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:
-
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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|
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 |
dc.type.coar.fl_str_mv |
http://purl.org/coar/resource_type/c_2df8fbb1 |
dc.type.coarversion.fl_str_mv |
http://purl.org/coar/version/c_970fb48d4fbd8a85 |
dc.type.local.spa.fl_str_mv |
artículo |
dc.type.coar.none.fl_str_mv |
http://purl.org/coar/resource_type/c_6501 |
dc.type.driver.none.fl_str_mv |
info:eu-repo/semantics/article |
format |
http://purl.org/coar/resource_type/c_6501 |
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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 |