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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.


As Figure 2 but with five Tulipa cultivars included (see text).
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Figure 3: As Figure 2 but with five Tulipa cultivars included (see text).

Mentions: Gene trees were constructed for each contig separately using POFAD. In 23 of the 26 gene trees, “Connecticut King” and “White Fox” grouped together, as well as “Star Gazer” and “Trumpet” (the exceptions being Contig_25751, contig_6165, and contig_34202). The same clustering resulted from constructing the Neighbor Network of the combined weighted genetic distance matrices of the 26 gene contigs (Figure 2A). As expected, introducing Tulipa as an out-group to the analysis did not introduce changes in the clustering among the Lilium cultivars (Figure 3A). The four cultivars are connected to multiple edges in the Network (Figure 3A), possibly indicating “non tree-like” behavior of the sequences involved. As for Tulipa, “Cantata” and “Princeps” that belong to T. fosteriana grouped together and “Ile de France,” “Kees Nelis” and “Bellona” that belong to T. gesneriana clustered together as well with multiple edges (Figure 3A).


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)

As Figure 2 but with five Tulipa cultivars included (see text).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 3: As Figure 2 but with five Tulipa cultivars included (see text).
Mentions: Gene trees were constructed for each contig separately using POFAD. In 23 of the 26 gene trees, “Connecticut King” and “White Fox” grouped together, as well as “Star Gazer” and “Trumpet” (the exceptions being Contig_25751, contig_6165, and contig_34202). The same clustering resulted from constructing the Neighbor Network of the combined weighted genetic distance matrices of the 26 gene contigs (Figure 2A). As expected, introducing Tulipa as an out-group to the analysis did not introduce changes in the clustering among the Lilium cultivars (Figure 3A). The four cultivars are connected to multiple edges in the Network (Figure 3A), possibly indicating “non tree-like” behavior of the sequences involved. As for Tulipa, “Cantata” and “Princeps” that belong to T. fosteriana grouped together and “Ile de France,” “Kees Nelis” and “Bellona” that belong to T. gesneriana clustered together as well with multiple edges (Figure 3A).

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.