IHB OpenIR  > 水生生物分子与细胞生物学研究中心  > 期刊论文
Transcriptome Analysis of the Model Protozoan, Tetrahymena thermophila, Using Deep RNA Sequencing
Xiong, Jie1,5; Lu, Xingyi1,5; Zhou, Zhemin2; Chang, Yue1,5; Yuan, Dongxia1; Tian, Miao1,5; Zhou, Zhigang4; Wang, Lei2; Fu, Chengjie1; Orias, Eduardo3; Miao, Wei1; Xiong, J (reprint author), Chinese Acad Sci, Inst Hydrobiol, Key Lab Aquat Biodivers & Conservat, Wuhan, Peoples R China.
2012-02-07
Source PublicationPLOS ONE
ISSN1932-6203
Volume7Issue:2Pages:e30630
AbstractBackground: 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. Methodology/Principal Findings: 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/Significance: 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.; 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.
SubtypeArticle
KeywordProgrammed Dna Elimination Activated Protein-kinase Genome-wide Analysis Gene-expression Functional Genomics Candida-albicans Splice Junctions Seq Annotation Yeast
Department[Xiong, Jie; Lu, Xingyi; Chang, Yue; Yuan, Dongxia; Tian, Miao; Fu, Chengjie; Miao, Wei] Chinese Acad Sci, Inst Hydrobiol, Key Lab Aquat Biodivers & Conservat, Wuhan, Peoples R China; [Zhou, Zhemin; Wang, Lei] Nankai Univ, Tianjin Econ Technol Dev Area, Sch Biol Sci & Biotechnol, Tianjin 300071, Peoples R China; [Orias, Eduardo] Univ Calif Santa Barbara, Dept Mol Cellular & Dev Biol, Santa Barbara, CA 93106 USA; [Zhou, Zhigang] Chinese Acad Agr Sci, Feed Res Inst, Beijing 100193, Peoples R China; [Xiong, Jie; Lu, Xingyi; Chang, Yue; Tian, Miao] Chinese Acad Sci, Grad Sch, Beijing, Peoples R China
DOI10.1371/journal.pone.0030630
WOS HeadingsScience & Technology
Funding OrganizationChinese Academy of Sciences[KSCX2-EW-G-6-4]; National Natural Science Foundation of China[Y11314-1-501, Y01307-1-501]; National Science Foundation, United States of America[MCB-1025069] ; Chinese Academy of Sciences[KSCX2-EW-G-6-4]; National Natural Science Foundation of China[Y11314-1-501, Y01307-1-501]; National Science Foundation, United States of America[MCB-1025069] ; Chinese Academy of Sciences[KSCX2-EW-G-6-4]; National Natural Science Foundation of China[Y11314-1-501, Y01307-1-501]; National Science Foundation, United States of America[MCB-1025069] ; Chinese Academy of Sciences[KSCX2-EW-G-6-4]; National Natural Science Foundation of China[Y11314-1-501, Y01307-1-501]; National Science Foundation, United States of America[MCB-1025069]
Indexed BySCI
Language英语
WOS Research AreaScience & Technology - Other Topics
WOS SubjectMultidisciplinary Sciences
WOS IDWOS:000302180600012
WOS KeywordPROGRAMMED DNA ELIMINATION ; ACTIVATED PROTEIN-KINASE ; GENOME-WIDE ANALYSIS ; GENE-EXPRESSION ; FUNCTIONAL GENOMICS ; CANDIDA-ALBICANS ; SPLICE JUNCTIONS ; SEQ ; ANNOTATION ; YEAST
Funding OrganizationChinese Academy of Sciences[KSCX2-EW-G-6-4]; National Natural Science Foundation of China[Y11314-1-501, Y01307-1-501]; National Science Foundation, United States of America[MCB-1025069] ; Chinese Academy of Sciences[KSCX2-EW-G-6-4]; National Natural Science Foundation of China[Y11314-1-501, Y01307-1-501]; National Science Foundation, United States of America[MCB-1025069] ; Chinese Academy of Sciences[KSCX2-EW-G-6-4]; National Natural Science Foundation of China[Y11314-1-501, Y01307-1-501]; National Science Foundation, United States of America[MCB-1025069] ; Chinese Academy of Sciences[KSCX2-EW-G-6-4]; National Natural Science Foundation of China[Y11314-1-501, Y01307-1-501]; National Science Foundation, United States of America[MCB-1025069]
Citation statistics
Document Type期刊论文
Identifierhttp://ir.ihb.ac.cn/handle/342005/17021
Collection水生生物分子与细胞生物学研究中心_期刊论文
Corresponding AuthorXiong, J (reprint author), Chinese Acad Sci, Inst Hydrobiol, Key Lab Aquat Biodivers & Conservat, Wuhan, Peoples R China.
Affiliation1.Chinese Acad Sci, Inst Hydrobiol, Key Lab Aquat Biodivers & Conservat, Wuhan, Peoples R China
2.Nankai Univ, Tianjin Econ Technol Dev Area, Sch Biol Sci & Biotechnol, Tianjin 300071, Peoples R China
3.Univ Calif Santa Barbara, Dept Mol Cellular & Dev Biol, Santa Barbara, CA 93106 USA
4.Chinese Acad Agr Sci, Feed Res Inst, Beijing 100193, Peoples R China
5.Chinese Acad Sci, Grad Sch, Beijing, Peoples R China
Recommended Citation
GB/T 7714
Xiong, Jie,Lu, Xingyi,Zhou, Zhemin,et al. Transcriptome Analysis of the Model Protozoan, Tetrahymena thermophila, Using Deep RNA Sequencing[J]. PLOS ONE,2012,7(2):e30630.
APA Xiong, Jie.,Lu, Xingyi.,Zhou, Zhemin.,Chang, Yue.,Yuan, Dongxia.,...&Xiong, J .(2012).Transcriptome Analysis of the Model Protozoan, Tetrahymena thermophila, Using Deep RNA Sequencing.PLOS ONE,7(2),e30630.
MLA Xiong, Jie,et al."Transcriptome Analysis of the Model Protozoan, Tetrahymena thermophila, Using Deep RNA Sequencing".PLOS ONE 7.2(2012):e30630.
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