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Mango (Mangifera indica L.) cv. Kent fruit mesocarp de novo transcriptome assembly identifies gene families important for ripening

Fruit ripening is a physiological and biochemical process genetically programmed to regulate fruit quality parameters like firmness, flavor, odor and color, as well as production of ethylene in climacteric fruit. In this study, a transcriptomic analysis of mango (Mangifera indica L.) mesocarp cv. “K...

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Autores principales: Dautt-Castro, Mitzuko, Ochoa-Leyva, Adrian, Contreras-Vergara, Carmen A., Pacheco-Sanchez, Magda A., Casas-Flores, Sergio, Sanchez-Flores, Alejandro, Kuhn, David N., Islas-Osuna, Maria A.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4332321/
https://www.ncbi.nlm.nih.gov/pubmed/25741352
http://dx.doi.org/10.3389/fpls.2015.00062
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author Dautt-Castro, Mitzuko
Ochoa-Leyva, Adrian
Contreras-Vergara, Carmen A.
Pacheco-Sanchez, Magda A.
Casas-Flores, Sergio
Sanchez-Flores, Alejandro
Kuhn, David N.
Islas-Osuna, Maria A.
author_facet Dautt-Castro, Mitzuko
Ochoa-Leyva, Adrian
Contreras-Vergara, Carmen A.
Pacheco-Sanchez, Magda A.
Casas-Flores, Sergio
Sanchez-Flores, Alejandro
Kuhn, David N.
Islas-Osuna, Maria A.
author_sort Dautt-Castro, Mitzuko
collection PubMed
description Fruit ripening is a physiological and biochemical process genetically programmed to regulate fruit quality parameters like firmness, flavor, odor and color, as well as production of ethylene in climacteric fruit. In this study, a transcriptomic analysis of mango (Mangifera indica L.) mesocarp cv. “Kent” was done to identify key genes associated with fruit ripening. Using the Illumina sequencing platform, 67,682,269 clean reads were obtained and a transcriptome of 4.8 Gb. A total of 33,142 coding sequences were predicted and after functional annotation, 25,154 protein sequences were assigned with a product according to Swiss-Prot database and 32,560 according to non-redundant database. Differential expression analysis identified 2,306 genes with significant differences in expression between mature-green and ripe mango [1,178 up-regulated and 1,128 down-regulated (FDR ≤ 0.05)]. The expression of 10 genes evaluated by both qRT-PCR and RNA-seq data was highly correlated (R = 0.97), validating the differential expression data from RNA-seq alone. Gene Ontology enrichment analysis, showed significantly represented terms associated to fruit ripening like “cell wall,” “carbohydrate catabolic process” and “starch and sucrose metabolic process” among others. Mango genes were assigned to 327 metabolic pathways according to Kyoto Encyclopedia of Genes and Genomes database, among them those involved in fruit ripening such as plant hormone signal transduction, starch and sucrose metabolism, galactose metabolism, terpenoid backbone, and carotenoid biosynthesis. This study provides a mango transcriptome that will be very helpful to identify genes for expression studies in early and late flowering mangos during fruit ripening.
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spelling pubmed-43323212015-03-04 Mango (Mangifera indica L.) cv. Kent fruit mesocarp de novo transcriptome assembly identifies gene families important for ripening Dautt-Castro, Mitzuko Ochoa-Leyva, Adrian Contreras-Vergara, Carmen A. Pacheco-Sanchez, Magda A. Casas-Flores, Sergio Sanchez-Flores, Alejandro Kuhn, David N. Islas-Osuna, Maria A. Front Plant Sci Plant Science Fruit ripening is a physiological and biochemical process genetically programmed to regulate fruit quality parameters like firmness, flavor, odor and color, as well as production of ethylene in climacteric fruit. In this study, a transcriptomic analysis of mango (Mangifera indica L.) mesocarp cv. “Kent” was done to identify key genes associated with fruit ripening. Using the Illumina sequencing platform, 67,682,269 clean reads were obtained and a transcriptome of 4.8 Gb. A total of 33,142 coding sequences were predicted and after functional annotation, 25,154 protein sequences were assigned with a product according to Swiss-Prot database and 32,560 according to non-redundant database. Differential expression analysis identified 2,306 genes with significant differences in expression between mature-green and ripe mango [1,178 up-regulated and 1,128 down-regulated (FDR ≤ 0.05)]. The expression of 10 genes evaluated by both qRT-PCR and RNA-seq data was highly correlated (R = 0.97), validating the differential expression data from RNA-seq alone. Gene Ontology enrichment analysis, showed significantly represented terms associated to fruit ripening like “cell wall,” “carbohydrate catabolic process” and “starch and sucrose metabolic process” among others. Mango genes were assigned to 327 metabolic pathways according to Kyoto Encyclopedia of Genes and Genomes database, among them those involved in fruit ripening such as plant hormone signal transduction, starch and sucrose metabolism, galactose metabolism, terpenoid backbone, and carotenoid biosynthesis. This study provides a mango transcriptome that will be very helpful to identify genes for expression studies in early and late flowering mangos during fruit ripening. Frontiers Media S.A. 2015-02-18 /pmc/articles/PMC4332321/ /pubmed/25741352 http://dx.doi.org/10.3389/fpls.2015.00062 Text en Copyright © 2015 Dautt-Castro, Ochoa-Leyva, Contreras-Vergara, Pacheco-Sanchez, Casas-Flores, Sanchez-Flores, Kuhn and Islas-Osuna. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Plant Science
Dautt-Castro, Mitzuko
Ochoa-Leyva, Adrian
Contreras-Vergara, Carmen A.
Pacheco-Sanchez, Magda A.
Casas-Flores, Sergio
Sanchez-Flores, Alejandro
Kuhn, David N.
Islas-Osuna, Maria A.
Mango (Mangifera indica L.) cv. Kent fruit mesocarp de novo transcriptome assembly identifies gene families important for ripening
title Mango (Mangifera indica L.) cv. Kent fruit mesocarp de novo transcriptome assembly identifies gene families important for ripening
title_full Mango (Mangifera indica L.) cv. Kent fruit mesocarp de novo transcriptome assembly identifies gene families important for ripening
title_fullStr Mango (Mangifera indica L.) cv. Kent fruit mesocarp de novo transcriptome assembly identifies gene families important for ripening
title_full_unstemmed Mango (Mangifera indica L.) cv. Kent fruit mesocarp de novo transcriptome assembly identifies gene families important for ripening
title_short Mango (Mangifera indica L.) cv. Kent fruit mesocarp de novo transcriptome assembly identifies gene families important for ripening
title_sort mango (mangifera indica l.) cv. kent fruit mesocarp de novo transcriptome assembly identifies gene families important for ripening
topic Plant Science
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4332321/
https://www.ncbi.nlm.nih.gov/pubmed/25741352
http://dx.doi.org/10.3389/fpls.2015.00062
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