title: Whole transcriptome analysis using next-generation sequencing of model species Setaria viridis to support C4 photosynthesis research.
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.
authors.affiliation: State Key Laboratory of Hybrid Rice Research, Shanghai Institute of Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
authors.forename: Jiajia
authors.initials: J
authors.lastname: Xu
authors.forename: Yuanyuan
authors.initials: Y
authors.lastname: Li
authors.forename: Xiuling
authors.initials: X
authors.lastname: Ma
authors.forename: Jianfeng
authors.initials: J
authors.lastname: Ding
authors.forename: Kai
authors.initials: K
authors.lastname: Wang
authors.forename: Sisi
authors.initials: S
authors.lastname: Wang
authors.forename: Ye
authors.initials: Y
authors.lastname: Tian
authors.forename: Hui
authors.initials: H
authors.lastname: Zhang
authors.forename: Xin-Guang
authors.initials: XG
authors.lastname: Zhu
mesh_terms: D002874:Chromosome Mapping; D032461:Chromosomes, Plant / Q000235:genetics / Q000378:metabolism; D020869:Gene Expression Profiling / Q000379:methods*; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D018745:Genome, Plant; D018525:Germination; D018895:Microsatellite Repeats; D008958:Models, Molecular; D058977:Molecular Sequence Annotation; D005810:Multigene Family; D010788:Photosynthesis; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D018749:RNA, Plant / Q000235:genetics / Q000378:metabolism*; D012098:Reproduction; D012639:Seeds / Q000235:genetics / Q000378:metabolism; D032983:Setaria Plant / Q000235:genetics / Q000254:growth & development / Q000378:metabolism*; D059467:Transcriptome
chemical_list: D012333:RNA, Messenger; D018749:RNA, Plant