Transcriptome mining for phylogenetic markers in a recently radiated genus of tropical plants (Renealmia L.f., Zingiberaceae)

The reconstruction of relationships within species-rich groups that have recently evolved in biodiversity hotspots is hampered by a lack of phylogenetically informative markers. It is also made difficult by the lack of sampling necessary to reconstruct a species-level phylogeny. We use transcriptome...

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Autores:
Tipo de recurso:
Fecha de publicación:
2018
Institución:
Universidad del Rosario
Repositorio:
Repositorio EdocUR - U. Rosario
Idioma:
eng
OAI Identifier:
oai:repository.urosario.edu.co:10336/22621
Acceso en línea:
https://doi.org/10.1016/j.ympev.2017.10.001
https://repository.urosario.edu.co/handle/10336/22621
Palabra clave:
Messenger RNA
Ribosome DNA
Transcriptome
Bayes theorem
Classification
DNA sequence
Genetic marker
Genetics
Intron
Metabolism
Phylogeny
Species difference
Tropic climate
Zingiberaceae
Bayes Theorem
Genetic Markers
Introns
Phylogeny
Species Specificity
Transcriptome
Tropical Climate
Zingiberaceae
Diversification
Markers
Neotropical
Phylogenetics
Transcriptomes
Zingiberaceae
Messenger
Ribosomal
DNA
DNA
RNA
Sequence Analysis
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License
Abierto (Texto Completo)
id EDOCUR2_e78d52de3e9ebe966987180471305271
oai_identifier_str oai:repository.urosario.edu.co:10336/22621
network_acronym_str EDOCUR2
network_name_str Repositorio EdocUR - U. Rosario
repository_id_str
spelling ab4ce66b-6fbd-4e61-9253-9433d2cf245c359328600b327704a-f8c3-4125-b940-82130e1ae0a220aaa981-a23f-40cb-8bfb-45cdf579d3b698636406-defa-4277-9a01-ae26bb6989af2020-05-25T23:57:10Z2020-05-25T23:57:10Z2018The reconstruction of relationships within species-rich groups that have recently evolved in biodiversity hotspots is hampered by a lack of phylogenetically informative markers. It is also made difficult by the lack of sampling necessary to reconstruct a species-level phylogeny. We use transcriptome mining to search for markers to reconstruct a phylogeny of the amphi-Atlantic genus Renealmia L. f. (Zingiberaceae). We recover seven introns from single copy genes and use them to reconstruct the phylogeny of the genus together with a commonly used phylogenetic marker, internal transcribed spacers of ribosomal DNA (ITS) that has previously been used to reconstruct the phylogeny of the genus. We targeted genes with low numbers of base pairs that improves sequencing success using highly degraded DNA from herbarium specimens. The use of herbarium specimens greatly increased the number of species in the study as these were readily available in historical collections. Data were obtained for 14 of the 17 African species and 54 of the 65 Neotropical species. The phylogeny was well-supported for a number of Renealmia subgroups although relationships among those clades remained poorly supported. © 2017 Elsevier Inc.application/pdfhttps://doi.org/10.1016/j.ympev.2017.10.0011095951310557903https://repository.urosario.edu.co/handle/10336/22621engAcademic Press Inc.2413Molecular Phylogenetics and EvolutionVol. 119Molecular Phylogenetics and Evolution, ISSN:10959513, 10557903, Vol.119,(2018); pp. 13-24https://www.scopus.com/inward/record.uri?eid=2-s2.0-85032944773&doi=10.1016%2fj.ympev.2017.10.001&partnerID=40&md5=f6f72d9b1025d88f2ec3e89ca6dabebdAbierto (Texto Completo)http://purl.org/coar/access_right/c_abf2instname:Universidad del Rosarioreponame:Repositorio Institucional EdocURMessenger RNARibosome DNATranscriptomeBayes theoremClassificationDNA sequenceGenetic markerGeneticsIntronMetabolismPhylogenySpecies differenceTropic climateZingiberaceaeBayes TheoremGenetic MarkersIntronsPhylogenySpecies SpecificityTranscriptomeTropical ClimateZingiberaceaeDiversificationMarkersNeotropicalPhylogeneticsTranscriptomesZingiberaceaeMessengerRibosomalDNADNARNASequence AnalysisTranscriptome mining for phylogenetic markers in a recently radiated genus of tropical plants (Renealmia L.f., Zingiberaceae)articleArtículohttp://purl.org/coar/version/c_970fb48d4fbd8a85http://purl.org/coar/resource_type/c_6501Valderrama, EugenioRichardson, James-EdwardKidner, Catherine A.Madriñán, SantiagoStone, Graham N.10336/22621oai:repository.urosario.edu.co:10336/226212022-05-02 07:37:17.13111https://repository.urosario.edu.coRepositorio institucional EdocURedocur@urosario.edu.co
dc.title.spa.fl_str_mv Transcriptome mining for phylogenetic markers in a recently radiated genus of tropical plants (Renealmia L.f., Zingiberaceae)
title Transcriptome mining for phylogenetic markers in a recently radiated genus of tropical plants (Renealmia L.f., Zingiberaceae)
spellingShingle Transcriptome mining for phylogenetic markers in a recently radiated genus of tropical plants (Renealmia L.f., Zingiberaceae)
Messenger RNA
Ribosome DNA
Transcriptome
Bayes theorem
Classification
DNA sequence
Genetic marker
Genetics
Intron
Metabolism
Phylogeny
Species difference
Tropic climate
Zingiberaceae
Bayes Theorem
Genetic Markers
Introns
Phylogeny
Species Specificity
Transcriptome
Tropical Climate
Zingiberaceae
Diversification
Markers
Neotropical
Phylogenetics
Transcriptomes
Zingiberaceae
Messenger
Ribosomal
DNA
DNA
RNA
Sequence Analysis
title_short Transcriptome mining for phylogenetic markers in a recently radiated genus of tropical plants (Renealmia L.f., Zingiberaceae)
title_full Transcriptome mining for phylogenetic markers in a recently radiated genus of tropical plants (Renealmia L.f., Zingiberaceae)
title_fullStr Transcriptome mining for phylogenetic markers in a recently radiated genus of tropical plants (Renealmia L.f., Zingiberaceae)
title_full_unstemmed Transcriptome mining for phylogenetic markers in a recently radiated genus of tropical plants (Renealmia L.f., Zingiberaceae)
title_sort Transcriptome mining for phylogenetic markers in a recently radiated genus of tropical plants (Renealmia L.f., Zingiberaceae)
dc.subject.keyword.spa.fl_str_mv Messenger RNA
Ribosome DNA
Transcriptome
Bayes theorem
Classification
DNA sequence
Genetic marker
Genetics
Intron
Metabolism
Phylogeny
Species difference
Tropic climate
Zingiberaceae
Bayes Theorem
Genetic Markers
Introns
Phylogeny
Species Specificity
Transcriptome
Tropical Climate
Zingiberaceae
Diversification
Markers
Neotropical
Phylogenetics
Transcriptomes
Zingiberaceae
topic Messenger RNA
Ribosome DNA
Transcriptome
Bayes theorem
Classification
DNA sequence
Genetic marker
Genetics
Intron
Metabolism
Phylogeny
Species difference
Tropic climate
Zingiberaceae
Bayes Theorem
Genetic Markers
Introns
Phylogeny
Species Specificity
Transcriptome
Tropical Climate
Zingiberaceae
Diversification
Markers
Neotropical
Phylogenetics
Transcriptomes
Zingiberaceae
Messenger
Ribosomal
DNA
DNA
RNA
Sequence Analysis
dc.subject.keyword.eng.fl_str_mv Messenger
Ribosomal
DNA
DNA
RNA
Sequence Analysis
description The reconstruction of relationships within species-rich groups that have recently evolved in biodiversity hotspots is hampered by a lack of phylogenetically informative markers. It is also made difficult by the lack of sampling necessary to reconstruct a species-level phylogeny. We use transcriptome mining to search for markers to reconstruct a phylogeny of the amphi-Atlantic genus Renealmia L. f. (Zingiberaceae). We recover seven introns from single copy genes and use them to reconstruct the phylogeny of the genus together with a commonly used phylogenetic marker, internal transcribed spacers of ribosomal DNA (ITS) that has previously been used to reconstruct the phylogeny of the genus. We targeted genes with low numbers of base pairs that improves sequencing success using highly degraded DNA from herbarium specimens. The use of herbarium specimens greatly increased the number of species in the study as these were readily available in historical collections. Data were obtained for 14 of the 17 African species and 54 of the 65 Neotropical species. The phylogeny was well-supported for a number of Renealmia subgroups although relationships among those clades remained poorly supported. © 2017 Elsevier Inc.
publishDate 2018
dc.date.created.spa.fl_str_mv 2018
dc.date.accessioned.none.fl_str_mv 2020-05-25T23:57:10Z
dc.date.available.none.fl_str_mv 2020-05-25T23:57:10Z
dc.type.eng.fl_str_mv article
dc.type.coarversion.fl_str_mv http://purl.org/coar/version/c_970fb48d4fbd8a85
dc.type.coar.fl_str_mv http://purl.org/coar/resource_type/c_6501
dc.type.spa.spa.fl_str_mv Artículo
dc.identifier.doi.none.fl_str_mv https://doi.org/10.1016/j.ympev.2017.10.001
dc.identifier.issn.none.fl_str_mv 10959513
10557903
dc.identifier.uri.none.fl_str_mv https://repository.urosario.edu.co/handle/10336/22621
url https://doi.org/10.1016/j.ympev.2017.10.001
https://repository.urosario.edu.co/handle/10336/22621
identifier_str_mv 10959513
10557903
dc.language.iso.spa.fl_str_mv eng
language eng
dc.relation.citationEndPage.none.fl_str_mv 24
dc.relation.citationStartPage.none.fl_str_mv 13
dc.relation.citationTitle.none.fl_str_mv Molecular Phylogenetics and Evolution
dc.relation.citationVolume.none.fl_str_mv Vol. 119
dc.relation.ispartof.spa.fl_str_mv Molecular Phylogenetics and Evolution, ISSN:10959513, 10557903, Vol.119,(2018); pp. 13-24
dc.relation.uri.spa.fl_str_mv https://www.scopus.com/inward/record.uri?eid=2-s2.0-85032944773&doi=10.1016%2fj.ympev.2017.10.001&partnerID=40&md5=f6f72d9b1025d88f2ec3e89ca6dabebd
dc.rights.coar.fl_str_mv http://purl.org/coar/access_right/c_abf2
dc.rights.acceso.spa.fl_str_mv Abierto (Texto Completo)
rights_invalid_str_mv Abierto (Texto Completo)
http://purl.org/coar/access_right/c_abf2
dc.format.mimetype.none.fl_str_mv application/pdf
dc.publisher.spa.fl_str_mv Academic Press Inc.
institution Universidad del Rosario
dc.source.instname.spa.fl_str_mv instname:Universidad del Rosario
dc.source.reponame.spa.fl_str_mv reponame:Repositorio Institucional EdocUR
repository.name.fl_str_mv Repositorio institucional EdocUR
repository.mail.fl_str_mv edocur@urosario.edu.co
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