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...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2014-10-01
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| Series: | Frontiers in Plant Science |
| Subjects: | |
| Online Access: | http://journal.frontiersin.org/Journal/10.3389/fpls.2014.00567/full |
| _version_ | 1818540444735242240 |
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| author | Arwa eShahin Marinus J M eSmulders Jaap eVan Tuyl Paul eArens Freek T Bakker |
| author_facet | Arwa eShahin Marinus J M eSmulders Jaap eVan Tuyl Paul eArens Freek T Bakker |
| author_sort | Arwa eShahin |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-12-11T21:55:27Z |
| format | Article |
| id | doaj.art-162e250a7a6a44e7bd4e4aafa9c728fa |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-12-11T21:55:27Z |
| publishDate | 2014-10-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-162e250a7a6a44e7bd4e4aafa9c728fa2022-12-22T00:49:19ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2014-10-01510.3389/fpls.2014.00567104779Using multi-locus allelic sequence data to estimate genetic divergence among four Lilium (Liliaceae) cultivarsArwa eShahin0Marinus J M eSmulders1Jaap eVan Tuyl2Paul eArens3Freek T Bakker4Wageningen University & Research CentreWageningen University & Research CentreWageningen University & Research CentreWageningen University & Research CentreWageningen University & Research CentreNext 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.http://journal.frontiersin.org/Journal/10.3389/fpls.2014.00567/fullLiliumTulipagenetic divergenceallelic variationPOFADRAxML |
| spellingShingle | Arwa eShahin Marinus J M eSmulders Jaap eVan Tuyl Paul eArens Freek T Bakker Using multi-locus allelic sequence data to estimate genetic divergence among four Lilium (Liliaceae) cultivars Frontiers in Plant Science Lilium Tulipa genetic divergence allelic variation POFAD RAxML |
| 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 | Lilium Tulipa genetic divergence allelic variation POFAD RAxML |
| url | http://journal.frontiersin.org/Journal/10.3389/fpls.2014.00567/full |
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