Genome encode analyses reveal the basis of convergent evolution of fleshy fruit ripening

Peitao Lü, Sheng Yu, Ning Zhu, Yun Ru Chen, Biyan Zhou, Yu Pan, David Tzeng, Joao Paulo Fabi, Jason Argyris, Jordi Garcia-Mas, Nenghui Ye, Jianhua ZHANG, Donald Grierson, Jenny Xiang, Zhangjun Fei, James Giovannoni, Silin Zhong*

*Corresponding author for this work

Research output: Contribution to journalJournal articlepeer-review

233 Citations (Scopus)


Fleshy fruits using ethylene to regulate ripening have developed multiple times in the history of angiosperms, presenting a clear case of convergent evolution whose molecular basis remains largely unknown. Analysis of the fruitENCODE data consisting of 361 transcriptome, 71 accessible chromatin, 147 histone and 45 DNA methylation profiles reveals three types of transcriptional feedback circuits controlling ethylene-dependent fruit ripening. These circuits are evolved from senescence or floral organ identity pathways in the ancestral angiosperms either by neofunctionalisation or repurposing pre-existing genes. The epigenome, H3K27me3 in particular, has played a conserved role in restricting ripening genes and their orthologues in dry and ethylene-independent fleshy fruits. Our findings suggest that evolution of ripening is constrained by limited hormone molecules and genetic and epigenetic materials, and whole-genome duplications have provided opportunities for plants to successfully circumvent these limitations.

Original languageEnglish
Pages (from-to)784-791
Number of pages8
JournalNature Plants
Issue number10
Publication statusPublished - 1 Oct 2018

Scopus Subject Areas

  • Plant Science


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