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

Shahin A, Smulders MJ, van Tuyl JM, Arens P, Bakker FT - Front Plant Sci (2014)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Wageningen UR Plant Breeding, Wageningen University and Research Centre Wageningen, Netherlands.

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.

No MeSH data available.


Floral morphology of the four Lilium L. cultivars used in this study.
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Figure 1: Floral morphology of the four Lilium L. cultivars used in this study.

Mentions: Transcriptome sequence data of four Lilium and five Tulipa cultivars (all diploid) used for this study were from Shahin et al. (2012). The four Lilium cultivars, representing the four main hybrid groups of the genus Lilium, are: “Star Gazer” (Oriental, Archelirion section), breeding line “Trumpet 061099” (Trumpet, Leucolirion subsection a), “White Fox” (Longiflorum, Leucolirion subsection b), and “Connecticut King” (Asiatic, Sinomartagon section) (Figure 1). The five Tulipa cultivars are: “Cantata” and “Princeps,” which belong to T. fosteriana (Eichleres section), and “Bellona,” “Kees Nelis” and “Ile de France,” which belong to T. gesneriana (Tulipa section).


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

Shahin A, Smulders MJ, van Tuyl JM, Arens P, Bakker FT - Front Plant Sci (2014)

Floral morphology of the four Lilium L. cultivars used in this study.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4202788&req=5

Figure 1: Floral morphology of the four Lilium L. cultivars used in this study.
Mentions: Transcriptome sequence data of four Lilium and five Tulipa cultivars (all diploid) used for this study were from Shahin et al. (2012). The four Lilium cultivars, representing the four main hybrid groups of the genus Lilium, are: “Star Gazer” (Oriental, Archelirion section), breeding line “Trumpet 061099” (Trumpet, Leucolirion subsection a), “White Fox” (Longiflorum, Leucolirion subsection b), and “Connecticut King” (Asiatic, Sinomartagon section) (Figure 1). The five Tulipa cultivars are: “Cantata” and “Princeps,” which belong to T. fosteriana (Eichleres section), and “Bellona,” “Kees Nelis” and “Ile de France,” which belong to T. gesneriana (Tulipa section).

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Wageningen UR Plant Breeding, Wageningen University and Research Centre Wageningen, Netherlands.

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.

No MeSH data available.