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Whole genome comparison between table and wine grapes reveals a comprehensive catalog of structural variants
BACKGROUND: Grapevine (Vitis vinifera L.) is the most important Mediterranean fruit crop, used to produce both wine and spirits as well as table grape and raisins. Wine and table grape cultivars represent two divergent germplasm pools with different origins and domestication history, as well as diff...
Autores principales: | , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2014
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3890619/ https://www.ncbi.nlm.nih.gov/pubmed/24397443 http://dx.doi.org/10.1186/1471-2229-14-7 |
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author | Di Genova, Alex Almeida, Andrea Miyasaka Muñoz-Espinoza, Claudia Vizoso, Paula Travisany, Dante Moraga, Carol Pinto, Manuel Hinrichsen, Patricio Orellana, Ariel Maass, Alejandro |
author_facet | Di Genova, Alex Almeida, Andrea Miyasaka Muñoz-Espinoza, Claudia Vizoso, Paula Travisany, Dante Moraga, Carol Pinto, Manuel Hinrichsen, Patricio Orellana, Ariel Maass, Alejandro |
author_sort | Di Genova, Alex |
collection | PubMed |
description | BACKGROUND: Grapevine (Vitis vinifera L.) is the most important Mediterranean fruit crop, used to produce both wine and spirits as well as table grape and raisins. Wine and table grape cultivars represent two divergent germplasm pools with different origins and domestication history, as well as differential characteristics for berry size, cluster architecture and berry chemical profile, among others. ‘Sultanina’ plays a pivotal role in modern table grape breeding providing the main source of seedlessness. This cultivar is also one of the most planted for fresh consumption and raisins production. Given its importance, we sequenced it and implemented a novel strategy for the de novo assembly of its highly heterozygous genome. RESULTS: Our approach produced a draft genome of 466 Mb, recovering 82% of the genes present in the grapevine reference genome; in addition, we identified 240 novel genes. A large number of structural variants and SNPs were identified. Among them, 45 (21 SNPs and 24 INDELs) were experimentally confirmed in ‘Sultanina’ and six SNPs in other 23 table grape varieties. Transposable elements corresponded to ca. 80% of the repetitive sequences involved in structural variants and more than 2,000 genes were affected in their structure by these variants. Some of these genes are likely involved in embryo development, suggesting that they may contribute to seedlessness, a key trait for table grapes. CONCLUSIONS: This work produced the first structural variants and SNPs catalog for grapevine, constituting a novel and very powerful tool for genomic studies in this key fruit crop, particularly useful to support marker assisted breeding in table grapes. |
format | Online Article Text |
id | pubmed-3890619 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-38906192014-01-15 Whole genome comparison between table and wine grapes reveals a comprehensive catalog of structural variants Di Genova, Alex Almeida, Andrea Miyasaka Muñoz-Espinoza, Claudia Vizoso, Paula Travisany, Dante Moraga, Carol Pinto, Manuel Hinrichsen, Patricio Orellana, Ariel Maass, Alejandro BMC Plant Biol Research Article BACKGROUND: Grapevine (Vitis vinifera L.) is the most important Mediterranean fruit crop, used to produce both wine and spirits as well as table grape and raisins. Wine and table grape cultivars represent two divergent germplasm pools with different origins and domestication history, as well as differential characteristics for berry size, cluster architecture and berry chemical profile, among others. ‘Sultanina’ plays a pivotal role in modern table grape breeding providing the main source of seedlessness. This cultivar is also one of the most planted for fresh consumption and raisins production. Given its importance, we sequenced it and implemented a novel strategy for the de novo assembly of its highly heterozygous genome. RESULTS: Our approach produced a draft genome of 466 Mb, recovering 82% of the genes present in the grapevine reference genome; in addition, we identified 240 novel genes. A large number of structural variants and SNPs were identified. Among them, 45 (21 SNPs and 24 INDELs) were experimentally confirmed in ‘Sultanina’ and six SNPs in other 23 table grape varieties. Transposable elements corresponded to ca. 80% of the repetitive sequences involved in structural variants and more than 2,000 genes were affected in their structure by these variants. Some of these genes are likely involved in embryo development, suggesting that they may contribute to seedlessness, a key trait for table grapes. CONCLUSIONS: This work produced the first structural variants and SNPs catalog for grapevine, constituting a novel and very powerful tool for genomic studies in this key fruit crop, particularly useful to support marker assisted breeding in table grapes. BioMed Central 2014-01-07 /pmc/articles/PMC3890619/ /pubmed/24397443 http://dx.doi.org/10.1186/1471-2229-14-7 Text en Copyright © 2014 Di Genova et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an open access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Article Di Genova, Alex Almeida, Andrea Miyasaka Muñoz-Espinoza, Claudia Vizoso, Paula Travisany, Dante Moraga, Carol Pinto, Manuel Hinrichsen, Patricio Orellana, Ariel Maass, Alejandro Whole genome comparison between table and wine grapes reveals a comprehensive catalog of structural variants |
title | Whole genome comparison between table and wine grapes reveals a comprehensive catalog of structural variants |
title_full | Whole genome comparison between table and wine grapes reveals a comprehensive catalog of structural variants |
title_fullStr | Whole genome comparison between table and wine grapes reveals a comprehensive catalog of structural variants |
title_full_unstemmed | Whole genome comparison between table and wine grapes reveals a comprehensive catalog of structural variants |
title_short | Whole genome comparison between table and wine grapes reveals a comprehensive catalog of structural variants |
title_sort | whole genome comparison between table and wine grapes reveals a comprehensive catalog of structural variants |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3890619/ https://www.ncbi.nlm.nih.gov/pubmed/24397443 http://dx.doi.org/10.1186/1471-2229-14-7 |
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