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

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Abstract

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.

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Abbreviations

GO:

Gene ontology

KEGG:

The Kyoto Encyclopedia of Genes and Genomes pathway database

SSR:

Simple sequence repeat

PPIS:

Photoperiod-insensitive

PPS:

Photoperiod-sensitive

FAO:

Food and Agriculture Organization of the United Nations

CDS:

Coding sequences

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Acknowledgments

We thank Guangdong Academy of Agricultural Sciences, Southern China Innovation Center for help in providing instruments and equipment. This work was supported by Guangdong Natural Science Foundation (No. S2012010010722), Guangdong Academy of Agricultural Sciences Dean Fund (No. 201203); Science and Technology Infrastructure Construction Project of Guangdong Key Laboratory for New Technology Research of Vegetables (Grant No. 2013112) and “948″ project from Ministry of Agriculture of China (2012-Z55).

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Authors and Affiliations

  1. Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China

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

  2. Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, 510640, China

    Tingquan Wu, Shaobo Luo, Rui Wang, Yujuan Zhong, Xiaomei Xu, Xiaoming He & Baojuan Sun

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  1. Tingquan Wu
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  2. Shaobo Luo
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  3. Rui Wang
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  4. Yujuan Zhong
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  5. Xiaomei Xu
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  6. Yu’e Lin
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  7. Xiaoming He
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  9. Hexun Huang
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Correspondence to Hexun Huang.

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Tingquan Wu and Shaobo Luo are co-first authors and contributed equally to this work.

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Wu, T., Luo, S., Wang, R. et al. The first Illumina-based de novo transcriptome sequencing and analysis of pumpkin (Cucurbita moschata Duch.) and SSR marker development. Mol Breeding 34, 1437–1447 (2014). https://doi.org/10.1007/s11032-014-0128-x

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  • DOI: https://doi.org/10.1007/s11032-014-0128-x

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