Main Conclusion A survey of developed fruit gene-specific datasets and the implementation of a novel cis -element analysis tool indicate specific transcription factors as novel regulatory actors under HT response and CI protection. Abstract Heat treatment (HT) prior to cold storage (CS) has been successfully applied to ameliorate fruit chilling injury (CI) disorders. Molecular studies have identified several HT-driven benefits and putative CI-protective molecules and mechanisms. However, bioinformatic tools and analyses able to integrate fruit-specific information are necessary to begin functional studies and breeding projects. In this work , a HT-responsive gene dataset (HTds) and four fruit expression datasets (FEds), containing gene-specific information from several species and postharvest conditions, were developed and characterized. FEds provided information about HT-responsive genes, not only validating their sensitivity to HT in different systems but also revealing most of them as CS-responsive. A special focus was given to peach heat treatment-sensitive transcriptional regulation by the development of a novel Perl motif analysis software ( cis Analyzer) and a curated plant cis -elements dataset (PASPds). cis Analyzer is able to assess sequence motifs presence, localization, enrichment and discovery on biological sequences. Its implementation for the enrichment analysis of PASPds motifs on the promoters of HTds genes rendered particular cis -elements that indicate certain transcription factor (TF) families as responsible of fruit HT-sensitive transcription regulation. Phylogenetic and postharvest expression data of these TFs showed a functional diversity of TF families, with members able to fulfil roles under HT, CS and/or both treatments. All integrated datasets and cis Analyzer tool were deposited in FruitGeneDB ( https://www.cefobi-conicet.gov.ar/FruitGeneDB/search1.php ), a new available database with a great potential for fruit gene functional studies, including the markers of HT and CS responses whose study will contribute to unravel HT-driven CI-protection and select tolerant cultivars.

中文翻译：

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水果采后基因数据集的生成和用于功能研究的新型基序分析工具：揭示桃果实热处理和冷藏反应之间的联系

主要结论 对已开发的水果基因特异性数据集的调查和新型顺式元素分析工具的实施表明，特定转录因子是 HT 反应和 CI 保护下的新型调节因子。摘要冷藏 (CS) 之前的热处理 (HT) 已成功应用于改善水果冷害 (CI) 疾病。分子研究已经确定了几种 HT 驱动的益处和推定的 CI 保护分子和机制。然而，能够整合水果特定信息的生物信息学工具和分析对于开始功能研究和育种项目是必要的。在这项工作中，开发和表征了一个 HT 响应基因数据集 (HTds) 和四个水果表达数据集 (FEds)，其中包含来自多个物种和收获后条件的基因特异性信息。FEds 提供了有关 HT 反应基因的信息，不仅验证了它们在不同系统中对 HT 的敏感性，而且还揭示了它们中的大多数是 CS 反应的。通过开发新的 Perl 基序分析软件 (cis Analyzer) 和策划的植物 cis 元素数据集 (PASPds)，特别关注桃热处理敏感的转录调控。cis Analyzer 能够评估生物序列上的序列基序存在、定位、富集和发现。其对 HTds 基因启动子上 PASPds 基序的富集分析的实施提供了特定的顺式元件，这些元件表明某些转录因子 (TF) 家族负责水果 HT 敏感的转录调节。这些 TF 的系统发育和收获后表达数据显示了 TF 家族的功能多样性，成员能够履行 HT、CS 和/或两种治疗下的角色。所有集成数据集和 cis Analyzer 工具都保存在 FruitGeneDB (https://www.cefobi-conicet.gov.ar/FruitGeneDB/search1.php) 中，这是一个新的可用数据库，具有巨大的水果基因功能研究潜力，包括标记HT 和 CS 反应的研究将有助于解开 HT 驱动的 CI 保护和选择耐受品种。