A Guide to Carrying Out a Phylogenomic Target Sequence Capture Project
Autor(a) principal: | |
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Data de Publicação: | 2020 |
Outros Autores: | , , , , , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional do INPA |
Texto Completo: | https://repositorio.inpa.gov.br/handle/1/15454 |
Resumo: | High-throughput DNA sequencing techniques enable time- and cost-effective sequencing of large portions of the genome. Instead of sequencing and annotating whole genomes, many phylogenetic studies focus sequencing effort on large sets of pre-selected loci, which further reduces costs and bioinformatic challenges while increasing coverage. One common approach that enriches loci before sequencing is often referred to as target sequence capture. This technique has been shown to be applicable to phylogenetic studies of greatly varying evolutionary depth. Moreover, it has proven to produce powerful, large multi-locus DNA sequence datasets suitable for phylogenetic analyses. However, target capture requires careful considerations, which may greatly affect the success of experiments. Here we provide a simple flowchart for designing phylogenomic target capture experiments. We discuss necessary decisions from the identification of target loci to the final bioinformatic processing of sequence data. We outline challenges and solutions related to the taxonomic scope, sample quality, and available genomic resources of target capture projects. We hope this review will serve as a useful roadmap for designing and carrying out successful phylogenetic target capture studies. © Copyright © 2020 Andermann, Torres Jiménez, Matos-Maraví, Batista, Blanco-Pastor, Gustafsson, Kistler, Liberal, Oxelman, Bacon and Antonelli. |
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Andermann, TobiasTorres-Jiminez, Maria FernandaMatos-Maraví, Pável F.Batista, Romina B.Blanco-Pastor, José LuisGustafsson, A. Lovisa S.Kistler, LoganLiberal, Isabel Mar?aOxelman, BengtBacon, Christine D.Antonelli, Alexandre2020-05-14T14:27:39Z2020-05-14T14:27:39Z2020https://repositorio.inpa.gov.br/handle/1/1545410.3389/fgene.2019.01407High-throughput DNA sequencing techniques enable time- and cost-effective sequencing of large portions of the genome. Instead of sequencing and annotating whole genomes, many phylogenetic studies focus sequencing effort on large sets of pre-selected loci, which further reduces costs and bioinformatic challenges while increasing coverage. One common approach that enriches loci before sequencing is often referred to as target sequence capture. This technique has been shown to be applicable to phylogenetic studies of greatly varying evolutionary depth. Moreover, it has proven to produce powerful, large multi-locus DNA sequence datasets suitable for phylogenetic analyses. However, target capture requires careful considerations, which may greatly affect the success of experiments. Here we provide a simple flowchart for designing phylogenomic target capture experiments. We discuss necessary decisions from the identification of target loci to the final bioinformatic processing of sequence data. We outline challenges and solutions related to the taxonomic scope, sample quality, and available genomic resources of target capture projects. We hope this review will serve as a useful roadmap for designing and carrying out successful phylogenetic target capture studies. © Copyright © 2020 Andermann, Torres Jiménez, Matos-Maraví, Batista, Blanco-Pastor, Gustafsson, Kistler, Liberal, Oxelman, Bacon and Antonelli.Volume 10Attribution-NonCommercial-NoDerivs 3.0 Brazilhttp://creativecommons.org/licenses/by-nc-nd/3.0/br/info:eu-repo/semantics/openAccessDna SequenceHigh Throughput SequencingPhylogenyReviewA Guide to Carrying Out a Phylogenomic Target Sequence Capture Projectinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleFrontiers in Geneticsengreponame:Repositório Institucional do INPAinstname:Instituto Nacional de Pesquisas da Amazônia (INPA)instacron:INPAORIGINALartigo-inpa.pdfartigo-inpa.pdfapplication/pdf4139551https://repositorio.inpa.gov.br/bitstream/1/15454/1/artigo-inpa.pdfd1f2ce9b99124fc25f1733d152987c2dMD511/154542020-05-14 11:14:13.515oai:repositorio:1/15454Repositório de PublicaçõesPUBhttps://repositorio.inpa.gov.br/oai/requestopendoar:2020-05-14T15:14:13Repositório Institucional do INPA - Instituto Nacional de Pesquisas da Amazônia (INPA)false |
dc.title.en.fl_str_mv |
A Guide to Carrying Out a Phylogenomic Target Sequence Capture Project |
title |
A Guide to Carrying Out a Phylogenomic Target Sequence Capture Project |
spellingShingle |
A Guide to Carrying Out a Phylogenomic Target Sequence Capture Project Andermann, Tobias Dna Sequence High Throughput Sequencing Phylogeny Review |
title_short |
A Guide to Carrying Out a Phylogenomic Target Sequence Capture Project |
title_full |
A Guide to Carrying Out a Phylogenomic Target Sequence Capture Project |
title_fullStr |
A Guide to Carrying Out a Phylogenomic Target Sequence Capture Project |
title_full_unstemmed |
A Guide to Carrying Out a Phylogenomic Target Sequence Capture Project |
title_sort |
A Guide to Carrying Out a Phylogenomic Target Sequence Capture Project |
author |
Andermann, Tobias |
author_facet |
Andermann, Tobias Torres-Jiminez, Maria Fernanda Matos-Maraví, Pável F. Batista, Romina B. Blanco-Pastor, José Luis Gustafsson, A. Lovisa S. Kistler, Logan Liberal, Isabel Mar?a Oxelman, Bengt Bacon, Christine D. Antonelli, Alexandre |
author_role |
author |
author2 |
Torres-Jiminez, Maria Fernanda Matos-Maraví, Pável F. Batista, Romina B. Blanco-Pastor, José Luis Gustafsson, A. Lovisa S. Kistler, Logan Liberal, Isabel Mar?a Oxelman, Bengt Bacon, Christine D. Antonelli, Alexandre |
author2_role |
author author author author author author author author author author |
dc.contributor.author.fl_str_mv |
Andermann, Tobias Torres-Jiminez, Maria Fernanda Matos-Maraví, Pável F. Batista, Romina B. Blanco-Pastor, José Luis Gustafsson, A. Lovisa S. Kistler, Logan Liberal, Isabel Mar?a Oxelman, Bengt Bacon, Christine D. Antonelli, Alexandre |
dc.subject.eng.fl_str_mv |
Dna Sequence High Throughput Sequencing Phylogeny Review |
topic |
Dna Sequence High Throughput Sequencing Phylogeny Review |
description |
High-throughput DNA sequencing techniques enable time- and cost-effective sequencing of large portions of the genome. Instead of sequencing and annotating whole genomes, many phylogenetic studies focus sequencing effort on large sets of pre-selected loci, which further reduces costs and bioinformatic challenges while increasing coverage. One common approach that enriches loci before sequencing is often referred to as target sequence capture. This technique has been shown to be applicable to phylogenetic studies of greatly varying evolutionary depth. Moreover, it has proven to produce powerful, large multi-locus DNA sequence datasets suitable for phylogenetic analyses. However, target capture requires careful considerations, which may greatly affect the success of experiments. Here we provide a simple flowchart for designing phylogenomic target capture experiments. We discuss necessary decisions from the identification of target loci to the final bioinformatic processing of sequence data. We outline challenges and solutions related to the taxonomic scope, sample quality, and available genomic resources of target capture projects. We hope this review will serve as a useful roadmap for designing and carrying out successful phylogenetic target capture studies. © Copyright © 2020 Andermann, Torres Jiménez, Matos-Maraví, Batista, Blanco-Pastor, Gustafsson, Kistler, Liberal, Oxelman, Bacon and Antonelli. |
publishDate |
2020 |
dc.date.accessioned.fl_str_mv |
2020-05-14T14:27:39Z |
dc.date.available.fl_str_mv |
2020-05-14T14:27:39Z |
dc.date.issued.fl_str_mv |
2020 |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
https://repositorio.inpa.gov.br/handle/1/15454 |
dc.identifier.doi.none.fl_str_mv |
10.3389/fgene.2019.01407 |
url |
https://repositorio.inpa.gov.br/handle/1/15454 |
identifier_str_mv |
10.3389/fgene.2019.01407 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.ispartof.pt_BR.fl_str_mv |
Volume 10 |
dc.rights.driver.fl_str_mv |
Attribution-NonCommercial-NoDerivs 3.0 Brazil http://creativecommons.org/licenses/by-nc-nd/3.0/br/ info:eu-repo/semantics/openAccess |
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Attribution-NonCommercial-NoDerivs 3.0 Brazil http://creativecommons.org/licenses/by-nc-nd/3.0/br/ |
eu_rights_str_mv |
openAccess |
dc.publisher.none.fl_str_mv |
Frontiers in Genetics |
publisher.none.fl_str_mv |
Frontiers in Genetics |
dc.source.none.fl_str_mv |
reponame:Repositório Institucional do INPA instname:Instituto Nacional de Pesquisas da Amazônia (INPA) instacron:INPA |
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INPA |
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Repositório Institucional do INPA |
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Repositório Institucional do INPA - Instituto Nacional de Pesquisas da Amazônia (INPA) |
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