Molecular Breeding

, Volume 34, Issue 3, pp 1437–1447 | Cite as

The first Illumina-based de novo transcriptome sequencing and analysis of pumpkin (Cucurbita moschata Duch.) and SSR marker development

  • Tingquan Wu
  • Shaobo Luo
  • Rui Wang
  • Yujuan Zhong
  • Xiaomei Xu
  • Yu’e Lin
  • Xiaoming He
  • Baojuan Sun
  • Hexun Huang


Pumpkin (Cucurbita moschata Duch.) is an important vegetable crop cultivated worldwide. In this study, the pumpkin transcriptome was sequenced by RNA-seq using the Illumina Hiseq 2000. A total of 52,849,316 clean sequencing reads, 66,621 contigs and 62,480 unigenes were postulated. Based on similarity searches with known proteins, 47,899 genes (76.66 % of the unigenes) were annotated: 47,596, 34,368 and 16,700 mapped in Nr, Swissprot and COG classifications, respectively; 21,164 were annotated with 44 gene ontology functional categories; and 13,728 were annotated to 269 pathways by searching the Kyoto Encyclopedia of Genes and Genomes pathway database. A total of 7,814 simple sequence repeats (SSRs) were identified in these unigenes and 4,794 pairs of primers were designed for application of SSRs. To date, 35 SSRs have been validated in 12 pumpkin varieties and can separate the pumpkin varieties into Cucurbita maxima and Cucurbita moschata. In addition, the expression of eight photoperiod-related unigenes were studied in different pumpkin plants and it was deduced that they may contribute to late flowering and light insensitiveness. This research will provide an important platform to facilitate gene discovery for functional genome studies of pumpkin and to conduct SSR discovery for breeders for use in pumpkin breeding.


Pumpkin Transcriptome SSR primers Illumina sequencing PPIS pumpkin plants 



Gene ontology


The Kyoto Encyclopedia of Genes and Genomes pathway database


Simple sequence repeat






Food and Agriculture Organization of the United Nations


Coding sequences

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Copyright information

© Springer Science+Business Media Dordrecht 2014

Authors and Affiliations

  • Tingquan Wu
    • 1
    • 2
  • Shaobo Luo
    • 1
    • 2
  • Rui Wang
    • 1
    • 2
  • Yujuan Zhong
    • 1
    • 2
  • Xiaomei Xu
    • 1
    • 2
  • Yu’e Lin
    • 1
  • Xiaoming He
    • 1
    • 2
  • Baojuan Sun
    • 1
    • 2
  • Hexun Huang
    • 1
  1. 1.Vegetable Research InstituteGuangdong Academy of Agricultural SciencesGuangzhouChina
  2. 2.Guangdong Key Laboratory for New Technology Research of VegetablesGuangzhouChina

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