J Integr Plant Biol. ›› 2011, Vol. 53 ›› Issue (10): 800-813.DOI: 10.1111/j.1744-7909.2011.01073.x

• Molecular Ecology and Evolution • Previous Articles     Next Articles

Exploring the Transcriptome Landscape of Pomegranate Fruit Peel for Natural Product Biosynthetic Gene and SSR Marker Discovery

Nadia Nicole Ono1, Monica Therese Britton2, Joseph Nathaniel Fass2, Charles Meyer Nicolet2, Dawei Lin2 and Li Tian1*   

  1. 1Department of Plant Sciences, University of California, Davis, CA 95616, USA
    2Genome Center, University of California, Davis, CA 95616, USA
  • Received:2011-07-01 Accepted:2011-09-04 Published:2011-09-12
  • About author:*Corresponding author Tel: +1 530 752 0940; Fax: +1 530 752 9659; Email: ltian@ucdavis.edu


Pomegranate fruit peel is rich in bioactive plant natural products, such as hydrolyzable tannins and anthocyanins. Despite their documented roles in human nutrition and fruit quality, genes involved in natural product biosynthesis have not been cloned from pomegranate and very little sequence information is available on pomegranate in the public domain. Shotgun transcriptome sequencing of pomegranate fruit peel cDNA was performed using RNA-Seq on the Illumina Genome Analyzer platform. Over 100 million raw sequence reads were obtained and assembled into 9,839 transcriptome assemblies (TAs) (>200 bp). Candidate genes for hydrolyzable tannin, anthocyanin, flavonoid, terpenoid and fatty acid biosynthesis and/or regulation were identified. Three lipid transfer proteins were obtained that may contribute to the previously reported IgE reactivity of pomegranate fruit extracts. In addition, 115 SSR markers were identified from the pomegranate fruit peel transcriptome and primers were designed for 77 SSR markers. The pomegranate fruit peel transcriptome set provides a valuable platform for natural product biosynthetic gene and SSR marker discovery in pomegranate. This work also demonstrates that next-generation transcriptome sequencing is an economical and effective approach for investigating natural product biosynthesis, identifying genes controlling important agronomic traits, and discovering molecular markers in non-model specialty crop species.

Ono NN, Britton MT, Fass JN, Nicolet CM, Lin D , Tian L (2011) Exploring the transcriptome, landscape of pomegranate fruit peel for natural product biosynthetic gene and SSR marker discovery. J. Integr. Plant Biol. 53(10), 800–813.

Key words: hydrolyzable tannin, natural product, pomegranate, SSR marker, transcriptome

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