Use of homologous and heterologous gene expression profiling tools to characterize transcription dynamics during apple fruit maturation and ripening.
Use of homologous and heterologous gene expression profiling tools to characterize transcription dynamics during apple fruit maturation and ripening.
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DOI：
10.1186/1471-2229-10-229
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发表时间：
2010-10-25
影响因子：
5.3
通讯作者：
Giovannoni J
中科院分区：
文献类型：
--
作者：
Costa F;Alba R;Schouten H;Soglio V;Gianfranceschi L;Serra S;Musacchi S;Sansavini S;Costa G;Fei Z;Giovannoni J
果实的发育、成熟和成熟是由一系列复杂的生化和生理变化组成的，在苹果和番茄等更年期水果中，这些变化是由气体激素乙烯协调的。这些变化导致最终的果实质量，了解这些过程背后的功能机制具有生物学和实践意义。迄今为止，对苹果基因表达的分析已有许多报道。在这项研究中，我们重点研究了乙烯在苹果成熟过程中的作用，特别是比较了激素受体竞争对手1-甲基环丙烯在正常成熟过程中的转录组学变化。为了深入了解苹果成熟的分子调控过程，并与番茄（成熟研究的模式物种）进行比较，我们利用同源和异源（番茄）微阵列分析了参与果实发育和成熟的基因转录组动力学，重点研究了乙烯调控的基因。使用这两种类型的微阵列促进了苹果和番茄之间的转录组比较（后者使用先前发表的数据，并可在TED：番茄表达数据库中获得），并突出了两个物种在成熟过程中保存的基因，这反过来又为进一步的比较基因组研究奠定了基础。跨种分析的第二个目的是检验异源（特别是番茄）微阵列杂交在成熟过程相关候选基因鉴定中的效率。转录组学数据揭示了成熟相关基因和乙烯响应基因在果实成熟过程中的协调表达，进一步促进了果实成熟和成熟过程中乙烯响应的分析。我们基于微阵列杂交的组合策略使正常更年期苹果成熟过程中的转录组特征，以及乙烯依赖性转录组变化的定义成为可能。与番茄果实成熟和乙烯应答转录组活性的比较，有助于鉴定出假定的保守的同源成熟相关基因，这些基因可作为评估果实植物物种基因组中基因活性保守性的初始候选基因。
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. 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. 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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影响因子：
4.4
作者：
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