Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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Record number 477452
Title Using multi-locus allelic sequence data to estimate genetic divergence among four Lilium (Liliaceae) cultivars
Author(s) Shahin, A.; Smulders, M.J.M.; Tuyl, J.M. van; Arens, P.F.P.; Bakker, F.T.
Source Frontiers in Plant Science 5 (2014). - ISSN 1664-462X
DOI https://doi.org/10.3389/fpls.2014.00567
Department(s) PRI Biodiversity and Breeding
WUR Plant Breeding
Biosystematics
Publication type Refereed Article in a scientific journal
Publication year 2014
Keyword(s) nuclear ribosomal dna - transcribed spacer region - phylogeny group classification - species trees - reticulate evolution - molecular phylogeny - flowering plants - genus lilium - apg iii - networks
Abstract 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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