fruitENCODE: An encyclopedia of DNA elements for fruit ripening

Fleshy fruits evolved independently multiple times during angiosperm history, including the use of ethylene for the initiation and maintenance of ripening. ENCODE data of 355 transcriptome, 66 accessible chromatin, 160 histone and 45 DNA methylation profiles from eleven fleshy fruit species revealed three types of transcriptional feedback loops controlling ripening. Eudicots peach, papaya and melon evolved their circuits using carpel senescence NAC genes, whereas tomato, apple and pear utilized floral identity MADS genes derived from recent whole-genome-duplications. The monocot banana used both, forming a unique dual-loop circuit. Genes in these circuits and their tissue-specific H3K27me3 mark could be traced back to both dry fruits and ethylene-independent fleshy fruits, suggesting that the ethylene-dependent ripening mechanisms evolved from pre-existing genetic and epigenetic pathways in the ancestral angiosperms. FruitENCODE provides a comprehensive annotation of functional elements for fleshy fruit crops and new insight into the origins of climacteric fruit ripening.

肉质果实在被子植物（angiosperm）演化历史中曾独立起源多次，其中包括利用乙烯启动并维持果实成熟的演化路径。本研究针对11种肉质果实生成的355份转录组、66份开放染色质、160份组蛋白修饰及45份DNA甲基化组的ENCODE数据，揭示了三类调控果实成熟的转录反馈环路。真双子叶植物（Eudicots）中的桃、番木瓜和甜瓜，通过心皮衰老相关NAC基因构建了成熟调控环路；而番茄、苹果和梨则利用了源自近期全基因组复制事件的花同源MADS基因。单子叶植物（monocot）香蕉则同时采用了两类基因，形成了独特的双环路调控电路。上述调控环路中的基因及其组织特异性H3K27me3修饰标记，均可追溯至干果与不依赖乙烯的肉质果实祖先类群，这表明依赖乙烯的成熟机制是由被子植物祖先中已存在的遗传与表观遗传通路演化而来。果实ENCODE（FruitENCODE）计划为肉质果实作物提供了全面的功能元件注释，并为呼吸跃变型果实成熟的起源提供了全新见解。

搜集汇总

背景与挑战

背景概述

fruitENCODE数据集是一个关于水果成熟过程中DNA元素的功能注释百科全书，包含355个转录组、66个可及染色质、160个组蛋白和45个DNA甲基化图谱，覆盖11种肉质水果物种。该数据集揭示了三种控制水果成熟的转录反馈环路类型，并提供了对乙烯依赖性成熟机制进化起源的新见解。