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Use of homologous and heterologous gene expression profiling tools to characterize transcription dynamics during apple fruit maturation and ripening

BACKGROUND: Fruit development, maturation and ripening consists of a complex series of biochemical and physiological changes that in climacteric fruits, including apple and tomato, are coordinated by the gaseous hormone ethylene. These changes lead to final fruit quality and understanding of the fun...

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Autores principales: Costa, Fabrizio, Alba, Rob, Schouten, Henk, Soglio, Valeria, Gianfranceschi, Luca, Serra, Sara, Musacchi, Stefano, Sansavini, Silviero, Costa, Guglielmo, Fei, Zhangjun, Giovannoni, James
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2010
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3095317/
https://www.ncbi.nlm.nih.gov/pubmed/20973957
http://dx.doi.org/10.1186/1471-2229-10-229
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author Costa, Fabrizio
Alba, Rob
Schouten, Henk
Soglio, Valeria
Gianfranceschi, Luca
Serra, Sara
Musacchi, Stefano
Sansavini, Silviero
Costa, Guglielmo
Fei, Zhangjun
Giovannoni, James
author_facet Costa, Fabrizio
Alba, Rob
Schouten, Henk
Soglio, Valeria
Gianfranceschi, Luca
Serra, Sara
Musacchi, Stefano
Sansavini, Silviero
Costa, Guglielmo
Fei, Zhangjun
Giovannoni, James
author_sort Costa, Fabrizio
collection PubMed
description BACKGROUND: Fruit development, maturation and ripening consists of a complex series of biochemical and physiological changes that in climacteric fruits, including apple and tomato, are coordinated by the gaseous hormone ethylene. These changes lead to final fruit quality and understanding of the functional machinery underlying these processes is of both biological and practical importance. To date many reports have been made on the analysis of gene expression in apple. In this study we focused our investigation on the role of ethylene during apple maturation, specifically comparing transcriptomics of normal ripening with changes resulting from application of the hormone receptor competitor 1-Methylcyclopropene. RESULTS: To gain insight into the molecular process regulating ripening in apple, and to compare to tomato (model species for ripening studies), we utilized both homologous and heterologous (tomato) microarray to profile transcriptome dynamics of genes involved in fruit development and ripening, emphasizing those which are ethylene regulated. The use of both types of microarrays facilitated transcriptome comparison between apple and tomato (for the later using data previously published and available at the TED: tomato expression database) and highlighted genes conserved during ripening of both species, which in turn represent a foundation for further comparative genomic studies. The cross-species analysis had the secondary aim of examining the efficiency of heterologous (specifically tomato) microarray hybridization for candidate gene identification as related to the ripening process. The resulting transcriptomics data revealed coordinated gene expression during fruit ripening of a subset of ripening-related and ethylene responsive genes, further facilitating the analysis of ethylene response during fruit maturation and ripening. CONCLUSION: Our combined strategy based on microarray hybridization enabled transcriptome characterization during normal climacteric apple ripening, as well as definition of ethylene-dependent transcriptome changes. Comparison with tomato fruit maturation and ethylene responsive transcriptome activity facilitated identification of putative conserved orthologous ripening-related genes, which serve as an initial set of candidates for assessing conservation of gene activity across genomes of fruit bearing plant species.
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spelling pubmed-30953172011-05-17 Use of homologous and heterologous gene expression profiling tools to characterize transcription dynamics during apple fruit maturation and ripening Costa, Fabrizio Alba, Rob Schouten, Henk Soglio, Valeria Gianfranceschi, Luca Serra, Sara Musacchi, Stefano Sansavini, Silviero Costa, Guglielmo Fei, Zhangjun Giovannoni, James BMC Plant Biol Research Article BACKGROUND: Fruit development, maturation and ripening consists of a complex series of biochemical and physiological changes that in climacteric fruits, including apple and tomato, are coordinated by the gaseous hormone ethylene. These changes lead to final fruit quality and understanding of the functional machinery underlying these processes is of both biological and practical importance. To date many reports have been made on the analysis of gene expression in apple. In this study we focused our investigation on the role of ethylene during apple maturation, specifically comparing transcriptomics of normal ripening with changes resulting from application of the hormone receptor competitor 1-Methylcyclopropene. RESULTS: To gain insight into the molecular process regulating ripening in apple, and to compare to tomato (model species for ripening studies), we utilized both homologous and heterologous (tomato) microarray to profile transcriptome dynamics of genes involved in fruit development and ripening, emphasizing those which are ethylene regulated. The use of both types of microarrays facilitated transcriptome comparison between apple and tomato (for the later using data previously published and available at the TED: tomato expression database) and highlighted genes conserved during ripening of both species, which in turn represent a foundation for further comparative genomic studies. The cross-species analysis had the secondary aim of examining the efficiency of heterologous (specifically tomato) microarray hybridization for candidate gene identification as related to the ripening process. The resulting transcriptomics data revealed coordinated gene expression during fruit ripening of a subset of ripening-related and ethylene responsive genes, further facilitating the analysis of ethylene response during fruit maturation and ripening. CONCLUSION: Our combined strategy based on microarray hybridization enabled transcriptome characterization during normal climacteric apple ripening, as well as definition of ethylene-dependent transcriptome changes. Comparison with tomato fruit maturation and ethylene responsive transcriptome activity facilitated identification of putative conserved orthologous ripening-related genes, which serve as an initial set of candidates for assessing conservation of gene activity across genomes of fruit bearing plant species. BioMed Central 2010-10-25 /pmc/articles/PMC3095317/ /pubmed/20973957 http://dx.doi.org/10.1186/1471-2229-10-229 Text en Copyright ©2010 Costa 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
Costa, Fabrizio
Alba, Rob
Schouten, Henk
Soglio, Valeria
Gianfranceschi, Luca
Serra, Sara
Musacchi, Stefano
Sansavini, Silviero
Costa, Guglielmo
Fei, Zhangjun
Giovannoni, James
Use of homologous and heterologous gene expression profiling tools to characterize transcription dynamics during apple fruit maturation and ripening
title Use of homologous and heterologous gene expression profiling tools to characterize transcription dynamics during apple fruit maturation and ripening
title_full Use of homologous and heterologous gene expression profiling tools to characterize transcription dynamics during apple fruit maturation and ripening
title_fullStr Use of homologous and heterologous gene expression profiling tools to characterize transcription dynamics during apple fruit maturation and ripening
title_full_unstemmed Use of homologous and heterologous gene expression profiling tools to characterize transcription dynamics during apple fruit maturation and ripening
title_short Use of homologous and heterologous gene expression profiling tools to characterize transcription dynamics during apple fruit maturation and ripening
title_sort use of homologous and heterologous gene expression profiling tools to characterize transcription dynamics during apple fruit maturation and ripening
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3095317/
https://www.ncbi.nlm.nih.gov/pubmed/20973957
http://dx.doi.org/10.1186/1471-2229-10-229
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