ArticlePlant molecular biology2013
Whole transcriptome analysis using next-generation sequencing of model species Setaria viridis to support C4 photosynthesis research.
Article in Plant molecular biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- Multi-omics intervention inFrontiers in plant science · 2022Review
- Transcriptome Characterization and Identification of Molecular Markers (SNP, SSR, and Indels) in the Medicinal PlantBioMed research international · 2021Article
- Transcriptomic analysis identifies novel genes and pathways for salt stress responses in Suaeda salsa leaves.Scientific reports · 2020Article
- Genetic mechanisms of salt stress responses in halophytes.Plant signaling & behavior · 2020Article
- Two responses to MeJA induction of R2R3-MYB transcription factors regulate flavonoid accumulation in Glycyrrhiza uralensis Fisch.PloS one · 2020Article
- Characterization of the complete plastome ofMitochondrial DNA. Part B, Resources · 2019Article
- Identification of Salt Stress Responding Genes Using Transcriptome Analysis in Green Alga Chlamydomonas reinhardtii.International journal of molecular sciences · 2018Article
- Diffusion of COPlant physiology · 2018Article
- Molecular mechanisms underlying stress response and adaptation.Thoracic cancer · 2018Review
- Survival Mechanisms to Selective Pressures and Implications.Open life sciences · 2018Article
- Strategies and tools to improve crop productivity by targeting photosynthesis.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2017Article
- Optimization of Phenotyping Assays for the Model MonocotFrontiers in plant science · 2017Article
- Molecular Approaches to Understand Nutritional Potential of Coarse Cereals.Current genomics · 2016Article
- Comparative transcriptome analyses of deltamethrin-susceptible and -resistant Culex pipiens pallens by RNA-seq.Molecular genetics and genomics : MGG · 2016Article
- Review
- Selecting Superior De Novo Transcriptome Assemblies: Lessons Learned by Leveraging the Best Plant Genome.PloS one · 2016Article
- A developing Setaria viridis internode: an experimental system for the study of biomass generation in a C4 model species.Biotechnology for biofuels · 2016Article
- De Novo Sequencing and Analysis of Lemongrass Transcriptome Provide First Insights into the Essential Oil Biosynthesis of Aromatic Grasses.Frontiers in plant science · 2016Article
- Genetics and physiology of cell wall polysaccharides in the model C4 grass, Setaria viridis spp.BMC plant biology · 2015Article
- Global analysis of WRKY transcription factor superfamily in Setaria identifies potential candidates involved in abiotic stress signaling.Frontiers in plant science · 2015Article
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Authors and funding
9 authors.
Funding
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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.
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