title: Using multi-locus allelic sequence data to estimate genetic divergence among four Lilium (Liliaceae) cultivars.
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.
authors.affiliation: Wageningen UR Plant Breeding, Wageningen University and Research Centre Wageningen, Netherlands.
authors.forename: Arwa
authors.initials: A
authors.lastname: Shahin
authors.affiliation: Wageningen UR Plant Breeding, Wageningen University and Research Centre Wageningen, Netherlands.
authors.forename: Marinus J M
authors.initials: MJ
authors.lastname: Smulders
authors.affiliation: Wageningen UR Plant Breeding, Wageningen University and Research Centre Wageningen, Netherlands.
authors.forename: Jaap M
authors.initials: JM
authors.lastname: van Tuyl
authors.affiliation: Wageningen UR Plant Breeding, Wageningen University and Research Centre Wageningen, Netherlands.
authors.forename: Paul
authors.initials: P
authors.lastname: Arens
authors.affiliation: Biosystematics Group, Wageningen University Wageningen, Netherlands.
authors.forename: Freek T
authors.initials: FT
authors.lastname: Bakker
keywords: Consensus Network; Lilium; POFAD; RAxML; Tulipa; allelic variation; genetic divergence