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Multi-omics data integration provides insights into the post-harvest biology of a long shelf-life tomato landrace
Horticulture Research ( IF 8.7 ) Pub Date : 2022-01-31 , DOI: 10.1093/hr/uhab042
Riccardo Aiese Cigliano 1 , Riccardo Aversano 2 , Antonio Di Matteo 2 , Samuela Palombieri 3 , Pasquale Termolino 3 , Claudia Angelini 4 , Hamed Bostan 2 , Maria Cammareri 3 , Federica Maria Consiglio 3 , Floriana Della Ragione 5 , Rosa Paparo 3 , Vladimir Totev Valkov 6 , Antonella Vitiello 3 , Domenico Carputo 2 , Maria Luisa Chiusano 2 , Maurizio D'Esposito 5 , Silvana Grandillo 3 , Maria Rosaria Matarazzo 5 , Luigi Frusciante 2 , Nunzio D'Agostino 2 , Clara Conicella 3
Affiliation  

Abstract
In this study we investigated the transcriptome and epigenome dynamics of the tomato fruit during post-harvest in a landrace belonging to a group of tomatoes (Solanum lycopersicum L.) collectively known as “Piennolo del Vesuvio”, all characterized by a long shelf-life. Expression of protein-coding genes and microRNAs as well as DNA methylation patterns and histone modifications were analysed in distinct post-harvest phases. Multi-omics data integration contributed to the elucidation of the molecular mechanisms underlying processes leading to long shelf-life. We unveiled global changes in transcriptome and epigenome. DNA methylation increased and the repressive histone mark H3K27me3 was lost as the fruit progressed from red ripe to 150 days post-harvest. Thousands of genes were differentially expressed, about half of which were potentially epi-regulated as they were engaged in at least one epi-mark change in addition to being microRNA targets in ~5% of cases. Down-regulation of the ripening regulator MADS-RIN and of genes involved in ethylene response and cell wall degradation was consistent with the delayed fruit softening. Large-scale epigenome reprogramming that occurred in the fruit during post-harvest likely contributed to delayed fruit senescence.


中文翻译:

多组学数据集成提供了对长保质期番茄地方品种收获后生物学的见解

摘要
在这项研究中,我们调查了番茄果实在收获后的转录组和表观基因组动态,该品种属于一组番茄(Solanum lycopersicum L.),统称为“Piennolo del Vesuvio”。, 所有的特点都是保质期长。在不同的收获后阶段分析了蛋白质编码基因和 microRNA 的表达以及 DNA 甲基化模式和组蛋白修饰。多组学数据集成有助于阐明导致长保质期的过程的分子机制。我们揭示了转录组和表观基因组的全球变化。随着果实从红熟到收获后 150 天,DNA 甲基化增加,抑制性组蛋白标记 H3K27me3 丢失。数千个基因被差异表达,其中大约一半可能受到表观调节,因为它们除了在约 5% 的病例中是 microRNA 靶标外,还参与至少一种表观标记变化。成熟调节剂MADS-RIN的下调与乙烯反应和细胞壁降解有关的基因与延迟的果实软化一致。收获后果实中发生的大规模表观基因组重编程可能导致果实衰老延迟。
更新日期:2022-01-31
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