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. Profiling of more than 300 transcriptome, more than 40 DNA methylome, more than 60 chromatin accessibility, more than 160 histone modification and bindings of several key ripening transcription factors in leaf, immature and ripe fruit tissues of 11 fleshy fruit bearing species. The raw data have beed deposited to SRA with Study accession number SRP102870 and Bioproject accession number PRJNA381300.