Function annotation of the rice transcriptome at single-nucleotide resolution by RNA-seq

Genome Research

Volumn 20, Issue 9, 2010, Pages 1238-1249

  Lu, Tingting ^a   Lu, Guojun ^a   Fan, Danlin ^a   Zhu, Chuanrang ^a   Li, Wei ^a   Zhao, Qiang ^a,b   Feng, Qi ^a   Zhao, Yan ^a   Guo, Yunli ^a   Li, Wenjun ^a   Huang, Xuehui ^a   Han, Bin ^a,c  

^a INSTITUTE OF PLANT PHYSIOLOGY AND ECOLOGY   (China)

^b SHANGHAI JIAO TONG UNIVERSITY   (China)

^c Chinese Academy of Sciences and China National Center for Bioinformation   (China)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTOME;

ARTICLE; DNA MICROARRAY; EXON; NONHUMAN; PLANT GENE; PLANT GENOME; PRIORITY JOURNAL; RICE; RNA SEQUENCE; SINGLE NUCLEOTIDE POLYMORPHISM;

ALTERNATIVE SPLICING; BASE SEQUENCE; GENE EXPRESSION PROFILING; GENES, PLANT; GENOME, PLANT; MOLECULAR SEQUENCE ANNOTATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; ORYZA SATIVA; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ANALYSIS, RNA;

JAPONICA; ORYZA SATIVA (INDICA CULTIVAR-GROUP);

EID: 77956277181     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.106120.110     Document Type: Article

References (33)

1. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. 1997. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402. (Pubitemid 27359211)
2. Apweiler R, Attwood TK, Bairoch A, Bateman A, Birney E, Biswas M, Bucher P, Cerutti L, Corpet F, Croning MD, et al. 2001. The InterPro database, an integrated documentation resource for protein families, domains and functional sites. Nucleic Acids Res 29: 37-41.
3. Campbell MA, Haas BJ, Hamilton JP, Mount SM, Buell CR. 2006. Comprehensive analysis of alternative splicing in rice and comparative analyses with Arabidopsis. BMC Genomics 7: 327. doi: 10.1186/1471-2164-7-327.
4. Cloonan N, Forrest AR, Kolle G, Gardiner BB, Faulkner GJ, Brown MK, Taylor DF, Steptoe AL, Wani S, Bethel G, et al. 2008. Stem cell transcriptome profiling via massive-scale mRNA sequencing. Nat Methods 5: 613-619. (Pubitemid 351911866)
5. Filichkin SA, Priest HD, Givan SA, Shen R, Bryant DW, Fox SE, Wong WK, Mockler TC. 2010. Genome-wide mapping of alternative splicing in Arabidopsis thaliana. Genome Res 20: 45-58.
6. Fullwood MJ, Wei CL, Liu ET, Ruan Y. 2009. Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses. Genome Res 19: 521-532.
7. Furutani I, Sukegawa S, Kyozuka J. 2006. Genome-wide analysis of spatial and temporal gene expression in rice panicle development. Plant J 46: 503-511.
8. Goff SA, Ricke D, Lan TH, Presting G, Wang R, Dunn M, Glazebrook J, Sessions A, Oeller P, Varma H, et al. 2002. A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296: 92-100. (Pubitemid 34280065)
9. He G, Zhu X, Elling AA, Chen L, Wang X, Guo L, Liang M, He H, Zhang H, Chen F, et al. 2010. Global epigenetic and transcriptional trends among two rice subspecies and their reciprocal hybrids. Plant Cell 22: 17-33.
10. International Rice Genome Sequencing Project. 2005. The map-based sequence of the rice genome. Nature 436: 793-800.
11. Jiao Y, Jia P, Wang X, Su N, Yu S, Zhang D, Ma L, Feng Q, Jin Z, Li L, et al. 2005. A tiling microarray expression analysis of rice chromosome 4 suggests a chromosome-level regulation of transcription. Plant Cell 17: 1641-1657.
12. Li L, Wang X, Stolc V, Li X, Zhang D, Su N, Tongprasit W, Li S, Cheng Z, Wang J, et al. 2006. Genome-wide transcription analyses in rice using tiling microarrays. Nat Genet 38: 124-129. (Pubitemid 43011893)
13. Li M, Xu W, Yang W, Kong Z, Xue Y. 2007. Genome-wide gene expression profiling reveals conserved and novel molecular functions of the stigma in rice. Plant Physiol 144: 1797-1812. (Pubitemid 47258104)
14. Li H, Ruan J, Durbin R. 2008. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res 18: 1851-1858.
15. Lister R, O'Malley RC, Tonti-Filippini J, Gregory BD, Berry CC, Millar AH, Ecker JR. 2008. Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133: 523-536.
16. Liu X, Lu T, Yu S, Li Y, Huang Y, Huang T, Zhang L, Zhu J, Zhao Q, Mu J, et al. 2007. A collection of 10,096 indica rice full-length cDNAs reveals highly expressed sequence divergence between Oryza sativa indica and japonica subspecies. Plant Mol Biol 65: 403-415. (Pubitemid 47598883)
17. Ma L, Chen C, Liu X, Jiao Y, Su N, Li L, Wang X, Cao M, Sun N, Zhang X, et al. 2005. A microarray analysis of the rice transcriptome and its comparison to Arabidopsis. Genome Res 15: 1274-1283. (Pubitemid 41247918)
18. Marioni J, Mason C, Mane S, Stephens M, Gilad Y. 2008. RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays. Genome Res 18: 1509-1517.
19. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. 2008. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5: 621-628. (Pubitemid 351911867)
20. Nagalakshmi U, Wang Z, Waern K, Shou C, Raha D, Gerstein M, Snyder M. 2008. The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 320: 1344-1349. (Pubitemid 351929471)
21. Pan Q, Shai O, Lee LJ, Frey BJ, Blencowe BJ. 2008. Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet 40: 1413-1415.
22. The Rice Full-Length cDNA Consortium. 2003. Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice. Science 301: 376-379.
23. Satoh K, Doi K, Nagata T, Kishimoto N, Suzuki K, Otomo Y, Kawai J, Nakamura M, Hirozane-Kishikawa T, Kanagawa S, et al. 2007. Gene organization in rice revealed by full-length cDNA mapping and gene expression analysis through microarray. PLoS ONE 2: e1235. doi: 10.1371/journal.pone.0001235.
24. Sultan M, Schulz MH, Richard H, Magen A, Klingenhoff A, Scherf M, Seifert M, Borodina T, Soldatov A, Parkhomchuk D, et al. 2008. A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science 321: 956-960.
25. Trapnell C, Pachter L, Salzberg S. 2009. TopHat: Discovering splice junctions with RNA-Seq. Bioinformatics 25: 1105-1111.
26. Wang BB, Brendel V. 2006. Genomewide comparative analysis of alternative splicing in plants. Proc Natl Acad Sci 103: 7175-7180.
27. Wang ET, Sandberg R, Luo S, Khrebtukova I, Zhang L, Mayr C, Kingsmore SF, Schroth GP, Burge CB. 2008. Alternative isoform regulation in human tissue transcriptomes. Nature 456: 470-476. (Pubitemid 352759009)
28. Wang L, Feng Z, Wang X, Wang X, Zhang X. 2010a. DEGseq: An R package for identifying differentially expressed genes from RNA-seq data. Bioinformatics 26: 136-138.
29. Wang L, Xie W, Chen Y, Tang W, Yang J, Ye R, Liu L, Lin Y, Xu C, Xiao J, et al. 2010b. A dynamic gene expression atlas covering the entire life cycle of rice. Plant J 61: 752-766.
30. Wilhelm BT, Marguerat S, Watt S, Schubert F, Wood V, Goodhead I, Penkett CJ, Rogers J, Bähler J. 2008. Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution. Nature 453: 1239-1243. (Pubitemid 351913597)
31. Yu J, Hu S, Wang J, Wong GK, Li S, Liu B, Deng Y, Dai L, Zhou Y, Zhang X, et al. 2002. A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296: 79-92. (Pubitemid 34280064)
32. Zhang J, Feng Q, Jin C, Qiu D, Zhang L, Xie K, Yuan D, Han B, Zhang Q, Wang S. 2005. Features of the expressed sequences revealed by a large-scale analysis of ESTs from a normalized cDNA library of the elite indica rice cultivar Minghui 63. Plant J 42: 772-780. (Pubitemid 40809893)
33. Zhang HY, He H, Chen LB, Li L, Liang MZ, Wang XF, Liu XG, He GM, Chen RS, Ma LG, et al. 2008. A Genome-wide transcription analysis reveals a close correlation of promoter INDEL polymorphism and heterotic gene expression in rice hybrids. Mol Plant 1: 720-731.