Plant Molecular Biology

, Volume 83, Issue 1–2, pp 77–87 | Cite as

Whole transcriptome analysis using next-generation sequencing of model species Setaria viridis to support C4 photosynthesis research

  • Jiajia Xu
  • Yuanyuan Li
  • Xiuling Ma
  • Jianfeng Ding
  • Kai Wang
  • Sisi Wang
  • Ye Tian
  • Hui Zhang
  • Xin-Guang Zhu


Setaria viridis is an emerging model species for genetic studies of C4 photosynthesis. Many basic molecular resources need to be developed to support for this species. In this paper, we performed a comprehensive transcriptome analysis from multiple developmental stages and tissues of S. viridis using next-generation sequencing technologies. Sequencing of the transcriptome from multiple tissues across three developmental stages (seed germination, vegetative growth, and reproduction) yielded a total of 71 million single end 100 bp long reads. Reference-based assembly using Setaria italica genome as a reference generated 42,754 transcripts. De novo assembly generated 60,751 transcripts. In addition, 9,576 and 7,056 potential simple sequence repeats (SSRs) covering S. viridis genome were identified when using the reference based assembled transcripts and the de novo assembled transcripts, respectively. This identified transcripts and SSR provided by this study can be used for both reverse and forward genetic studies based on S. viridis.


Setaria viridis Whole transcriptome analysis Next-generation sequencing technologies C4 photosynthesis 

Supplementary material

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Copyright information

© Springer Science+Business Media Dordrecht 2013

Authors and Affiliations

  • Jiajia Xu
    • 1
    • 2
  • Yuanyuan Li
    • 1
    • 2
  • Xiuling Ma
    • 3
  • Jianfeng Ding
    • 3
  • Kai Wang
    • 3
  • Sisi Wang
    • 2
    • 3
  • Ye Tian
    • 1
    • 2
  • Hui Zhang
    • 2
    • 3
  • Xin-Guang Zhu
    • 1
    • 2
  1. 1.State Key Laboratory of Hybrid Rice Research, Shanghai Institute of Biological SciencesChinese Academy of SciencesShanghaiChina
  2. 2.Key Laboratory of Computational Biology, CAS-MPG (Chinese Academy of Sciences-German Max Planck Society) Partner Institute for Computational Biology, Shanghai Institute of Biological SciencesChinese Academy of SciencesShanghaiChina
  3. 3.Key Lab of Plant Stress ResearchShandong Normal UniversityJinanChina

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