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Genome-wide analysis of starch metabolism genes in potato (Solanum tuberosum L.)

BACKGROUND: Starch is the principle constituent of potato tubers and is of considerable importance for food and non-food applications. Its metabolism has been subject of extensive research over the past decades. Despite its importance, a description of the complete inventory of genes involved in sta...

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Autores principales: Van Harsselaar, Jessica K., Lorenz, Julia, Senning, Melanie, Sonnewald, Uwe, Sonnewald, Sophia
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5217216/
https://www.ncbi.nlm.nih.gov/pubmed/28056783
http://dx.doi.org/10.1186/s12864-016-3381-z
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author Van Harsselaar, Jessica K.
Lorenz, Julia
Senning, Melanie
Sonnewald, Uwe
Sonnewald, Sophia
author_facet Van Harsselaar, Jessica K.
Lorenz, Julia
Senning, Melanie
Sonnewald, Uwe
Sonnewald, Sophia
author_sort Van Harsselaar, Jessica K.
collection PubMed
description BACKGROUND: Starch is the principle constituent of potato tubers and is of considerable importance for food and non-food applications. Its metabolism has been subject of extensive research over the past decades. Despite its importance, a description of the complete inventory of genes involved in starch metabolism and their genome organization in potato plants is still missing. Moreover, mechanisms regulating the expression of starch genes in leaves and tubers remain elusive with regard to differences between transitory and storage starch metabolism, respectively. This study aimed at identifying and mapping the complete set of potato starch genes, and to study their expression pattern in leaves and tubers using different sets of transcriptome data. Moreover, we wanted to uncover transcription factors co-regulated with starch accumulation in tubers in order to get insight into the regulation of starch metabolism. RESULTS: We identified 77 genomic loci encoding enzymes involved in starch metabolism. Novel isoforms of many enzymes were found. Their analysis will help to elucidate mechanisms of starch biosynthesis and degradation. Expression analysis of starch genes led to the identification of tissue-specific isoenzymes suggesting differences in the transcriptional regulation of starch metabolism between potato leaf and tuber tissues. Selection of genes predominantly expressed in developing potato tubers and exhibiting an expression pattern indicative for a role in starch biosynthesis enabled the identification of possible transcriptional regulators of tuber starch biosynthesis by co-expression analysis. CONCLUSIONS: This study provides the annotation of the complete set of starch metabolic genes in potato plants and their genomic localizations. Novel, so far undescribed, enzyme isoforms were revealed. Comparative transcriptome analysis enabled the identification of tuber- and leaf-specific isoforms of starch genes. This finding suggests distinct regulatory mechanisms in transitory and storage starch metabolism. Putative regulatory proteins of starch biosynthesis in potato tubers have been identified by co-expression and their expression was verified by quantitative RT-PCR. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-016-3381-z) contains supplementary material, which is available to authorized users.
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spelling pubmed-52172162017-01-09 Genome-wide analysis of starch metabolism genes in potato (Solanum tuberosum L.) Van Harsselaar, Jessica K. Lorenz, Julia Senning, Melanie Sonnewald, Uwe Sonnewald, Sophia BMC Genomics Research Article BACKGROUND: Starch is the principle constituent of potato tubers and is of considerable importance for food and non-food applications. Its metabolism has been subject of extensive research over the past decades. Despite its importance, a description of the complete inventory of genes involved in starch metabolism and their genome organization in potato plants is still missing. Moreover, mechanisms regulating the expression of starch genes in leaves and tubers remain elusive with regard to differences between transitory and storage starch metabolism, respectively. This study aimed at identifying and mapping the complete set of potato starch genes, and to study their expression pattern in leaves and tubers using different sets of transcriptome data. Moreover, we wanted to uncover transcription factors co-regulated with starch accumulation in tubers in order to get insight into the regulation of starch metabolism. RESULTS: We identified 77 genomic loci encoding enzymes involved in starch metabolism. Novel isoforms of many enzymes were found. Their analysis will help to elucidate mechanisms of starch biosynthesis and degradation. Expression analysis of starch genes led to the identification of tissue-specific isoenzymes suggesting differences in the transcriptional regulation of starch metabolism between potato leaf and tuber tissues. Selection of genes predominantly expressed in developing potato tubers and exhibiting an expression pattern indicative for a role in starch biosynthesis enabled the identification of possible transcriptional regulators of tuber starch biosynthesis by co-expression analysis. CONCLUSIONS: This study provides the annotation of the complete set of starch metabolic genes in potato plants and their genomic localizations. Novel, so far undescribed, enzyme isoforms were revealed. Comparative transcriptome analysis enabled the identification of tuber- and leaf-specific isoforms of starch genes. This finding suggests distinct regulatory mechanisms in transitory and storage starch metabolism. Putative regulatory proteins of starch biosynthesis in potato tubers have been identified by co-expression and their expression was verified by quantitative RT-PCR. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-016-3381-z) contains supplementary material, which is available to authorized users. BioMed Central 2017-01-05 /pmc/articles/PMC5217216/ /pubmed/28056783 http://dx.doi.org/10.1186/s12864-016-3381-z Text en © The Author(s). 2017 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research Article
Van Harsselaar, Jessica K.
Lorenz, Julia
Senning, Melanie
Sonnewald, Uwe
Sonnewald, Sophia
Genome-wide analysis of starch metabolism genes in potato (Solanum tuberosum L.)
title Genome-wide analysis of starch metabolism genes in potato (Solanum tuberosum L.)
title_full Genome-wide analysis of starch metabolism genes in potato (Solanum tuberosum L.)
title_fullStr Genome-wide analysis of starch metabolism genes in potato (Solanum tuberosum L.)
title_full_unstemmed Genome-wide analysis of starch metabolism genes in potato (Solanum tuberosum L.)
title_short Genome-wide analysis of starch metabolism genes in potato (Solanum tuberosum L.)
title_sort genome-wide analysis of starch metabolism genes in potato (solanum tuberosum l.)
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5217216/
https://www.ncbi.nlm.nih.gov/pubmed/28056783
http://dx.doi.org/10.1186/s12864-016-3381-z
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