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.
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
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
Brown NJ, Parsley K, Hibberd JM (2005) The future of C4 research—maize, Flaveria or Cleome? Trends Plant Sci 10(5):215–221
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
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
Covshoff S, Hibberd JM (2012) Integrating C4 photosynthesis into C3 crops to increase yield potential. Curr Opin Biotechnol 23(2):209–214
Doust AN, Kellogg EA, Devos KM, Bennetzen JL (2009) Foxtail millet: a sequence-driven grass model system. Plant Physiol 149(1):137–141
Furbank RT (2011) Evolution of the C4 photosynthetic mechanism: are there really three C4 acid decarboxylation types? J Exp Bot 62(9):3103–3108
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
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
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
Hibberd JM, Covshoff S (2010) The regulation of gene expression required for C4 photosynthesis. Annu Rev Plant Biol 61(1):181–207
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
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
Langdale JA (2011) C4 cycles: past, present, and future research on C4 photosynthesis. Plant Cell 23(11):3879–3892
Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9(4):357–359
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
Li P, Brutnell TP (2011) Setaria viridis and Setaria italica, model genetic systems for the Panicoid grasses. J Exp Bot 62(9):3031–3037
Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25(14):1754–1760
Li Y-C, Korol AB, Fahima T, Nevo E (2004) Microsatellites within genes: structure, function, and evolution. Mol Biol Evol 21(6):991–1007
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
Martin JA, Wang Z (2011) Next-generation transcriptome assembly. Nat Rev Genet 12(10):671–682
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
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
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
Morgante M, Hanafey M, Powell W (2002) Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes. Nat Genet 30(2):194–200
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
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
Peterhansel C (2011) Best practice procedures for the establishment of a C4 cycle in transgenic C3 plants. J Exp Bot 62(9):3011–3019
Powell W, Machray GC, Provan J (1996) Polymorphism revealed by simple sequence repeats. Trends Plant Sci 1(7):215–222
Sage RF, Zhu X-G (2011) Exploiting the engine of C4 photosynthesis. J Exp Bot 62(9):2989–3000
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
Sheen J (1999) C4 gene expression. Annu Rev Plant Physiol Plant Mol Biol 50(1):187–217
Tóth G, Gáspári Z, Jurka J (2000) Microsatellites in different eukaryotic genomes: survey and analysis. Genome Res 10(7):967–981
Trapnell C, Pachter L, Salzberg SL (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25(9):1105–1111
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
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
Varshney RK, Graner A, Sorrells ME (2005) Genic microsatellite markers in plants: features and applications. Trends Biotechnol 23(1):48–55
Wang L, Peterson RB, Brutnell TP (2011) Regulatory mechanisms underlying C4 photosynthesis. New Phytol 190(1):9–20
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
Williams BP, Aubry S, Hibberd JM (2012) Molecular evolution of genes recruited into C4 photosynthesis. Trends Plant Sci 17(4):213–220
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
Ye Y, Choi J-H, Tang H (2011) RAPSearch: a fast protein similarity search tool for short reads. BMC Bioinform 12(1):159
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
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
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
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
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
Author information
Authors and Affiliations
Corresponding author
Additional information
Jiajia Xu, Yuanyuan Li contributed equally to this work.
Electronic supplementary material
Below is the link to the electronic supplementary material.
Rights 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
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s11103-013-0025-4