbiologia
dc.subject.none.fl_str_mv Genòmica
Genómica
Genomics
Bioinformàtica
Bioinformática
Bioinformatics
Evolució
Evolución
Evolution
Ciències Experimentals57
575
topic Genòmica
Genómica
Genomics
Bioinformàtica
Bioinformática
Bioinformatics
Evolució
Evolución
Evolution
Ciències Experimentals57
575
description High-throughput sequencing technologies are allowing the description of genome-wide variation patterns for an ever-growing number of organisms. However, we still lack a thorough comprehension of the relative amount of different types of genetic variation, their phenotypic effects, and the detection and quantification of distinct selection regimes acting on genomes. The recent compilation of more than one thousand of worldwide wild-derived Drosophila melanogaster genome sequences reassembled using a standardized pipeline (Drosophila Genome Nexus, DGN, Lack et al. 2015, 2016) provides a unique resource to test molecular population genetics hypotheses, and ultimately understand the evolutionary dynamics of genetic variation in the populations. Besides, the increasing amount of genomic data available requires the continuous development and optimization of bioinformatics tools able to handle and analyze such information. Thus, the development and implementation of new biologically-oriented software addressing several steps from data acquisition, filtering, processing, display or analysis to the final reporting step is a constantly growing need, especially in fields dealing with large data sets, such as population genomics. This thesis is conceived as a comprehensive bioinformatics and population genomics project. It is centered in the development and application of bioinformatics tools for the analysis and visualization of nucleotide variation patterns and the detection of selective events in the genome of D. melanogaster, using the DGN data. The main goal is accomplished in three sequential steps: (i) capture the evolutionary properties of the analyzed sequences (i.e., create a catalog of population genetics metrics) and implement a tool for the graphical display of such information; (ii) develop a statistical package for the computation of the diverse selection regimes acting on genomes (positive and purifying selection), and finally (iii) perform an initial population genomics analysis in D. melanogaster using the previously developed tools. The common approach applied to process the data, starting at the assembly of genome sequences and ending up at the estimates of population genetics metrics, allows performing, for the first time, a comprehensive comparison and interpretation of results using samples from five continents. Overall, this work provides a global overview of the nucleotide variation and adaptation patterns along the genome, and a general assessment of the relative impact of the major genomic determinants of genetic variation, in Drosophila meta-populations with different geographical origin.
publishDate 2018
dc.date.none.fl_str_mv 2018
2019
2019
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/10803/665851
url http://hdl.handle.net/10803/665851
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.rights.none.fl_str_mv http://creativecommons.org/licenses/by-nc-nd/4.0/
info:eu-repo/semantics/openAccess
rights_invalid_str_mv http://creativecommons.org/licenses/by-nc-nd/4.0/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv 252 p.
application/pdf
application/pdf
dc.publisher.none.fl_str_mv Universitat Autònoma de Barcelona
publisher.none.fl_str_mv Universitat Autònoma de Barcelona
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
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