Evolution of Lineage-Specific Gene Networks Underlying the Considerable Fruit Shape Diversity in Persimmon

Haruka Maeda, Takashi Akagi, Noriyuki Onoue, Atsushi Kono, Ryutaro Tao

Research output: Contribution to journalArticlepeer-review

5 Citations (Scopus)


The shapes of plant organs reflect the evolution of each lineage and have been diversified according to lineage-specific adaptations to environment. Research on the molecular pathways responsible for organ shapes has traditionally been focused mainly on leaves or flowers. Thus, little is known about the pathways controlling fruit shapes, despite their diversity in some plant species. In this study, we analyzed oriental persimmon (Diospyros kaki), which exhibits considerable diversity in fruit shapes among cultivars, to elucidate the underlying molecular mechanism using transcriptomic data and quantitative evaluation. First, to filter the candidate genes associated with persimmon fruit shapes, the whole gene expression patterns obtained using mRNA-Seq analysis from 100 individuals, including a segregated population and various cultivars, were assessed to detect correlations with principal component scores for fruit shapes characterized with elliptic Fourier descriptors. Next, a gene co-expression network analysis with weighted gene co-expression network analysis (WGCNA) package revealed that class 1 KNOX family genes and SEEDSTICK function as integrators along with some phytohormone-related genes, to regulate the fruit shape diversity. On the other hand, the OVATE family genes also contribute to fruit shape diversity, of which pathway would be potentially shared with other plant species. Evolutionary aspects suggest that acquisition of a high lineage-specific and variable expression of class 1 KNOX gene, knotted-like homeobox of Arabidopsis thaliana 1 (KNAT1), in young fruit is important for establishing the persimmon-specific mechanism that determines fruit shape diversity.

Original languageEnglish
Pages (from-to)2464-2477
Number of pages14
JournalPlant and Cell Physiology
Issue number11
Publication statusPublished - Nov 1 2019
Externally publishedYes


  • Class 1 KNOX
  • Co-expression network analysis
  • Diospyros
  • Fruit shape
  • Image analysis
  • mRNA-seq

ASJC Scopus subject areas

  • Physiology
  • Plant Science
  • Cell Biology


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