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Using multi-locus allelic sequence data to estimate genetic divergence among four Lilium (Liliaceae) cultivars

Next Generation Sequencing (NGS) may enable estimating relationships among genotypes using allelic variation of multiple nuclear genes simultaneously. We explored the potential and caveats of this strategy in four genetically distant Lilium cultivars to estimate their genetic divergence from transcr...

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Autores principales: Shahin, Arwa, Smulders, Marinus J. M., van Tuyl, Jaap M., Arens, Paul, Bakker, Freek T.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4202788/
https://www.ncbi.nlm.nih.gov/pubmed/25368628
http://dx.doi.org/10.3389/fpls.2014.00567
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author Shahin, Arwa
Smulders, Marinus J. M.
van Tuyl, Jaap M.
Arens, Paul
Bakker, Freek T.
author_facet Shahin, Arwa
Smulders, Marinus J. M.
van Tuyl, Jaap M.
Arens, Paul
Bakker, Freek T.
author_sort Shahin, Arwa
collection PubMed
description Next Generation Sequencing (NGS) may enable estimating relationships among genotypes using allelic variation of multiple nuclear genes simultaneously. We explored the potential and caveats of this strategy in four genetically distant Lilium cultivars to estimate their genetic divergence from transcriptome sequences using three approaches: POFAD (Phylogeny of Organisms from Allelic Data, uses allelic information of sequence data), RAxML (Randomized Accelerated Maximum Likelihood, tree building based on concatenated consensus sequences) and Consensus Network (constructing a network summarizing among gene tree conflicts). Twenty six gene contigs were chosen based on the presence of orthologous sequences in all cultivars, seven of which also had an orthologous sequence in Tulipa, used as out-group. The three approaches generated the same topology. Although the resolution offered by these approaches is high, in this case there was no extra benefit in using allelic information. We conclude that these 26 genes can be widely applied to construct a species tree for the genus Lilium.
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spelling pubmed-42027882014-11-03 Using multi-locus allelic sequence data to estimate genetic divergence among four Lilium (Liliaceae) cultivars Shahin, Arwa Smulders, Marinus J. M. van Tuyl, Jaap M. Arens, Paul Bakker, Freek T. Front Plant Sci Plant Science Next Generation Sequencing (NGS) may enable estimating relationships among genotypes using allelic variation of multiple nuclear genes simultaneously. We explored the potential and caveats of this strategy in four genetically distant Lilium cultivars to estimate their genetic divergence from transcriptome sequences using three approaches: POFAD (Phylogeny of Organisms from Allelic Data, uses allelic information of sequence data), RAxML (Randomized Accelerated Maximum Likelihood, tree building based on concatenated consensus sequences) and Consensus Network (constructing a network summarizing among gene tree conflicts). Twenty six gene contigs were chosen based on the presence of orthologous sequences in all cultivars, seven of which also had an orthologous sequence in Tulipa, used as out-group. The three approaches generated the same topology. Although the resolution offered by these approaches is high, in this case there was no extra benefit in using allelic information. We conclude that these 26 genes can be widely applied to construct a species tree for the genus Lilium. Frontiers Media S.A. 2014-10-20 /pmc/articles/PMC4202788/ /pubmed/25368628 http://dx.doi.org/10.3389/fpls.2014.00567 Text en Copyright © 2014 Shahin, Smulders, van Tuyl, Arens and Bakker. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Plant Science
Shahin, Arwa
Smulders, Marinus J. M.
van Tuyl, Jaap M.
Arens, Paul
Bakker, Freek T.
Using multi-locus allelic sequence data to estimate genetic divergence among four Lilium (Liliaceae) cultivars
title Using multi-locus allelic sequence data to estimate genetic divergence among four Lilium (Liliaceae) cultivars
title_full Using multi-locus allelic sequence data to estimate genetic divergence among four Lilium (Liliaceae) cultivars
title_fullStr Using multi-locus allelic sequence data to estimate genetic divergence among four Lilium (Liliaceae) cultivars
title_full_unstemmed Using multi-locus allelic sequence data to estimate genetic divergence among four Lilium (Liliaceae) cultivars
title_short Using multi-locus allelic sequence data to estimate genetic divergence among four Lilium (Liliaceae) cultivars
title_sort using multi-locus allelic sequence data to estimate genetic divergence among four lilium (liliaceae) cultivars
topic Plant Science
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4202788/
https://www.ncbi.nlm.nih.gov/pubmed/25368628
http://dx.doi.org/10.3389/fpls.2014.00567
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