Tree Genetics & Genomes

, 15:22 | Cite as

Gene expression and metabolite profiling analyses of developing pomegranate fruit peel reveal interactions between anthocyanin and punicalagin production

  • Rotem Harel-Beja
  • Li Tian
  • Shiri Freilich
  • Rida Habashi
  • Hamutal Borochov-Neori
  • Tamar Lahav
  • Taly Trainin
  • Adi Doron-Faigenboim
  • Ron Ophir
  • Irit Bar-Ya’akov
  • Rachel Amir
  • Doron HollandEmail author
Original Article
Part of the following topical collections:
  1. Genome Biology


The fruit peel of pomegranate (Punica granatum L.) contains high concentrations of polyphenols, which play a critical role in determining the color and nutritional value of fruits. This study evaluated and compared the production of two major classes of polyphenols in the pomegranate fruit skin, i.e., anthocyanins, the main pigments in pomegranate, and punicalagin, a highly bioactive hydrolyzable tannin that is synthesized from an intermediate of the shikimate pathway. Gene expression and metabolite (anthocyanins and punicalagin) accumulation were determined, at three stages of fruit development, in the peel of red and pink cultivars, containing high and low levels of anthocyanins, respectively. Red and pink pomegranate cultivars showed the highest difference in gene expression during the transition from early to late fruit developmental stages, while differences between the cultivars were relatively small at each developmental stage. Positive correlations were found between anthocyanin and total punicalagin content. Of the differentially expressed contigs, 3093 and 312 contigs were correlated (Pearson’s r, |0.75|; P < = 0.02) with anthocyanins and punicalagin content, respectively. Interestingly, 143 contigs positively correlated with both anthocyanin and punicalagin. The differentially expressed contigs could be further divided into five groups representing a distinct characteristic correlation with each of the analyzed metabolites. Overall, the presented information provides a comprehensive view of the interplay between the hydrolyzable tannin and the anthocyanin pathways and points to genetic factors potentially involved in this interaction.


Punica granatum Anthocyanin Punicalagin Fruit development Polyphenols Differential expression 



We thank Kamel Hatib for orchard management.

Data archiving statement

The raw sequencing data is archived in NCBI No. PRJNA521857.

Authors’ contribution

RHB and DH conducted the study and wrote the manuscript, DH LT and RA initiated the study, RHB and IBY collected and prepared the plant material, RH and RA did the punicalagin analysis, HBN did the AT analysis, TT purified the RNA, and SF, TL, ADF, and RO did the bioinformatics analysis.


This research was supported by research grant award No. IS-4822-15 R from BARD, The United States—Israel Binational Agricultural Research and Development Fund.

Compliance with ethical standards

Competing interests

The authors declare that they have no competing interests.

Supplementary material

11295_2019_1329_MOESM1_ESM.docx (64 kb)
ESM 1 (DOCX 63 kb)
11295_2019_1329_MOESM2_ESM.xlsx (412 kb)
ESM 2 (XLSX 411 kb)


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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  • Rotem Harel-Beja
    • 1
  • Li Tian
    • 2
  • Shiri Freilich
    • 1
  • Rida Habashi
    • 3
  • Hamutal Borochov-Neori
    • 4
  • Tamar Lahav
    • 1
  • Taly Trainin
    • 1
  • Adi Doron-Faigenboim
    • 5
  • Ron Ophir
    • 5
  • Irit Bar-Ya’akov
    • 1
  • Rachel Amir
    • 3
  • Doron Holland
    • 1
    Email author
  1. 1.Newe Ya’ar Research Center, Agricultural Research OrganizationRamat YishayIsrael
  2. 2.Department of Plant SciencesUniversity of California DavisDavisUSA
  3. 3.MIGAL - Galilee Research InstituteKiryat ShmonaIsrael
  4. 4.Southern Arava R&DHevel EilotIsrael
  5. 5.Plant Sciences, Agricultural Research OrganizationBet DaganIsrael

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