GSE116581 fruitENCODE: An encyclopedia of DNA elements for fruit ripening

Contributor : Silin ZhongSeries Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencing ; Methylation profiling by high throughput sequencingOrganism : Arabidopsis thaliana ; Carica papaya ; Citrullus lanatus ; Cucumis melo ; Cucumis sativus ; Fragaria vesca ; Malus domestica ; Musa acuminata AAA Group ; Oryza sativa ; Prunus persica ; Pyrus x bretschneideri ; Solanum lycopersicum ; Vitis viniferaFleshy 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 n...

Source: GEO: Gene Expression Omnibus - July 4, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing Methylation profiling by high throughput sequencing Arabidopsis thaliana Carica papaya Citrullus lanatus Cucumis melo Cucumis Source Type: research