Transcriptomic analysis of developmental features of Bombyx mori wing disc during metamorphosis

BMC Genomics

Lin Liu¹  Qi-Li Feng¹  Li-Hua Huang¹  Si-Chun Zheng¹  Hui-Min Deng¹  Jun Ou¹ 

[1]Laboratory of Molecular and Developmental Entomology, Guangdong Provincial Key Lab of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou 510631, China

关键词: RNA-Seq;    Transcriptome;    Metamorphosis;    Wing disc;    B. mori;   

Others  :  1139511
DOI  :  10.1186/1471-2164-15-820

 received in 2014-03-20, accepted in 2014-09-17,  发布年份 2014

【 摘 要 】

Background

Wing discs of B. mori are transformed to pupal wings during the larva-to-pupa metamorphosis with dramatic morphological and structural changes. To understand these changes at a transcriptional level, RNA-seq of the wing discs from 6-day-old fifth instar larvae (L5D6), prepupae (PP) and pupae (P0) was performed.

Results

In total, 12,254 transcripts were obtained from the wing disc, out of which 5,287 were identified to be differentially expressed from L5D6 to PP and from PP to P0. The results of comprehensive analysis of RNA-seq data showed that during larvae-to-pupae metamorphosis, many genes of 20E signaling pathway were up-regulated and those of JH signaling pathway were down-regulated. Seventeen transcription factors were significantly up-regulated. Cuticle protein genes (especially wing cuticle protein genes), were most abundant and significantly up-regulated at P0 stage. Genes responsible for the degradation and de novo synthesis of chitin were significantly up-regulated. There were A and B two types of chitin synthases in B. mori, whereas only chitin synthase A was up-regulated. Both trehalose and D-fructose, which are precursors of chitin synthesis, were detected in the hemolymph of L5D6, PP and P0, suggesting de novo synthesis of chitin. However, most of the genes that are related to early wing disc differentiation were down-regulated.

Conclusions

Extensive transcriptome and DGE profiling data of wing disc during metamorphosis of silkworm have been generated, which provided comprehensive gene expression information at the transcriptional level. These results implied that during the larva-to-pupa metamorphosis, pupal wing development and transition might be mainly controlled by 20E signaling in B. mori. The 17 up-regulated transcription factors might be involved in wing development. Chitin required for pupal wing development might be generated from both degradation of componential chitin and de novo synthesis. Chitin synthase A might be responsible for the chitin synthesis in the pupal wing, while both trehalose and D-fructose might contribute to the de novo synthesis of chitin during the formation of pupal wing.

【 授权许可】

   
2014 Ou et al.; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

Figure 2.

Figure 3.

Figure 4.

Figure 5.

Figure 6.

Figure 7.

【 参考文献 】

• [1]Xia Q, Zhou Z, Lu C, Cheng D, Dai F, Li B, Zhao P, Zha X, Cheng T, Chai C, Pan G, Xu J, Liu C, Lin Y, Qian J, Hou Y, Wu Z, Li G, Pan M, Li C, Shen Y, Lan X, Yuan L, Li T, Xu H, Yang G, Wan Y, Zhu Y, Yu M, Shen W, et al.: A draft sequence for the genome of the domesticated silkworm (Bombyx mori). Science 2004, 306(5703):1937-1940.
• [2]International Silkworm Genome C: The genome of a lepidopteran model insect, the silkworm Bombyx mori. Insect Biochem Mol Biol 2008, 38(12):1036-1045.
• [3]Wang J, Xia Q, He X, Dai M, Ruan J, Chen J, Yu G, Yuan H, Hu Y, Li R, Feng T, Ye C, Lu C, Wang J, Li S, Wong GK, Yang H, Wang J, Xiang Z, Zhou Z, Yu J: SilkDB: a knowledgebase for silkworm biology and genomics. Nucleic Acids Res 2005, 33(Database issue):D399-D402.
• [4]Shimomura M, Minami H, Suetsugu Y, Ohyanagi H, Satoh C, Antonio B, Nagamura Y, Kadono-Okuda K, Kajiwara H, Sezutsu H, Nagaraju J, Goldsmith MR, Xia Q, Yamamoto K, Mita K: KAIKObase: an integrated silkworm genome database and data mining tool. BMC Genomics 2009, 10:486. BioMed Central Full Text
• [5]Klein T: Wing disc development in the fly: the early stages. Curr Opinion Genetics Dev 2001, 11(4):470-475.
• [6]Deng H, Zhang J, Li Y, Zheng S, Liu L, Huang L, Xu WH, Palli SR, Feng Q: Homeodomain POU and Abd-A proteins regulate the transcription of pupal genes during metamorphosis of the silkworm, Bombyx mori. Proc Natl Acad Sci U S A 2012, 109(31):12598-12603.
• [7]Dubrovsky EB: Hormonal cross talk in insect development. Trends in Endocrinol Metab TEM 2005, 16(1):6-11.
• [8]Thummel CS: Molecular mechanisms of developmental timing in C. elegans and Drosophila. Dev Cell 2001, 1(4):453-465.
• [9]Truman JW, Riddiford LM: The origins of insect metamorphosis. Nature 1999, 401(6752):447-452.
• [10]Truman JW, Riddiford LM: Endocrine insights into the evolution of metamorphosis in insects. Annu Rev Entomol 2002, 47:467-500.
• [11]Riddiford LM, Hiruma K, Zhou X, Nelson CA: Insights into the molecular basis of the hormonal control of molting and metamorphosis from Manduca sexta and Drosophila melanogaster. Insect Biochem Mol Biol 2003, 33(12):1327-1338.
• [12]Thummel CS: Ecdysone-regulated puff genes 2000. Insect Biochem Mol Biol 2002, 32(2):113-120.
• [13]Huet F, Ruiz C, Richards G: Sequential gene activation by ecdysone in Drosophila melanogaster: the hierarchical equivalence of early and early late genes. Development 1995, 121(4):1195-1204.
• [14]Ashok M, Turner C, Wilson TG: Insect juvenile hormone resistance gene homology with the bHLH-PAS family of transcriptional regulators. Proc Natl Acad Sci U S A 1998, 95(6):2761-2766.
• [15]Charles JP, Iwema T, Epa VC, Takaki K, Rynes J, Jindra M: Ligand-binding properties of a juvenile hormone receptor, Methoprene-tolerant. Proc Natl Acad Sci U S A 2011, 108(52):21128-21133.
• [16]Konopova B, Jindra M: Juvenile hormone resistance gene Methoprene-tolerant controls entry into metamorphosis in the beetle Tribolium castaneum. Proc Natl Acad Sci U S A 2007, 104(25):10488-10493.
• [17]Parthasarathy R, Tan A, Palli SR: bHLH-PAS family transcription factor methoprene-tolerant plays a key role in JH action in preventing the premature development of adult structures during larval-pupal metamorphosis. Mech Dev 2008, 125(7):601-616.
• [18]Kayukawa T, Minakuchi C, Namiki T, Togawa T, Yoshiyama M, Kamimura M, Mita K, Imanishi S, Kiuchi M, Ishikawa Y, Shinoda T: Transcriptional regulation of juvenile hormone-mediated induction of Kruppel homolog 1, a repressor of insect metamorphosis. Proc Natl Acad Sci U S A 2012, 109(29):11729-11734.
• [19]Obara Y, Miyatani M, Ishiguro Y, Hirota K, Koyama T, Izumi S, Iwami M, Sakurai S: Pupal commitment and its hormonal control in wing imaginal discs. J Insect Physiol 2002, 48(10):933-944.
• [20]Koyama T, Obara Y, Iwami M, Sakurai S: Commencement of pupal commitment in late penultimate instar and its hormonal control in wing imaginal discs of the silkworm, Bombyx mori. J Insect Physiol 2004, 50(2–3):123-133.
• [21]Sato K, Matsunaga TM, Futahashi R, Kojima T, Mita K, Banno Y, Fujiwara H: Positional cloning of a Bombyx wingless locus flugellos (fl) reveals a crucial role for fringe that is specific for wing morphogenesis. Genetics 2008, 179(2):875-885.
• [22]Kubota K, Goto S, Eto K, Hayashi S: EGF receptor attenuates Dpp signaling and helps to distinguish the wing and leg cell fates in Drosophila. Development 2000, 127(17):3769-3776.
• [23]Bray S: Drosophila development: Scalloped and Vestigial take wing. Current Biol CB 1999, 9(7):R245-R247.
• [24]Morata G: How Drosophila appendages develop. Nat Rev Mol Cell Biol 2001, 2(2):89-97.
• [25]Schwank G, Basler K: Regulation of organ growth by morphogen gradients. Cold Spring Harbor Perspect Biol 2010, 2(1):a001669.
• [26]Swarup S, Verheyen EM: Wnt/Wingless signaling in Drosophila. Cold Spring Harbor Perspect Biol 2012, 4:6.
• [27]Neto-Silva RM, Wells BS, Johnston LA: Mechanisms of growth and homeostasis in the Drosophila wing. Annu Rev Cell Dev Biol 2009, 25:197-220.
• [28]Merzendorfer H, Zimoch L: Chitin metabolism in insects: structure, function and regulation of chitin synthases and chitinases. J Exp Biol 2003, 206(Pt 24):4393-4412.
• [29]Takeda M, Mita K, Quan GX, Shimada T, Okano K, Kanke E, Kawasaki H: Mass isolation of cuticle protein cDNAs from wing discs of Bombyx mori and their characterizations. Insect Biochem Mol Biol 2001, 31(10):1019-1028.
• [30]Noji T, Ote M, Takeda M, Mita K, Shimada T, Kawasaki H: Isolation and comparison of different ecdysone-responsive cuticle protein genes in wing discs of Bombyx mori. Insect Biochem Mol Biol 2003, 33(7):671-679.
• [31]Futahashi R, Okamoto S, Kawasaki H, Zhong YS, Iwanaga M, Mita K, Fujiwara H: Genome-wide identification of cuticular protein genes in the silkworm, Bombyx mori. Insect Biochem Mol Biol 2008, 38(12):1138-1146.
• [32]Gan LP, Zhang WY, Niu YS, Xu L, Xi J, Ji MM, Xu SQ: 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 2010, 10:114.
• [33]Mita K, Morimyo M, Okano K, Koike Y, Nohata J, Kawasaki H, Kadono-Okuda K, Yamamoto K, Suzuki MG, Shimada T, Goldsmith MR, Maeda S: The construction of an EST database for Bombyx mori and its application. Proc Natl Acad Sci U S A 2003, 100(24):14121-14126.
• [34]Funaguma S, Hashimoto S, Suzuki Y, Omuro N, Sugano S, Mita K, Katsuma S, Shimada T: SAGE analysis of early oogenesis in the silkworm, Bombyx mori. Insect Biochem Mol Biol 2007, 37(2):147-154.
• [35]Zhang Y, Huang J, Jia S, Liu W, Li M, Wang S, Miao X, Xiao H, Huang Y: SAGE tag based cDNA microarray analysis during larval to pupal development and isolation of novel cDNAs in Bombyx mori. Genomics 2007, 90(3):372-379.
• [36]Liang J, Zhang L, Xiang Z, He N: Expression profile of cuticular genes of silkworm, Bombyx mori. BMC Genomics 2010, 11:173. BioMed Central Full Text
• [37]Xia Q, Cheng D, Duan J, Wang G, Cheng T, Zha X, Liu C, Zhao P, Dai F, Zhang Z, He N, Zhang L, Xiang Z: Microarray-based gene expression profiles in multiple tissues of the domesticated silkworm, Bombyx mori. Genome Biol 2007, 8(8):R162. BioMed Central Full Text
• [38]Li Y, Wang G, Tian J, Liu H, Yang H, Yi Y, Wang J, Shi X, Jiang F, Yao B, Zhang Z: Transcriptome analysis of the silkworm (Bombyx mori) by high-throughput RNA sequencing. PLoS One 2012, 7(8):e43713.
• [39]Wang Z, Gerstein M, Snyder M: RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 2009, 10(1):57-63.
• [40]Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A: Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 2011, 29(7):644-652.
• [41]Li R, Yu C, Li Y, Lam TW, Yiu SM, Kristiansen K, Wang J: SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 2009, 25(15):1966-1967.
• [42]Curtis K, Youngquist ST: Part 21: categoric analysis: Pearson chi-square test. Air Med J 2013, 32(4):179-180.
• [43]Matsuoka T, Fujiwara H: Expression of ecdysteroid-regulated genes is reduced specifically in the wing discs of the wing-deficient mutant (fl) of Bombyx mori. Dev Genes Evol 2000, 210(3):120-128.
• [44]Ote M, Mita K, Kawasaki H, Seki M, Nohata J, Kobayashi M, Shimada T: Microarray analysis of gene expression profiles in wing discs of Bombyx mori during pupal ecdysis. Insect Biochem Mol Biol 2004, 34(8):775-784.
• [45]Zhou Q, Yu L, Shen X, Li Y, Xu W, Yi Y, Zhang Z: Homology of dipteran bristles and lepidopteran scales: requirement for the Bombyx mori achaete-scute homologue ASH2. Genetics 2009, 183(2):619-627. 611SI-613SI
• [46]Besson MT, Chareyre P, Deleage G, Demont J, Quennedey B, Courrent A, Fourche J, Bosquet G: Isolation and characterization of Urbain, a 20-hydroxyecdysone-inducible gene expressed during morphogenesis of Bombyx mori wing imaginal discs. Rouxs Arch Dev Biol 1996, 205(7–8):333-343.
• [47]Abdou M, Peng C, Huang J, Zyaan O, Wang S, Li S, Wang J: Wnt signaling cross-talks with JH signaling by suppressing Met and gce expression. PLoS One 2011, 6(11):e26772.
• [48]Muramatsu D, Kinjoh T, Shinoda T, Hiruma K: The role of 20-hydroxyecdysone and juvenile hormone in pupal commitment of the epidermis of the silkworm, Bombyx mori. Mech Dev 2008, 125(5–6):411-420.
• [49]Kozlova T, Lam G, Thummel CS: Drosophila DHR38 nuclear receptor is required for adult cuticle integrity at eclosion. Dev Dyn Off Publ Am Assoc Anatomists 2009, 238(3):701-707.
• [50]Charles JP, Shinoda T, Chinzei Y: Characterization and DNA-binding properties of GRF, a novel monomeric binding orphan receptor related to GCNF and betaFTZ-F1. Eur J Biochem/FEBS 1999, 266(1):181-190.
• [51]Wang HB, Nita M, Iwanaga M, Kawasaki H: betaFTZ-F1 and Broad-Complex positively regulate the transcription of the wing cuticle protein gene, BMWCP5, in wing discs of Bombyx mori. Insect Biochem Mol Biol 2009, 39(9):624-633.
• [52]Deng H, Zheng S, Yang X, Liu L, Feng Q: Transcription factors BmPOUM2 and BmbetaFTZ-F1 are involved in regulation of the expression of the wing cuticle protein gene BmWCP4 in the silkworm, Bombyx mori. Insect Mol Biol 2011, 20(1):45-60.
• [53]Ali MS, Iwanaga M, Kawasaki H: Ecdysone-responsive transcriptional regulation determines the temporal expression of cuticular protein genes in wing discs of Bombyx mori. Gene 2013, 512(2):337-347.
• [54]Lundell MJ, Hirsh J: eagle is required for the specification of serotonin neurons and other neuroblast 7–3 progeny in the Drosophila CNS. Development 1998, 125(3):463-472.
• [55]Gritzan U, Weiss C, Brennecke J, Bohmann D: Transrepression of AP-1 by nuclear receptors in Drosophila. Mech Dev 2002, 115(1–2):91-100.
• [56]Sourmeli S, Papantonis A, Lecanidou R: A novel role for the Bombyx Slbo homologue, BmC/EBP, in insect choriogenesis. Biochem Biophys Res Commun 2005, 337(2):713-719.
• [57]Armand P, Knapp AC, Hirsch AJ, Wieschaus EF, Cole MD: A novel basic helix-loop-helix protein is expressed in muscle attachment sites of the Drosophila epidermis. Mol Cell Biol 1994, 14(6):4145-4154.
• [58]Staudt N, Molitor A, Somogyi K, Mata J, Curado S, Eulenberg K, Meise M, Siegmund T, Hader T, Hilfiker A, Bronner G, Ephrussi A, Rorth P, Cohen SM, Fellert S, Chung HR, Piepenburg O, Schafer U, Jackle H, Vorbruggen G: Gain-of-function screen for genes that affect Drosophila muscle pattern formation. PLoS Genet 2005, 1(4):e55.
• [59]Biehs B, Sturtevant MA, Bier E: Boundaries in the Drosophila wing imaginal disc organize vein-specific genetic programs. Development 1998, 125(21):4245-4257.
• [60]Wessells RJ, Grumbling G, Donaldson T, Wang SH, Simcox A: Tissue-specific regulation of vein/EGF receptor signaling in Drosophila. Dev Biol 1999, 216(1):243-259.
• [61]Bergsland M, Werme M, Malewicz M, Perlmann T, Muhr J: The establishment of neuronal properties is controlled by Sox4 and Sox11. Genes Dev 2006, 20(24):3475-3486.
• [62]Dang DT, Pevsner J, Yang VW: The biology of the mammalian Kruppel-like family of transcription factors. Int J Biochem Cell Biol 2000, 32(11–12):1103-1121.
• [63]de Celis JF, Bray S, Garcia-Bellido A: Notch signalling regulates veinlet expression and establishes boundaries between veins and interveins in the Drosophila wing. Development 1997, 124(10):1919-1928.
• [64]Wang S, Jayaram SA, Hemphala J, Senti KA, Tsarouhas V, Jin H, Samakovlis C: Septate-junction-dependent luminal deposition of chitin deacetylases restricts tube elongation in the Drosophila trachea. Curr Biol CB 2006, 16(2):180-185.
• [65]Zhao Y, Park RD, Muzzarelli RA: Chitin deacetylases: properties and applications. Marine Drugs 2010, 8(1):24-46.
• [66]Moussian B, Tang E, Tonning A, Helms S, Schwarz H, Nusslein-Volhard C, Uv AE: Drosophila Knickkopf and Retroactive are needed for epithelial tube growth and cuticle differentiation through their specific requirement for chitin filament organization. Development 2006, 133(1):163-171.
• [67]Chaudhari SS, Arakane Y, Specht CA, Moussian B, Boyle DL, Park Y, Kramer KJ, Beeman RW, Muthukrishnan S: Knickkopf protein protects and organizes chitin in the newly synthesized insect exoskeleton. Proc Natl Acad Sci U S A 2011, 108(41):17028-17033.
• [68]Milan M, Perez L, Cohen SM: Short-range cell interactions and cell survival in the Drosophila wing. Dev Cell 2002, 2(6):797-805.
• [69]Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B: Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 2008, 5(7):621-628.
• [70]Benjamini Y, Yekutieli D: The control of the false discovery rate in multiple testing under dependency. Ann Stat 2001, 29:1165-1188.
• [71]Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, Itoh M, Katayama T, Kawashima S, Okuda S, Tokimatsu T, Yamanishi Y: KEGG for linking genomes to life and the environment. Nucleic Acids Res 2008, 36(Database issue):D480-D484.
• [72]Ye J, Fang L, Zheng H, Zhang Y, Chen J, Zhang Z, Wang J, Li S, Li R, Bolund L, Wang J: WEGO: a web tool for plotting GO annotations. Nucleic Acids Res 2006, 34(Web Server issue):W293-W297.