Skip to main content
SpringerLink
Log in

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

  • Published:
Plant Molecular Biology Aims and scope Submit manuscript

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.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5

Similar content being viewed by others

References

  • Andrews S (2010) Fastqc. http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/

  • 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 (2012) Reference genome sequence of the model plant Setaria. Nat Biotechnol 30(6):555–561

    Article  PubMed  CAS  Google Scholar 

  • Brown RH, Bouton JH (1993) Physiology and genetics of interspecific hybrids between photosynthetic types. Annu Rev Plant Physiol Plant Mol Biol 44(1):435–456

    Article  Google Scholar 

  • Brown NJ, Parsley K, Hibberd JM (2005) The future of C4 research—maize, Flaveria or Cleome? Trends Plant Sci 10(5):215–221

    Article  PubMed  CAS  Google Scholar 

  • Brutnell TP, Wang L, Swartwood K, Goldschmidt A, Jackson D, Zhu X-G, Kellogg E, Van Eck J (2010) Setaria viridis: a model for C4 photosynthesis. Plant Cell 22(8):2537–2544

    Article  PubMed  CAS  Google Scholar 

  • Cheung F, Haas BJ, Goldberg SMD, May GD, Xiao Y, Town CD (2006) Sequencing Medicago truncatula expressed sequenced tags using 454 Life Sciences technology. BMC Genomics 7(1):272

    Article  PubMed  Google Scholar 

  • Covshoff S, Hibberd JM (2012) Integrating C4 photosynthesis into C3 crops to increase yield potential. Curr Opin Biotechnol 23(2):209–214

    Article  PubMed  CAS  Google Scholar 

  • Doust AN, Kellogg EA, Devos KM, Bennetzen JL (2009) Foxtail millet: a sequence-driven grass model system. Plant Physiol 149(1):137–141

    Article  PubMed  CAS  Google Scholar 

  • Furbank RT (2011) Evolution of the C4 photosynthetic mechanism: are there really three C4 acid decarboxylation types? J Exp Bot 62(9):3103–3108

    Article  PubMed  CAS  Google Scholar 

  • Ghannoum O, Evans JR, von Caemmerer S (2010) Nitrogen and water use efficiency of C4 plants. In: Raghavendra AS, Sage RF (eds) C4 photosynthesis and related CO2 concentrating mechanisms, vol 32. Advances in photosynthesis and respiration. Springer, The Netherlands, pp 129–146

    Chapter  Google Scholar 

  • Giussani LM, Cota-Sánchez JH, Zuloaga FO, Kellogg EA (2001) A molecular phylogeny of the grass subfamily Panicoideae (Poaceae) shows multiple origins of C4 photosynthesis. Am J Bot 88(11):1993–2012

    Article  PubMed  CAS  Google Scholar 

  • Gordon A (2009) Fastx-toolkit. http://hannonlab.cshl.edu/fastx_toolkit/

  • Hatch MD (1987) C4 photosynthesis: a unique blend of modified biochemistry, anatomy and ultrastructure. Biochim Biophys Acta 895:81–106

    Article  CAS  Google Scholar 

  • Hibberd JM, Covshoff S (2010) The regulation of gene expression required for C4 photosynthesis. Annu Rev Plant Biol 61(1):181–207

    Article  PubMed  CAS  Google Scholar 

  • Huang L, Yang X, Sun P, Tang W, Hu S (2012) The first Illumina-based de novo transcriptome sequencing and analysis of safflower flowers. PLoS One 7(6):e38653

  • Kent WJ (2002) BLAT—the BLAST-like alignment tool. Genome Res 12(4):656–664

    PubMed  CAS  Google Scholar 

  • Krzywinski M, Schein J, Birol İ, Connors J, Gascoyne R, Horsman D, Jones SJ, Marra MA (2009) Circos: an information aesthetic for comparative genomics. Genome Res 19(9):1639–1645

    Article  PubMed  CAS  Google Scholar 

  • Langdale JA (2011) C4 cycles: past, present, and future research on C4 photosynthesis. Plant Cell 23(11):3879–3892

    Article  PubMed  CAS  Google Scholar 

  • Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9(4):357–359

    Article  PubMed  CAS  Google Scholar 

  • Lavagi I, Estelle M, Weckwerth W, Beynon J, Bastow RM (2012) From bench to bountiful harvests: a road map for the next decade of Arabidopsis research. Plant Cell 24:2240–2247

    Article  PubMed  CAS  Google Scholar 

  • Li P, Brutnell TP (2011) Setaria viridis and Setaria italica, model genetic systems for the Panicoid grasses. J Exp Bot 62(9):3031–3037

    Article  PubMed  CAS  Google Scholar 

  • Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25(14):1754–1760

    Article  PubMed  CAS  Google Scholar 

  • Li Y-C, Korol AB, Fahima T, Nevo E (2004) Microsatellites within genes: structure, function, and evolution. Mol Biol Evol 21(6):991–1007

    Article  PubMed  CAS  Google Scholar 

  • Li C, Zhang Y, Wang R, Lu J, Nandi S, Mohanty S, Terhune J, Liu Z, Peatman E (2012) RNA-seq analysis of mucosal immune responses reveals signatures of intestinal barrier disruption and pathogen entry following Edwardsiella ictaluri infection in channel catfish, Ictalurus punctatus. Fish Shellfish Immunol 32(5):816–827

    Article  PubMed  CAS  Google Scholar 

  • Martin JA, Wang Z (2011) Next-generation transcriptome assembly. Nat Rev Genet 12(10):671–682

    Article  PubMed  CAS  Google Scholar 

  • Matsuoka M, Furbank RT, Fukayama H, Miyao M (2001) Molecular engineering of C4 photosynthesis. Annu Rev Plant Physiol Plant Mol Biol 52(1):297–314

    Article  PubMed  CAS  Google Scholar 

  • Mayer C (2006–2010) Phobos 3.3.11. http://www.rub.de/spezzoo/cm/cm_phobos.htm

  • Metzker ML (2010) Sequencing technologies—the next generation. Nat Rev Genet 11(1):31–46

    Article  PubMed  CAS  Google Scholar 

  • Meyer E, Logan TL, Juenger TE (2012) Transcriptome analysis and gene expression atlas for Panicum hallii var. filipes, a diploid model for biofuel research. Plant J 70(5):879–890

    Article  PubMed  CAS  Google Scholar 

  • Morgante M, Hanafey M, Powell W (2002) Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes. Nat Genet 30(2):194–200

    Article  PubMed  CAS  Google Scholar 

  • Ogata H, Goto S, Sato K, Fujibuchi W, Bono H, Kanehisa M (1999) KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res 27(1):29–34

    Article  PubMed  CAS  Google Scholar 

  • Parkinson J, Blaxter M (2009) Expressed sequence tags: an overview. In: Parkinson J (ed) Expressed sequence tags (ESTs), vol 533. Methods in molecular biology. Humana Press, New York, pp 1–12

    Chapter  Google Scholar 

  • Peterhansel C (2011) Best practice procedures for the establishment of a C4 cycle in transgenic C3 plants. J Exp Bot 62(9):3011–3019

    Article  PubMed  CAS  Google Scholar 

  • Powell W, Machray GC, Provan J (1996) Polymorphism revealed by simple sequence repeats. Trends Plant Sci 1(7):215–222

    Google Scholar 

  • Sage RF, Zhu X-G (2011) Exploiting the engine of C4 photosynthesis. J Exp Bot 62(9):2989–3000

    Article  PubMed  CAS  Google Scholar 

  • Schulz MH, Zerbino DR, Vingron M, Birney E (2012) Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels. Bioinformatics 28(8):1086–1092

    Article  PubMed  CAS  Google Scholar 

  • Sheen J (1999) C4 gene expression. Annu Rev Plant Physiol Plant Mol Biol 50(1):187–217

    Article  PubMed  CAS  Google Scholar 

  • Tóth G, Gáspári Z, Jurka J (2000) Microsatellites in different eukaryotic genomes: survey and analysis. Genome Res 10(7):967–981

    Article  PubMed  Google Scholar 

  • Trapnell C, Pachter L, Salzberg SL (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25(9):1105–1111

    Article  PubMed  CAS  Google Scholar 

  • Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L (2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 28(5):511–515

    Article  PubMed  CAS  Google Scholar 

  • Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L (2012) Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc 7(3):562–578

    Article  PubMed  CAS  Google Scholar 

  • Varshney RK, Graner A, Sorrells ME (2005) Genic microsatellite markers in plants: features and applications. Trends Biotechnol 23(1):48–55

    Article  PubMed  CAS  Google Scholar 

  • Wang L, Peterson RB, Brutnell TP (2011) Regulatory mechanisms underlying C4 photosynthesis. New Phytol 190(1):9–20

    Article  CAS  Google Scholar 

  • Wang Y, Zeng X, Iyer NJ, Bryant DW, Mockler TC, Mahalingam R (2012) Exploring the switchgrass transcriptome using second-generation sequencing technology. PLoS One 7(3):e34225

    Article  PubMed  CAS  Google Scholar 

  • Williams BP, Aubry S, Hibberd JM (2012) Molecular evolution of genes recruited into C4 photosynthesis. Trends Plant Sci 17(4):213–220

    Article  PubMed  CAS  Google Scholar 

  • Xie F, Burklew CE, Yang Y, Liu M, Xiao P, Zhang B, Qiu D (2012) De novo sequencing and a comprehensive analysis of purple sweet potato (Impomoea batatas L.) transcriptome. Planta 236(1):101–113

    Article  PubMed  CAS  Google Scholar 

  • Ye Y, Choi J-H, Tang H (2011) RAPSearch: a fast protein similarity search tool for short reads. BMC Bioinform 12(1):159

    Article  CAS  Google Scholar 

  • Zalapa JE, Cuevas H, Zhu H, Steffan S, Senalik D, Zeldin E, McCown B, Harbut R, Simon P (2012) Using next-generation sequencing approaches to isolate simple sequence repeat (SSR) loci in the plant sciences. Am J Bot 99(2):193–208

    Article  PubMed  CAS  Google Scholar 

  • Zhang G, Liu X, Quan Z, Cheng S, Xu X, Pan S, Xie M, Zeng P, Yue Z, Wang W, Tao Y, Bian C, Han C, Xia Q, Peng X, Cao R, Yang X, Zhan D, Hu J, Zhang Y, Li H, Li H, Li N, Wang J, Wang C, Wang R, Guo T, Cai Y, Liu C, Xiang H, Shi Q, Huang P, Chen Q, Li Y, Wang J, Zhao Z, Wang J (2012a) Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potential. Nat Biotechnol 30(6):549–554

    Article  PubMed  CAS  Google Scholar 

  • Zhang Y, Jiang R, Wu H, Liu P, Xie J, He Y, Pang H (2012b) Next-generation sequencing-based transcriptome analysis of Cryptolaemus montrouzieri under insecticide stress reveals resistance-relevant genes in ladybirds. Genomics 100(1):35–41

    Article  PubMed  CAS  Google Scholar 

  • Zhu X-G, Long SP, Ort DR (2008) What is the maximum efficiency with which photosynthesis can convert solar energy into biomass? Curr Opin Biotechnol 19(2):153–159

    Article  PubMed  CAS  Google Scholar 

  • Zhu X-G, Shan LL, Wang Y, Quick WP (2010) C4 rice—an ideal arena for systems biology research. J Integr Plant Biol 52(8):762–770

    Article  PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. State Key Laboratory of Hybrid Rice Research, Shanghai Institute of Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China

    Jiajia Xu, Yuanyuan Li, Ye Tian & Xin-Guang Zhu

  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 Sciences, Chinese Academy of Sciences, Shanghai, 200031, China

    Jiajia Xu, Yuanyuan Li, Sisi Wang, Ye Tian, Hui Zhang & Xin-Guang Zhu

  3. Key Lab of Plant Stress Research, Shandong Normal University, Jinan, 250014, Shandong, China

    Xiuling Ma, Jianfeng Ding, Kai Wang, Sisi Wang & Hui Zhang

Authors
  1. Jiajia Xu
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Yuanyuan Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Xiuling Ma
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Jianfeng Ding
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Kai Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Sisi Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Ye Tian
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Hui Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Xin-Guang Zhu
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Xin-Guang Zhu.

Additional information

Jiajia Xu, Yuanyuan Li contributed equally to this work.

Electronic supplementary material

Rights and permissions

Reprints and permissions

About this article

Cite this article

Xu, J., Li, Y., Ma, X. et al. Whole transcriptome analysis using next-generation sequencing of model species Setaria viridis to support C4 photosynthesis research. Plant Mol Biol 83, 77–87 (2013). https://doi.org/10.1007/s11103-013-0025-4

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11103-013-0025-4

Keywords

Search

Navigation