Transcriptome analysis of the Silkworm (Bombyx mori) by high-throughput RNA sequencing

PLoS ONE

Volumn 7, Issue 8, 2012, Pages

  Li, Yinü ^a   Wang, Guozeng ^a   Tian, Jian ^a   Liu, Huifen ^a   Yang, Huipeng ^a   Yi, Yongzhu ^a   Wang, Jinhui ^a   Shi, Xiaofeng ^a   Jiang, Feng ^a   Yao, Bin ^a   Zhang, Zhifang ^a  

^a INSTITUTE OF PLANT PROTECTION   (China)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTOME;

ANIMAL TISSUE; ARTICLE; CONTROLLED STUDY; DATA ANALYSIS; DEVELOPMENTAL STAGE; EXON; GENE EXPRESSION PROFILING; GENE MAPPING; GENETIC DATABASE; HIGH THROUGHPUT SEQUENCING; INSECT GENOME; NONHUMAN; RNA SEQUENCE; SILKWORM; WEB BROWSER;

ANIMALS; BOMBYX; DATABASES, GENETIC; FEMALE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, DEVELOPMENTAL; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MALE; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS, RNA;

EID: 84865279627     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0043713     Document Type: Article

References (33)

1. Xia Q, Zhou Z, Lu C, Cheng D, Dai F, et al. (2004) A draft sequence for the genome of the domesticated silkworm (Bombyx mori). Science 306: 1937-1940.
2. Qian Y, Liu W, Yang X, (2011) Analysis in 2010 and prospects in 2011 of Chinese silk industry (I). SILK (Chinese) 04: 57-60.
3. Li Z, Yi Y, Yin X, Zhang Z, Liu J, (2008) Expression of foot-and-mouth disease virus capsid proteins in silkworm-baculovirus expression system and its utilization as a subunit vaccine. PLoS One 3: e2273.
4. Li XH, Zhang P, Wang MX, Zhou F, Malik FA, et al. (2011) Expression of Trichoderma viride endoglucanase III in the larvae of silkworm, Bombyx mori L. and characteristic analysis of the recombinant protein. Mol Biol Rep 38: 3897-3902.
5. Chen J, Wu XF, Zhang YZ, (2006) Expression, purification and characterization of human GM-CSF using silkworm pupae (Bombyx mori) as a bioreactor. J Biotechnol 123: 236-247.
6. Xia Q, Guo Y, Zhang Z, Li D, Xuan Z, et al. (2009) Complete resequencing of 40 genomes reveals domestication events and genes in silkworm (Bombyx). Science 326: 433-436.
7. Xiang H, Zhu J, Chen Q, Dai F, Li X, et al. (2010) Single base-resolution methylome of the silkworm reveals a sparse epigenomic map. Nat Biotechnol 28: 516-520.
8. Mita K, Morimyo M, Okano K, Koike Y, Nohata J, et al. (2003) The construction of an EST database for Bombyx mori and its application. Proc Natl Acad Sci U S A 100: 14121-14126.
9. Gan LP, Zhang WY, Niu YS, Xu L, Xi J, et al. (2010) Construction and application of an electronic spatiotemporal expression profile and gene ontology analysis platform based on the EST database of the silkworm, Bombyx mori. J Insect Sci 10: 114.
10. Funaguma S, Hashimoto S, Suzuki Y, Omuro N, Sugano S, et al. (2007) SAGE analysis of early oogenesis in the silkworm, Bombyx mori. Insect Biochem Mol Biol 37: 147-154.
11. Zhang Y, Huang J, Jia S, Liu W, Li M, et al. (2007) SAGE tag based cDNA microarray analysis during larval to pupal development and isolation of novel cDNAs in Bombyx mori. Genomics 90: 372-379.
12. Ote M, Mita K, Kawasaki H, Seki M, Nohata J, et al. (2004) Microarray analysis of gene expression profiles in wing discs of Bombyx mori during pupal ecdysis. Insect Biochem Mol Biol 34: 775-784.
13. Duan J, Li R, Cheng D, Fan W, Zha X, et al. (2010) SilkDB v2.0 a platform for silkworm (Bombyx mori) genome biology. Nucleic Acids Res 38: D453-456.
14. Shimomura M, Minami H, Suetsugu Y, Ohyanagi H, Satoh C, et al. (2009) KAIKObase an integrated silkworm genome database and data mining tool. BMC Genomics 10: 486.
15. Wang Z, Gerstein M, Snyder M, (2009) RNA-Seq a revolutionary tool for transcriptomics. Nat Rev Genet 10: 57-63.
16. Marguerat S, Bahler J, (2010) RNA-seq: from technology to biology. Cell Mol Life Sci 67: 569-579.
17. Wang ET, Sandberg R, Luo S, Khrebtukova I, Zhang L, et al. (2008) Alternative isoform regulation in human tissue transcriptomes. Nature 456: 470-476.
18. Wang B, Guo G, Wang C, Lin Y, Wang X, et al. (2010) Survey of the transcriptome of Aspergillus oryzae via massively parallel mRNA sequencing. Nucleic Acids Res 38: 5075-5087.
19. Zhang G, Guo G, Hu X, Zhang Y, Li Q, et al. (2010) Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome. Genome Res 20: 646-654.
20. Maher CA, Kumar-Sinha C, Cao X, Kalyana-Sundaram S, Han B, et al. (2009) Transcriptome sequencing to detect gene fusions in cancer. Nature 458: 97-101.
21. Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, et al. (2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 28: 511-515.
22. Stein LD, Mungall C, Shu S, Caudy M, Mangone M, et al. (2002) The generic genome browser a building block for a model organism system database. Genome Res 12: 1599-1610.
23. Modrek B, Lee C, (2002) A genomic view of alternative splicing. Nat Genet 30: 13-19.
24. Malko DB, Makeev VJ, Mironov AA, Gelfand MS, (2006) Evolution of exon-intron structure and alternative splicing in fruit flies and malarial mosquito genomes. Genome Res 16: 505-509.
25. Liu HF, Li YN, Jia R, Cui WZ, Mu ZM, et al. (2011) Alternative splicing of the antitrypsin gene in the silkworm, Bombyx mori. Mol Biol Rep 38: 2793-2799.
26. Nagaoka S, Takata Y, Kato K, (2011) Identification of two arginases generated by alternative splicing in the silkworm, Bombyx mori. Arch Insect Biochem Physiol 76: 97-113.
27. Gopalapillai R, Kadono-Okuda K, Tsuchida K, Yamamoto K, Nohata J, et al. (2006) Lipophorin receptor of Bombyx mori cDNA cloning, genomic structure, alternative splicing, and isolation of a new isoform. J Lipid Res 47: 1005-1013.
28. Niu BL, Meng ZQ, Tao YZ, Lu SL, Weng HB, et al. (2005) Cloning and alternative splicing analysis of Bombyx mori transformer-2 gene using silkworm EST database. Acta Biochim Biophys Sin (Shanghai) 37: 728-736.
29. Abdel-Banat BM, Koga D, (2002) Alternative splicing of the primary transcript generates heterogeneity within the products of the gene for Bombyx mori chitinase. J Biol Chem 277: 30524-30534.
30. Xia QY, Fujii H, Kusakabe T, Banno Y, (2001) Identification of three annexin IX isoforms generated by alternative splicing of the carboxyl-terminal exon in silkworm, Bombyx mori. Insect Biochem Mol Biol 32: 9-14.
31. Drevet JR, Swevers L, Iatrou K, (1995) Developmental regulation of a silkworm gene encoding multiple GATA-type transcription factors by alternative splicing. J Mol Biol 246: 43-53.
32. Zha XF, Xia QY, Zhao P, Li J, Duan J, et al. (2005) Detection and analysis of alternative splicing in the silkworm by aligning expressed sequence tags with the genomic sequence. Insect Mol Biol 14: 113-119.
33. The International SilkwormGenome Consortium, (2008) The genome of a lepidopteran model insect, the silkworm Bombyx mori. Insect Biochem Mol Biol 38: 1036-1045.