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

E. Valderrama, J.E. Richardson, C.A. Kidner, S. Madriñán, G.N. Stone

Resultado de la investigación: Contribución a RevistaArtículo

5 Citas (Scopus)

Resumen

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.
Idioma originalEnglish
Páginas (desde-hasta)13-24
Número de páginas12
PublicaciónMolecular Phylogenetics and Evolution
Volumen119
DOI
EstadoPublished - 2018

Huella dactilar

Zingiberaceae
Phylogeny
Transcriptome
transcriptome
phylogeny
phylogenetics
herbarium
herbaria
Ribosomal Spacer DNA
DNA
gene
Biodiversity
Base Pairing
Introns
Genes
intergenic DNA
ribosomal DNA
internal transcribed spacers
Renealmia (Zingiberaceae)
tropical plant

Citar esto

@article{6ceceefe92844a54b0340d2e39950128,
title = "Transcriptome mining for phylogenetic markers in a recently radiated genus of tropical plants (Renealmia L.f., Zingiberaceae)",
abstract = "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. {\circledC} 2017 Elsevier Inc.",
author = "E. Valderrama and J.E. Richardson and C.A. Kidner and S. Madri{\~n}{\'a}n and G.N. Stone",
note = "Export Date: 14 December 2017 CODEN: MPEVE Correspondence Address: Valderrama, E.; Facultad de Psicolog{\'i}a y Programa de Biolog{\'i}a, Universidad El BosqueColombia; email: e.valderrama.e@gmail.com References: Abbott, R.J., James, J.K., Milne, R.I., Gillies, A.C.M., Plant introductions, hybridization and gene flow (2003) Philos. Trans. R. Soc. B: Biol. Sci., 358, pp. 1123-1132; Altschul, S.F., Gish, W., Miller, W., Myers, E.W., Lipman, D.J., Basic local alignment search tool (1990) J. Mol. Biol., 215, pp. 403-410; Andrews, S., Lindenbaum, P., Howard, B., Ewels, P., (2015), FastQC; Armstrong, K.E., Stone, G.N., Nicholls, J.A., Valderrama, E., Anderberg, A.A., Smedmark, J., Gautier, L., Richardson, J.E., Patterns of diversification amongst tropical regions compared: a case study in Sapotaceae (2014) Front. Genet., 5, pp. 1-13; Auvray, G., Harris, D.J., Richardson, J.E., Newman, M.F., S{\"a}rkinen, T.E., Phylogeny and Dating of Aframomum (Zingiberaceae) (2010) Diversity, Phylogeny and Evolution in the Monocotyledons, pp. 287-305. , O. Seberg A. S{\'a}nchez Barfod G. Petersen J.I. Davis Aarhus Denmark; {\'A}lvarez, I., Wendel, J.F., Ribosomal ITS sequences and plant phylogenetic inference (2003) Mol. Phylogenet. Evol., 29, pp. 417-434; Bakker, F.T., Lei, D., Yu, J., Mohammadin, S., Wei, Z., van de Kerke, S., Gravendeel, B., Holmer, R., Herbarium genomics: plastome sequence assembly from a range of herbarium specimens using an Iterative Organelle Genome Assembly pipeline (2015) Biol. J. Lin. 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Transcriptome mining for phylogenetic markers in a recently radiated genus of tropical plants (Renealmia L.f., Zingiberaceae). / Valderrama, E.; Richardson, J.E.; Kidner, C.A.; Madriñán, S.; Stone, G.N.

En: Molecular Phylogenetics and Evolution, Vol. 119, 2018, p. 13-24.

Resultado de la investigación: Contribución a RevistaArtículo

TY - JOUR

T1 - Transcriptome mining for phylogenetic markers in a recently radiated genus of tropical plants (Renealmia L.f., Zingiberaceae)

AU - Valderrama, E.

AU - Richardson, J.E.

AU - Kidner, C.A.

AU - Madriñán, S.

AU - Stone, G.N.

N1 - Export Date: 14 December 2017 CODEN: MPEVE Correspondence Address: Valderrama, E.; Facultad de Psicología y Programa de Biología, Universidad El BosqueColombia; email: e.valderrama.e@gmail.com References: Abbott, R.J., James, J.K., Milne, R.I., Gillies, A.C.M., Plant introductions, hybridization and gene flow (2003) Philos. Trans. R. Soc. B: Biol. Sci., 358, pp. 1123-1132; Altschul, S.F., Gish, W., Miller, W., Myers, E.W., Lipman, D.J., Basic local alignment search tool (1990) J. Mol. Biol., 215, pp. 403-410; Andrews, S., Lindenbaum, P., Howard, B., Ewels, P., (2015), FastQC; Armstrong, K.E., Stone, G.N., Nicholls, J.A., Valderrama, E., Anderberg, A.A., Smedmark, J., Gautier, L., Richardson, J.E., Patterns of diversification amongst tropical regions compared: a case study in Sapotaceae (2014) Front. Genet., 5, pp. 1-13; Auvray, G., Harris, D.J., Richardson, J.E., Newman, M.F., Särkinen, T.E., Phylogeny and Dating of Aframomum (Zingiberaceae) (2010) Diversity, Phylogeny and Evolution in the Monocotyledons, pp. 287-305. , O. Seberg A. Sánchez Barfod G. Petersen J.I. Davis Aarhus Denmark; Álvarez, I., Wendel, J.F., Ribosomal ITS sequences and plant phylogenetic inference (2003) Mol. Phylogenet. Evol., 29, pp. 417-434; Bakker, F.T., Lei, D., Yu, J., Mohammadin, S., Wei, Z., van de Kerke, S., Gravendeel, B., Holmer, R., Herbarium genomics: plastome sequence assembly from a range of herbarium specimens using an Iterative Organelle Genome Assembly pipeline (2015) Biol. J. Lin. Soc., 117, pp. 33-43; Bi, K., Vanderpool, D., Singhal, S., Linderoth, T., Moritz, C., Good, J.M., Transcriptome-based exon capture enables highly cost-effective comparative genomic data collection at moderate evolutionary scales (2012) BMC Genomics, 13, p. 403; (2010), Geneious Pro; Bolger, A.M., Lohse, M., Usadel, B., Trimmomatic: a flexible trimmer for Illumina sequence data (2014) Bioinformatics, 30, pp. 2114-2120; Bouckaert, R., Heled, J., Kühnert, D., Vaughan, T., Wu, C.-H., Xie, D., Suchard, M.A., Drummond, A.J., BEAST 2: a software platform for Bayesian evolutionary analysis (2014) PLoS Comput. Biol., 10. , e1003537–6; Bouckaert, R.R., DensiTree: making sense of sets of phylogenetic trees (2010) Bioinformatics, 26, pp. 1372-1373; Brassac, J., Blattner, F.R., Species-Level Phylogeny and Polyploid Relationships in Hordeum (Poaceae) Inferred by Next-Generation Sequencing and In Silico Cloning of Multiple Nuclear Loci (2015) Syst. Biol., 64, pp. 792-808; Castillo-Ramírez, S., Liu, L., Pearl, D., Edwards, S.V., Bayesian estimation of species trees: a practical guide to optimal sampling and analysis (2011) Estimating Species Trees, pp. 15-34. , L.L. Knowles L.S. Kubatko John Wiley & Sons Hoboken, New Jersey; Chamala, S., García, N., Godden, G.T., Krishnakumar, V., Jordon-Thaden, I.E., Smet, R.D., Barbazuk, W.B., Soltis, P.S., MarkerMiner 1.0: a new application for phylogenetic marker development using angiosperm transcriptomes (2015) Appl. Plant Sci., 3, pp. 1400115-1400118; Comes, H.P., Abbott, R.J., Molecular phylogeography, reticulation, and lineage sorting in Mediterranean Senecio sect. Senecio (Asteraceae) (2001) Evolution, 55, p. 1943; Cronn, R., Knaus, B.J., Liston, A., Maughan, P.J., Parks, M., Syring, J.V., Udall, J., Targeted enrichment strategies for next-generation plant biology (2012) Am. J. 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PY - 2018

Y1 - 2018

N2 - 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.

AB - 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.

U2 - 10.1016/j.ympev.2017.10.001

DO - 10.1016/j.ympev.2017.10.001

M3 - Artículo

VL - 119

SP - 13

EP - 24

JO - Molecular Phylogenetics and Evolution

JF - Molecular Phylogenetics and Evolution

SN - 1055-7903

ER -