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The Transcriptome of the Reference Potato Genome Solanum tuberosum Group Phureja Clone DM1-3 516R44

Advances in molecular breeding in potato have been limited by its complex biological system, which includes vegetative propagation, autotetraploidy, and extreme heterozygosity. The availability of the potato genome and accompanying gene complement with corresponding gene structure, location, and fun...

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Autores principales: Massa, Alicia N., Childs, Kevin L., Lin, Haining, Bryan, Glenn J., Giuliano, Giovanni, Buell, C. Robin
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2011
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3203163/
https://www.ncbi.nlm.nih.gov/pubmed/22046362
http://dx.doi.org/10.1371/journal.pone.0026801
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author Massa, Alicia N.
Childs, Kevin L.
Lin, Haining
Bryan, Glenn J.
Giuliano, Giovanni
Buell, C. Robin
author_facet Massa, Alicia N.
Childs, Kevin L.
Lin, Haining
Bryan, Glenn J.
Giuliano, Giovanni
Buell, C. Robin
author_sort Massa, Alicia N.
collection PubMed
description Advances in molecular breeding in potato have been limited by its complex biological system, which includes vegetative propagation, autotetraploidy, and extreme heterozygosity. The availability of the potato genome and accompanying gene complement with corresponding gene structure, location, and functional annotation are powerful resources for understanding this complex plant and advancing molecular breeding efforts. Here, we report a reference for the potato transcriptome using 32 tissues and growth conditions from the doubled monoploid Solanum tuberosum Group Phureja clone DM1-3 516R44 for which a genome sequence is available. Analysis of greater than 550 million RNA-Seq reads permitted the detection and quantification of expression levels of over 22,000 genes. Hierarchical clustering and principal component analyses captured the biological variability that accounts for gene expression differences among tissues suggesting tissue-specific gene expression, and genes with tissue or condition restricted expression. Using gene co-expression network analysis, we identified 18 gene modules that represent tissue-specific transcriptional networks of major potato organs and developmental stages. This information provides a powerful resource for potato research as well as studies on other members of the Solanaceae family.
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spelling pubmed-32031632011-11-01 The Transcriptome of the Reference Potato Genome Solanum tuberosum Group Phureja Clone DM1-3 516R44 Massa, Alicia N. Childs, Kevin L. Lin, Haining Bryan, Glenn J. Giuliano, Giovanni Buell, C. Robin PLoS One Research Article Advances in molecular breeding in potato have been limited by its complex biological system, which includes vegetative propagation, autotetraploidy, and extreme heterozygosity. The availability of the potato genome and accompanying gene complement with corresponding gene structure, location, and functional annotation are powerful resources for understanding this complex plant and advancing molecular breeding efforts. Here, we report a reference for the potato transcriptome using 32 tissues and growth conditions from the doubled monoploid Solanum tuberosum Group Phureja clone DM1-3 516R44 for which a genome sequence is available. Analysis of greater than 550 million RNA-Seq reads permitted the detection and quantification of expression levels of over 22,000 genes. Hierarchical clustering and principal component analyses captured the biological variability that accounts for gene expression differences among tissues suggesting tissue-specific gene expression, and genes with tissue or condition restricted expression. Using gene co-expression network analysis, we identified 18 gene modules that represent tissue-specific transcriptional networks of major potato organs and developmental stages. This information provides a powerful resource for potato research as well as studies on other members of the Solanaceae family. Public Library of Science 2011-10-28 /pmc/articles/PMC3203163/ /pubmed/22046362 http://dx.doi.org/10.1371/journal.pone.0026801 Text en Massa et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Massa, Alicia N.
Childs, Kevin L.
Lin, Haining
Bryan, Glenn J.
Giuliano, Giovanni
Buell, C. Robin
The Transcriptome of the Reference Potato Genome Solanum tuberosum Group Phureja Clone DM1-3 516R44
title The Transcriptome of the Reference Potato Genome Solanum tuberosum Group Phureja Clone DM1-3 516R44
title_full The Transcriptome of the Reference Potato Genome Solanum tuberosum Group Phureja Clone DM1-3 516R44
title_fullStr The Transcriptome of the Reference Potato Genome Solanum tuberosum Group Phureja Clone DM1-3 516R44
title_full_unstemmed The Transcriptome of the Reference Potato Genome Solanum tuberosum Group Phureja Clone DM1-3 516R44
title_short The Transcriptome of the Reference Potato Genome Solanum tuberosum Group Phureja Clone DM1-3 516R44
title_sort transcriptome of the reference potato genome solanum tuberosum group phureja clone dm1-3 516r44
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3203163/
https://www.ncbi.nlm.nih.gov/pubmed/22046362
http://dx.doi.org/10.1371/journal.pone.0026801
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