Comparative analysis of the silk gland transcriptomes between the domestic and wild silkworms

BMC Genomics

Volumn 16, Issue 1, 2015, Pages

  Fang, Shou Min ^a,c   Hu, Bi Li ^b   Zhou, Qiu Zhong ^a   Yu, Quan You ^a   Zhang, Ze ^a  

^a CHONGQING UNIVERSITY   (China)

^b ANKANG UNIVERSITY   (China)

^c CHINA WEST NORMAL UNIVERSITY   (China)

Author keywords

Bombyx mori; Differentially expressed gene; Domestication; RNA seq; Silk gland

Indexed keywords

MESSENGER RNA; OXIDOREDUCTASE; TRANSCRIPTOME; SILK;

ARTICLE; BOMBYX MANDARINA; BOMBYX MORI; CONTROLLED STUDY; DIFFERENTIALLY EXPRESSED GENE; ENZYME ACTIVITY; GENE; GENE EXPRESSION REGULATION; GENE IDENTIFICATION; GENE ONTOLOGY; NONHUMAN; PROTEIN METABOLISM; PROTEIN SECRETION; QUANTITATIVE ANALYSIS; REAL TIME POLYMERASE CHAIN REACTION; RNA SEQUENCE; UPREGULATION; ANIMAL; BIOSYNTHESIS; BOMBYX; GENE EXPRESSION; GENETICS; MOLECULAR EVOLUTION; MOLECULAR GENETICS;

BOMBYX MANDARINA; BOMBYX MORI;

ANIMALS; BOMBYX; EVOLUTION, MOLECULAR; GENE EXPRESSION; MOLECULAR SEQUENCE ANNOTATION; SILK; TRANSCRIPTOME;

EID: 84924286420     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/s12864-015-1287-9     Document Type: Article

References (46)

1. Goldsmith MR, Shimada T, Abe H. The genetics and genomics of the silkworm, Bombyx mori. Annu Rev Entomol. 2005;50:71-100.
2. Xia Q, Guo Y, Zhang Z, Li D, Xuan Z, Li Z, et al. Complete resequencing of 40 genomes reveals domestication events and genes in silkworm (Bombyx). Science. 2009;326(5951):433-6.
3. Sun W, Yu H, Shen Y, Banno Y, Xiang Z, Zhang Z. Phylogeny and evolutionary history of the silkworm. Sci China Life Sci. 2012;55(6):483-96.
4. Normile D. Insect genetics. Sequencing 40 silkworm genomes unravels history of cultivation. Science. 2009;325(5944):1058-9.
5. Ma L, Xu H, Zhu J, Ma S, Liu Y, Jiang RJ, et al. Ras1(CA) overexpression in the posterior silk gland improves silk yield. Cell Res. 2011;21(6):934-43.
6. Grzelak K. Control of expression of silk protein genes. Comp Biochem Physiol B Biochem Mol Biol. 1995;110(4):671-81.
7. Zhou CZ, Confalonieri F, Jacquet M, Perasso R, Li ZG, Janin J. Silk fibroin: structural implications of a remarkable amino acid sequence. Proteins. 2001;44(2):119-22.
8. Inoue S, Tanaka K, Arisaka F, Kimura S, Ohtomo K, Mizuno S. Silk fibroin of Bombyx mori is secreted, assembling a high molecular mass elementary unit consisting of H-chain, L-chain, and P25, with a 6:6:1 molar ratio. J Biol Chem. 2000;275(51):40517-28.
9. Takasu Y, Hata T, Uchino K, Zhang Q. Identification of Ser2 proteins as major sericin components in the non-cocoon silk of Bombyx mori. Insect Biochem Mol Biol. 2010;40(4):339-44.
10. Zhong B, Yu Y, Xu Y, Yu H, Lu X, Miao Y, et al. Analysis of ESTs and gene expression patterns of the posterior silkgland in the fifth instar larvae of silkworm, Bombyx mori L. Sci China C Life Sci. 2005;48(1):25-33.
11. Xia Q, Cheng D, Duan J, Wang G, Cheng T, Zha X, et al. Microarray-based gene expression profiles in multiple tissues of the domesticated silkworm, Bombyx mori. Genome Biol. 2007;8(8):R162.
12. Tang J, Li WF, Zhang X, Zhou CZ. The gene expression profile of Bombyx mori silkgland. Gene. 2007;396(2):369-72.
13. Royer C, Briolay J, Garel A, Brouilly P, Sasanuma S, Sasanuma M, et al. Novel genes differentially expressed between posterior and median silk gland identified by SAGE-aided transcriptome analysis. Insect Biochem Mol Biol. 2011;41(2):118-24.
14. Duan J, Li R, Cheng D, Fan W, Zha X, Cheng T, et al. SilkDB v2.0: a platform for silkworm (Bombyx mori) genome biology. Nucleic Acids Res. 2010;38(Database issue):D453-456.
15. Roberts A, Pimentel H, Trapnell C, Pachter L. Identification of novel transcripts in annotated genomes using RNA-Seq. Bioinformatics. 2011;27(17):2325-9.
16. Li Y, Wang G, Tian J, Liu H, Yang H, Yi Y, et al. Transcriptome analysis of the silkworm (Bombyx mori) by high-throughput RNA sequencing. PLoS One. 2012;7(8):e43713.
17. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods. 2008;5(7):621-8.
18. Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010;26(1):139-40.
19. Wang L, Feng Z, Wang X, Zhang X. DEGseq: an R package for identifying differentially expressed genes from RNA-seq data. Bioinformatics. 2010;26(1):136-8.
20. Conesa A, Gotz S, Garcia-Gomez JM, Terol J, Talon M, Robles M. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics. 2005;21(18):3674-6.
21. Xie C, Mao X, Huang J, Ding Y, Wu J, Dong S, et al. KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases. Nucleic Acids Res. 2011;39(Web Server issue):W316-322.
22. Koepsell H, Schmitt BM, Gorboulev V. Organic cation transporters. Rev Physiol Biochem Pharmacol. 2003;150:36-90.
23. De Gregorio E, Spellman PT, Rubin GM, Lemaitre B. Genome-wide analysis of the Drosophila immune response by using oligonucleotide microarrays. Proc Natl Acad Sci U S A. 2001;98(22):12590-5.
24. Dittmer NT, Suderman RJ, Jiang H, Zhu YC, Gorman MJ, Kramer KJ, et al. Characterization of cDNAs encoding putative laccase-like multicopper oxidases and developmental expression in the tobacco hornworm, Manduca sexta, and the malaria mosquito, Anopheles gambiae. Insect Biochem Mol Biol. 2004;34(1):29-41.
25. Schenkman JB, Jansson I. The many roles of cytochrome b5. Pharmacol Ther. 2003;97(2):139-52.
26. Sakudoh T, Iizuka T, Narukawa J, Sezutsu H, Kobayashi I, Kuwazaki S, et al. A CD36-related transmembrane protein is coordinated with an intracellular lipid-binding protein in selective carotenoid transport for cocoon coloration. J Biol Chem. 2010;285(10):7739-51.
27. Zhou Z, Yang J, Wang L, Zhang H, Gao Y, Shi X, et al. A dopa decarboxylase modulating the immune response of scallop Chlamys farreri. PLoS One. 2011;6(4):e18596.
28. Wesley UV, McGroarty M, Homoyouni A. Dipeptidyl peptidase inhibits malignant phenotype of prostate cancer cells by blocking basic fibroblast growth factor signaling pathway. Cancer Res. 2005;65(4):1325-34.
29. Zhao P, Dong Z, Duan J, Wang G, Wang L, Li Y, et al. Genome-wide identification and immune response analysis of serine protease inhibitor genes in the silkworm, Bombyx mori. PLoS One. 2012;7(2):e31168.
30. Lee TV, Ding T, Chen Z, Rajendran V, Scherr H, Lackey M, et al. The E1 ubiquitin-activating enzyme Uba1 in Drosophila controls apoptosis autonomously and tissue growth non-autonomously. Development. 2008;135(1):43-52.
31. Perdomo G, Henry Dong H. Apolipoprotein D in lipid metabolism and its functional implication in atherosclerosis and aging. Aging (Albany NY). 2009;1(1):17-27.
32. Yang SY, Jeon SK, Kang JH, Yoo HI, Kim YS, Moon JS, et al. Synaptic vesicle protein 2b is expressed temporospatially in (pre)odontoblasts in developing molars. Eur J Oral Sci. 2012;120(6):505-12.
33. Victoriano E, Gregorio EA. Ultrastructure of the excretory duct in the silk gland of the sugarcane borer Diatraea saccharalis (Lepidoptera: Pyralidae). Arthropod Struct Dev. 2002;31(1):15-21.
34. Vrontou E, Economou A. Structure and function of SecA, the preprotein translocase nanomotor. Biochim Biophys Acta. 2004;1694(1-3):67-80.
35. Boot RG, Verhoek M, Donker-Koopman W, Strijland A, van Marle J, Overkleeft HS, et al. Identification of the non-lysosomal glucosylceramidase as beta-glucosidase 2. J Biol Chem. 2007;282(2):1305-12.
36. Ma L, Liu S, Shi M, Chen XX, Li S. Ras1CA-upregulated BCPI inhibits cathepsin activity to prevent tissue destruction of the Bombyx posterior silk gland. J Proteome Res. 2013;12(4):1924-34.
37. Li J, Cai Y, Ye L, Wang S, Che J, You Z, et al. MicroRNA expression profiling of the fifth-instar posterior silk gland of Bombyx mori. BMC Genomics. 2014;15:410.
38. Vella MC, Choi EY, Lin SY, Reinert K, Slack FJ. The C. elegans microRNA let-7 binds to imperfect let-7 complementary sites from the lin-41 3'UTR. Genes Dev. 2004;18(2):132-7.
39. Eulalio A, Huntzinger E, Izaurralde E. Getting to the root of miRNA-mediated gene silencing. Cell. 2008;132(1):9-14.
40. Long D, Lu W, Zhang Y, Guo Q, Xiang Z, Zhao A. New insight into the mechanism underlying fibroin secretion in silkworm, Bombyx mori. FEBS J. 2015;282(1):89-101.
41. Hoegger PJ, Kilaru S, James TY, Thacker JR, Kues U. Phylogenetic comparison and classification of laccase and related multicopper oxidase protein sequences. FEBS J. 2006;273(10):2308-26.
42. Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009;10(3):R25.
43. Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 2013;14(4):R36.
44. Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Statist Soc B. 1995;57:289-300.
45. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, et al. Clustal W and Clustal X version 2.0. Bioinformatics. 2007;23(21):2947-8.
46. Livak KJ, Schmittgen TD. Analysis of relative gene expression data using real-time quantitative PCR and the 2 (-Delta Delta C(T)) Method. Methods. 2001;25(4):402-8.