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...

Full description

Autores:
Valderrama, Eugenio
Richardson, James E.
Kidner, Catherine A.
Madriñán, Santiago
Stone, Graham N.
Tipo de recurso:
Article of journal
Fecha de publicación:
2018
Institución:
Universidad El Bosque
Repositorio:
Repositorio U. El Bosque
Idioma:
eng
OAI Identifier:
oai:repositorio.unbosque.edu.co:20.500.12495/2944
Acceso en línea:
http://hdl.handle.net/20.500.12495/2944
https://doi.org/10.1016/j.ympev.2017.10.001
https://repositorio.unbosque.edu.co
Palabra clave:
Phylogenetics
Transcriptomes
Markers
Diversification
Zingiberaceae
Neotropical
Región neotropical
Plantas
Fitogenética
Rights
openAccess
License
Acceso cerrado
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repository_id_str
dc.title.spa.fl_str_mv Transcriptome mining for phylogenetic markers in a recently radiated genus of tropical plants (Renealmia L.f., Zingiberaceae)
dc.title.translated.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)
Phylogenetics
Transcriptomes
Markers
Diversification
Zingiberaceae
Neotropical
Región neotropical
Plantas
Fitogenética
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.creator.fl_str_mv Valderrama, Eugenio
Richardson, James E.
Kidner, Catherine A.
Madriñán, Santiago
Stone, Graham N.
dc.contributor.author.none.fl_str_mv Valderrama, Eugenio
Richardson, James E.
Kidner, Catherine A.
Madriñán, Santiago
Stone, Graham N.
dc.subject.keywords.spa.fl_str_mv Phylogenetics
Transcriptomes
Markers
Diversification
Zingiberaceae
Neotropical
topic Phylogenetics
Transcriptomes
Markers
Diversification
Zingiberaceae
Neotropical
Región neotropical
Plantas
Fitogenética
dc.subject.agrovoc.spa.fl_str_mv Región neotropical
Plantas
Fitogenética
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.
publishDate 2018
dc.date.issued.none.fl_str_mv 2018
dc.date.accessioned.none.fl_str_mv 2020-05-18T11:15:39Z
dc.date.available.none.fl_str_mv 2020-05-18T11:15:39Z
dc.type.spa.fl_str_mv article
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dc.type.local.spa.fl_str_mv artículo
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dc.identifier.issn.none.fl_str_mv 1055-7903
dc.identifier.uri.none.fl_str_mv http://hdl.handle.net/20.500.12495/2944
dc.identifier.doi.none.fl_str_mv https://doi.org/10.1016/j.ympev.2017.10.001
dc.identifier.instname.spa.fl_str_mv instname:Universidad El Bosque
dc.identifier.reponame.spa.fl_str_mv reponame:Repositorio Institucional Universidad El Bosque
dc.identifier.repourl.none.fl_str_mv https://repositorio.unbosque.edu.co
identifier_str_mv 1055-7903
instname:Universidad El Bosque
reponame:Repositorio Institucional Universidad El Bosque
url http://hdl.handle.net/20.500.12495/2944
https://doi.org/10.1016/j.ympev.2017.10.001
https://repositorio.unbosque.edu.co
dc.language.iso.none.fl_str_mv eng
language eng
dc.relation.ispartofseries.spa.fl_str_mv Molecular Phylogenetics and Evolution, 1055-7903, Vol 119, 2018, pag 13-24
dc.relation.uri.none.fl_str_mv https://www.sciencedirect.com/science/article/abs/pii/S1055790317307157?via%3Dihub
dc.rights.local.spa.fl_str_mv Acceso cerrado
dc.rights.accessrights.none.fl_str_mv http://purl.org/coar/access_right/c_abf2
info:eu-repo/semantics/openAccess
Acceso abierto
dc.rights.creativecommons.none.fl_str_mv 2018
rights_invalid_str_mv Acceso cerrado
http://purl.org/coar/access_right/c_abf2
Acceso abierto
2018
eu_rights_str_mv openAccess
dc.format.mimetype.none.fl_str_mv application/pdf
dc.publisher.spa.fl_str_mv Elsevier
dc.publisher.journal.spa.fl_str_mv Molecular Phylogenetics and Evolution
institution Universidad El Bosque
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spelling Valderrama, EugenioRichardson, James E.Kidner, Catherine A.Madriñán, SantiagoStone, Graham N.2020-05-18T11:15:39Z2020-05-18T11:15:39Z20181055-7903http://hdl.handle.net/20.500.12495/2944https://doi.org/10.1016/j.ympev.2017.10.001instname:Universidad El Bosquereponame:Repositorio Institucional Universidad El Bosquehttps://repositorio.unbosque.edu.coapplication/pdfengElsevierMolecular Phylogenetics and EvolutionMolecular Phylogenetics and Evolution, 1055-7903, Vol 119, 2018, pag 13-24https://www.sciencedirect.com/science/article/abs/pii/S1055790317307157?via%3DihubTranscriptome mining for phylogenetic markers in a recently radiated genus of tropical plants (Renealmia L.f., Zingiberaceae)Transcriptome mining for phylogenetic markers in a recently radiated genus of tropical plants (Renealmia L.f., Zingiberaceae)articleartículohttp://purl.org/coar/resource_type/c_6501http://purl.org/coar/resource_type/c_2df8fbb1info:eu-repo/semantics/articlehttp://purl.org/coar/version/c_970fb48d4fbd8a85PhylogeneticsTranscriptomesMarkersDiversificationZingiberaceaeNeotropicalRegión neotropicalPlantasFitogenéticaThe 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.Acceso cerradohttp://purl.org/coar/access_right/c_abf2info:eu-repo/semantics/openAccessAcceso abierto2018ORIGINALValderrama_Eugenio_2018.pdfValderrama_Eugenio_2018.pdfapplication/pdf2016184http://18.204.144.38/bitstreams/3923543e-c6b5-4984-9277-8dadbcbd17b7/download2d440ab1150460e350f6b839fcd43070MD53LICENSElicense.txtlicense.txttext/plain; charset=utf-81748http://18.204.144.38/bitstreams/7ca681fb-e9c5-4705-9b45-43d24306ece9/download8a4605be74aa9ea9d79846c1fba20a33MD52THUMBNAILValderrama_Eugenio_2018.pdf.jpgValderrama_Eugenio_2018.pdf.jpgimage/jpeg5775http://18.204.144.38/bitstreams/c61f2ccb-1212-46e4-9ab4-6c4e7c9806eb/download7210a811635d1799e7c05fee5d259be7MD54TEXTValderrama_Eugenio_2018.pdf.txtValderrama_Eugenio_2018.pdf.txtExtracted texttext/plain74958http://18.204.144.38/bitstreams/630f2569-35c5-4337-8f51-e4f02ff3eef5/download7325ea25f43928b4eb53f9fc45b87b7aMD5520.500.12495/2944oai:18.204.144.38:20.500.12495/29442024-02-06 22:22:12.708restrictedhttp://18.204.144.38DSpace Pre-instalado Biteca S.A.Sbibliotecas@biteca.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