Access the full text.
Sign up today, get DeepDyve free for 14 days.
O Ghannoum, JR Evans, S Caemmerer (2010)
C4 photosynthesis and related CO2 concentrating mechanisms, vol 32. Advances in photosynthesis and respiration
M Krzywinski, J Schein, İ Birol, J Connors, R Gascoyne, D Horsman, SJ Jones, MA Marra (2009)
Circos: an information aesthetic for comparative genomicsGenome Res, 19
F Xie, CE Burklew, Y Yang, M Liu, P Xiao, B Zhang, D Qiu (2012)
De novo sequencing and a comprehensive analysis of purple sweet potato (Impomoea batatas L.) transcriptomePlanta, 236
JA Martin, Z Wang (2011)
Next-generation transcriptome assemblyNat Rev Genet, 12
BP Williams, S Aubry, JM Hibberd (2012)
Molecular evolution of genes recruited into C4 photosynthesisTrends Plant Sci, 17
Y Ye, J-H Choi, H Tang (2011)
RAPSearch: a fast protein similarity search tool for short readsBMC Bioinform, 12
M Morgante, M Hanafey, W Powell (2002)
Microsatellites are preferentially associated with nonrepetitive DNA in plant genomesNat Genet, 30
M Matsuoka, RT Furbank, H Fukayama, M Miyao (2001)
Molecular engineering of C4 photosynthesisAnnu Rev Plant Physiol Plant Mol Biol, 52
J Sheen (1999)
C4 gene expressionAnnu Rev Plant Physiol Plant Mol Biol, 50
C Trapnell, L Pachter, SL Salzberg (2009)
TopHat: discovering splice junctions with RNA-SeqBioinformatics, 25
Y Wang, X Zeng, NJ Iyer, DW Bryant, TC Mockler, R Mahalingam (2012)
Exploring the switchgrass transcriptome using second-generation sequencing technologyPLoS One, 7
W Powell, GC Machray, J Provan (1996)
Polymorphism revealed by simple sequence repeatsTrends Plant Sci, 1
RF Sage, X-G Zhu (2011)
Exploiting the engine of C4 photosynthesisJ Exp Bot, 62
WJ Kent (2002)
BLAT—the BLAST-like alignment toolGenome Res, 12
E Meyer, TL Logan, TE Juenger (2012)
Transcriptome analysis and gene expression atlas for Panicum hallii var. filipes, a diploid model for biofuel researchPlant J, 70
H Li, R Durbin (2009)
Fast and accurate short read alignment with Burrows–Wheeler transformBioinformatics, 25
ML Metzker (2010)
Sequencing technologies—the next generationNat Rev Genet, 11
J Parkinson, M Blaxter (2009)
Expressed sequence tags (ESTs), vol 533. Methods in molecular biology
AN Doust, EA Kellogg, KM Devos, JL Bennetzen (2009)
Foxtail millet: a sequence-driven grass model systemPlant Physiol, 149
RK Varshney, A Graner, ME Sorrells (2005)
Genic microsatellite markers in plants: features and applicationsTrends Biotechnol, 23
Y Zhang, R Jiang, H Wu, P Liu, J Xie, Y He, H Pang (2012)
Next-generation sequencing-based transcriptome analysis of Cryptolaemus montrouzieri under insecticide stress reveals resistance-relevant genes in ladybirdsGenomics, 100
RH Brown, JH Bouton (1993)
Physiology and genetics of interspecific hybrids between photosynthetic typesAnnu Rev Plant Physiol Plant Mol Biol, 44
C Peterhansel (2011)
Best practice procedures for the establishment of a C4 cycle in transgenic C3 plantsJ Exp Bot, 62
G Zhang, X Liu, Z Quan, S Cheng, X Xu, S Pan, M Xie, P Zeng, Z Yue, W Wang, Y Tao, C Bian, C Han, Q Xia, X Peng, R Cao, X Yang, D Zhan, J Hu, Y Zhang, H Li, H Li, N Li, J Wang, C Wang, R Wang, T Guo, Y Cai, C Liu, H Xiang, Q Shi, P Huang, Q Chen, Y Li, J Wang, Z Zhao, J Wang (2012)
Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potentialNat Biotechnol, 30
G Tóth, Z Gáspári, J Jurka (2000)
Microsatellites in different eukaryotic genomes: survey and analysisGenome Res, 10
C Trapnell, BA Williams, G Pertea, A Mortazavi, G Kwan, MJ Baren, SL Salzberg, BJ Wold, L Pachter (2010)
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiationNat Biotechnol, 28
JE Zalapa, H Cuevas, H Zhu, S Steffan, D Senalik, E Zeldin, B McCown, R Harbut, P Simon (2012)
Using next-generation sequencing approaches to isolate simple sequence repeat (SSR) loci in the plant sciencesAm J Bot, 99
Y-C Li, AB Korol, T Fahima, E Nevo (2004)
Microsatellites within genes: structure, function, and evolutionMol Biol Evol, 21
C Trapnell, A Roberts, L Goff, G Pertea, D Kim, DR Kelley, H Pimentel, SL Salzberg, JL Rinn, L Pachter (2012)
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and CufflinksNat Protoc, 7
TP Brutnell, L Wang, K Swartwood, A Goldschmidt, D Jackson, X-G Zhu, E Kellogg, J Eck (2010)
Setaria viridis: a model for C4 photosynthesisPlant Cell, 22
X-G Zhu, LL Shan, Y Wang, WP Quick (2010)
C4 rice—an ideal arena for systems biology researchJ Integr Plant Biol, 52
LM Giussani, JH Cota-Sánchez, FO Zuloaga, EA Kellogg (2001)
A molecular phylogeny of the grass subfamily Panicoideae (Poaceae) shows multiple origins of C4 photosynthesisAm J Bot, 88
H Ogata, S Goto, K Sato, W Fujibuchi, H Bono, M Kanehisa (1999)
KEGG: Kyoto encyclopedia of genes and genomesNucleic Acids Res, 27
MD Hatch (1987)
C4 photosynthesis: a unique blend of modified biochemistry, anatomy and ultrastructureBiochim Biophys Acta, 895
I Lavagi, M Estelle, W Weckwerth, J Beynon, RM Bastow (2012)
From bench to bountiful harvests: a road map for the next decade of Arabidopsis researchPlant Cell, 24
C Li, Y Zhang, R Wang, J Lu, S Nandi, S Mohanty, J Terhune, Z Liu, E Peatman (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 punctatusFish Shellfish Immunol, 32
JL Bennetzen, J Schmutz, H Wang, R Percifield, J Hawkins, AC Pontaroli, M Estep, L Feng, JN Vaughn, J Grimwood, J Jenkins, K Barry, E Lindquist, U Hellsten, S Deshpande, X Wang, X Wu, T Mitros, J Triplett, X Yang, C-Y Ye, M Mauro-Herrera, L Wang, P Li, M Sharma, R Sharma, PC Ronald, O Panaud, EA Kellogg, TP Brutnell, AN Doust, GA Tuskan, D Rokhsar, KM Devos (2012)
Reference genome sequence of the model plant SetariaNat Biotechnol, 30
MH Schulz, DR Zerbino, M Vingron, E Birney (2012)
Oases: robust de novo RNA-seq assembly across the dynamic range of expression levelsBioinformatics, 28
L Wang, RB Peterson, TP Brutnell (2011)
Regulatory mechanisms underlying C4 photosynthesisNew Phytol, 190
S Covshoff, JM Hibberd (2012)
Integrating C4 photosynthesis into C3 crops to increase yield potentialCurr Opin Biotechnol, 23
P Li, TP Brutnell (2011)
Setaria viridis and Setaria italica, model genetic systems for the Panicoid grassesJ Exp Bot, 62
NJ Brown, K Parsley, JM Hibberd (2005)
The future of C4 research—maize, Flaveria or Cleome?Trends Plant Sci, 10
X-G Zhu, SP Long, DR Ort (2008)
What is the maximum efficiency with which photosynthesis can convert solar energy into biomass?Curr Opin Biotechnol, 19
JA Langdale (2011)
C4 cycles: past, present, and future research on C4 photosynthesisPlant Cell, 23
RT Furbank (2011)
Evolution of the C4 photosynthetic mechanism: are there really three C4 acid decarboxylation types?J Exp Bot, 62
JM Hibberd, S Covshoff (2010)
The regulation of gene expression required for C4 photosynthesisAnnu Rev Plant Biol, 61
B Langmead, SL Salzberg (2012)
Fast gapped-read alignment with Bowtie 2Nat Methods, 9
F Cheung, BJ Haas, SMD Goldberg, GD May, Y Xiao, CD Town (2006)
Sequencing Medicago truncatula expressed sequenced tags using 454 Life Sciences technologyBMC Genomics, 7
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.
Plant Molecular Biology – Springer Journals
Published: Mar 20, 2013
Read and print from thousands of top scholarly journals.
Already have an account? Log in
Bookmark this article. You can see your Bookmarks on your DeepDyve Library.
To save an article, log in first, or sign up for a DeepDyve account if you don’t already have one.
Copy and paste the desired citation format or use the link below to download a file formatted for EndNote
Access the full text.
Sign up today, get DeepDyve free for 14 days.
All DeepDyve websites use cookies to improve your online experience. They were placed on your computer when you launched this website. You can change your cookie settings through your browser.