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

Whole transcriptome analysis using next-generation sequencing of model species Setaria viridis to... 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. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Plant Molecular Biology Springer Journals

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

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Publisher
Springer Journals
Copyright
Copyright © 2013 by Springer Science+Business Media Dordrecht
Subject
Life Sciences; Plant Sciences; Biochemistry, general; Plant Pathology
ISSN
0167-4412
eISSN
1573-5028
D.O.I.
10.1007/s11103-013-0025-4
Publisher site
See Article on Publisher Site

Abstract

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.

Journal

Plant Molecular BiologySpringer Journals

Published: Mar 20, 2013

References

  • Reference genome sequence of the model plant Setaria
    Bennetzen, JL; Schmutz, J; Wang, H; Percifield, R; Hawkins, J; Pontaroli, AC; Estep, M; Feng, L; Vaughn, JN; Grimwood, J; Jenkins, J; Barry, K; Lindquist, E; Hellsten, U; Deshpande, S; Wang, X; Wu, X; Mitros, T; Triplett, J; Yang, X; Ye, C-Y; Mauro-Herrera, M; Wang, L; Li, P; Sharma, M; Sharma, R; Ronald, PC; Panaud, O; Kellogg, EA; Brutnell, TP; Doust, AN; Tuskan, GA; Rokhsar, D; Devos, KM
  • Physiology and genetics of interspecific hybrids between photosynthetic types
    Brown, RH; Bouton, JH
  • Setaria viridis: a model for C4 photosynthesis
    Brutnell, TP; Wang, L; Swartwood, K; Goldschmidt, A; Jackson, D; Zhu, X-G; Kellogg, E; Eck, J
  • Integrating C4 photosynthesis into C3 crops to increase yield potential
    Covshoff, S; Hibberd, JM
  • Foxtail millet: a sequence-driven grass model system
    Doust, AN; Kellogg, EA; Devos, KM; Bennetzen, JL

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