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...
- 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
- Rights
- License
- Abierto (Texto Completo)
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oai:repository.urosario.edu.co:10336/22621 |
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network_name_str |
Repositorio EdocUR - U. Rosario |
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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 |
_version_ |
1814167507621117952 |