title: Transcriptome analysis of the model protozoan, Tetrahymena thermophila, using Deep RNA sequencing.
abstract: BACKGROUND
  The ciliated protozoan Tetrahymena thermophila is a well-studied single-celled eukaryote model organism for cellular and molecular biology. However, the lack of extensive T. thermophila cDNA libraries or a large expressed sequence tag (EST) database limited the quality of the original genome annotation.
  
  
  RESULTS
  This RNA-seq study describes the first deep sequencing analysis of the T. thermophila transcriptome during the three major stages of the life cycle: growth, starvation and conjugation. Uniquely mapped reads covered more than 96% of the 24,725 predicted gene models in the somatic genome. More than 1,000 new transcribed regions were identified. The great dynamic range of RNA-seq allowed detection of a nearly six order-of-magnitude range of measurable gene expression orchestrated by this cell. RNA-seq also allowed the first prediction of transcript untranslated regions (UTRs) and an updated (larger) size estimate of the T. thermophila transcriptome: 57 Mb, or about 55% of the somatic genome. Our study identified nearly 1,500 alternative splicing (AS) events distributed over 5.2% of T. thermophila genes. This percentage represents a two order-of-magnitude increase over previous EST-based estimates in Tetrahymena. Evidence of stage-specific regulation of alternative splicing was also obtained. Finally, our study allowed us to completely confirm about 26.8% of the genes originally predicted by the gene finder, to correct coding sequence boundaries and intron-exon junctions for about a third, and to reassign microarray probes and correct earlier microarray data.
  
  
  CONCLUSIONS
  RNA-seq data significantly improve the genome annotation and provide a fully comprehensive view of the global transcriptome of T. thermophila. To our knowledge, 5.2% of T. thermophila genes with AS is the highest percentage of genes showing AS reported in a unicellular eukaryote. Tetrahymena thus becomes an excellent unicellular model eukaryote in which to investigate mechanisms of alternative splicing.
authors.affiliation: Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, People's Republic of China.
authors.forename: Jie
authors.initials: J
authors.lastname: Xiong
authors.forename: Xingyi
authors.initials: X
authors.lastname: Lu
authors.forename: Zhemin
authors.initials: Z
authors.lastname: Zhou
authors.forename: Yue
authors.initials: Y
authors.lastname: Chang
authors.forename: Dongxia
authors.initials: D
authors.lastname: Yuan
authors.forename: Miao
authors.initials: M
authors.lastname: Tian
authors.forename: Zhigang
authors.initials: Z
authors.lastname: Zhou
authors.forename: Lei
authors.initials: L
authors.lastname: Wang
authors.forename: Chengjie
authors.initials: C
authors.lastname: Fu
authors.forename: Eduardo
authors.initials: E
authors.lastname: Orias
authors.forename: Wei
authors.initials: W
authors.lastname: Miao
mesh_terms: D020869:Gene Expression Profiling / Q000379:methods*; D017125:Genes, Protozoan; D058977:Molecular Sequence Annotation; D016053:RNA, Protozoan / Q000235:genetics*; D017423:Sequence Analysis, RNA / Q000379:methods*; D016808:Tetrahymena thermophila / Q000235:genetics*; D059467:Transcriptome
chemical_list: D016053:RNA, Protozoan