Background The Eastern hive honey bee, Apis cerana cerana is a native and widely bred honey bee species in China. Molecular biology research about this honey bee species is scarce, and genomic information for A. c. cerana is not currently available. Transcriptome and expression profiling data for this species are therefore important resources needed to better understand the biological mechanisms of A. c. cerana. In this study, we obtained the transcriptome information of A. c. cerana by RNA-sequencing and compared gene expression differences between queens and workers of A. c. cerana by digital gene expression (DGE) analysis. Results Using high-throughput Illumina RNA sequencing we obtained 51,581,510 clean reads corresponding to 4.64 Gb total nucleotides from a single run. These reads were assembled into 46,999 unigenes with a mean length of 676 bp. Based on a sequence similarity search against the five public databases (NR, Swissport, GO, COG, KEGG) with a cut-off E-value of 10?5 using BLASTX, a total of 24,630 unigenes were annotated with gene descriptions, gene ontology terms, or metabolic pathways. Using these transcriptome data as references we analyzed the gene expression differences between the queens and workers of A. c. cerana using a tag-based digital gene expression method. We obtained 5.96 and 5.66 million clean tags from the queen and worker samples, respectively. A total of 414 genes were differentially expressed between them, with 189 up-regulated and 225 down-regulated in queens. Conclusions Our transcriptome data provide a comprehensive sequence resource for future A. c. cerana study, establishing an important public information platform for functional genomic studies in A. c. cerana. Furthermore, the DGE data provide comprehensive gene expression information for the queens and workers, which will facilitate our understanding of the molecular mechanisms of the different physiological aspects of the two castes.
References
[1]
Peng YS, Fang ZY, Xu SY, Ge LS (1987) The resistance mechanism of the Asian honey bee, Apis cerana cerana Fabr., to ectoparasitic mite, Varroa jacbsoni Oudemans. J Inver Patho 47: 54–60.
[2]
Cheng SL (2001) Special management of Apis cerana cerana. In: Liu BH, editor. The Apicultural Science in China. Beijing: Chinese Agricultural Press. 488–512.
[3]
Page RE Jr, Peng CY (2001) Aging and development in social insects with emphasis on the honey bee, Apis mellifera L. Experimental Gerontology. 36(4–6): 695–711.
[4]
Severson DW, Williamson JL, Aiken JM (1989) Caste-specific transcription in the female honey bee. Insect Biochem 19(2): 215–220.
[5]
Evans JD, Wheeler DE (1999) Differential gene expression between developing queens and workers in the honey bee, Apis mellifera. Proc Natl Acad Sci U S A 96(10): 5575–5580.
[6]
Evans JD, Wheeler DE (2001) Expression profiles during honeybee caste determination. Genome Biol 2(1): RESEARCH0001.
[7]
Barchuk AR, Cristino AS, Kucharski R, Costa LF, Sim?es ZL, et al. (2007) Molecular determinants of caste differentiation in the highly eusocial honeybee Apis mellifera. BMC Dev Biol 7: 70.
[8]
Azevedo SV, Caranton OA, de Oliveira TL, Hartfelder K (2011) Differential expression of hypoxia pathway genes in honey bee (Apis mellifera L.) caste development. J Insect Physiol 57(1): 38–45.
[9]
Patel A, Fondrk MK, Kaftanoglu O, Emore C, Hunt G, et al. (2007) The making of a queen: TOR pathway is a key player in diphenic caste development. PLoS One 2(6): e509.
[10]
Mutti NS, Dolezal AG, Wolschin F, Mutti JS, Gill KS, et al. (2011) IRS and TOR nutrient-signaling pathways act via juvenile hormone to influence honey bee caste fate. J Exp Biol 214(Pt 23): 3977–3984.
[11]
Wheeler DE, Buck N, Evans JD (2006) Expression of insulin pathway genes during the period of caste determination in the honey bee, Apis mellifera. Insect Mol Biol 15(5): 597–602.
[12]
de Azevedo SV, Hartfelder K (2008) The insulin signaling pathway in honey bee (Apis mellifera) caste development – differential expression of insulin-like peptides and insulin receptors in queen and worker larvae. J Insect Physiol 54(6): 1064–1071.
[13]
Corona M, Hughes KA, Weaver DB, Robinson GE (2005) Gene expression patterns associated with queen honey bee longevity. Mech Ageing Dev 126(11): 1230–1238.
[14]
Grozinger CM, Fan Y, Hoover SE, Winston ML (2007) Genome-wide analysis reveals differences in brain gene expression patterns associated with caste and reproductive status in honey bees (Apis mellifera). Mol Ecol 16(22): 4837–4848.
[15]
Humann FC, Hartfelder K (2011) Representational Difference Analysis (RDA) reveals differential expression of conserved as well as novel genes during caste-specific development of the honey bee (Apis mellifera L.) ovary. Insect Biochem Mol Biol 41(8): 602–612.
[16]
Thompson GJ, Yockey H, Lim J, Oldroyd BP (2007) Experimental manipulation of ovary activation and gene expression in honey bee (Apis mellifera) queens and workers: testing hypotheses of reproductive regulation. J Exp Zool A Ecol Genet Physiol 307(10): 600–610.
[17]
Li J, Wu J, Begna Rundassa D, Song F, et al. (2010) Differential protein expression in honeybee (Apis mellifera L.) larvae: underlying caste differentiation. PLoS One 5(10): e13455.
[18]
Begna D, Fang Y, Feng M, Li J (2011) Mitochondrial proteins differential expression during honeybee (Apis mellifera L.) queen and worker larvae caste determination. J Proteome Res 10(9): 4263–4280.
[19]
Begna D, Han B, Feng M, Fang Y, Li J (2012) Differential Expressions of Nuclear Proteomes between Honeybee (Apis mellifera L.) Queen and Worker Larvae: A Deep Insight into Caste Pathway Decisions. J Proteome Res 11(2): 1317–1329.
[20]
Pereboom JJ, Jordan WC, Sumner S, Hammond RL, Bourke AF (2005) Differential gene expression in queen-worker caste determination in bumble-bees. Proc Biol Sci 272(1568): 1145–1152.
[21]
Judice C, Hartfelder K, Pereira GAG (2004) Caste-specific gene expression in the stingless bee Melipona quadrifasciata – Are there common patterns in highly eusocial bees? Insect Soc 51(4): 352–358.
[22]
Judice CC, Carazzole MF, Festa F, Sogayar MC, Hartfelder K, et al. (2006) Gene expression profiles underlying alternative caste phenotypes in a highly eusocial bee, Melipona quadrifasciata. Insect Mol Biol 15(1): 33–44.
[23]
Gr?ff J, Jemielity S, Parker JD, Parker KM, Keller L (2007) Differential gene expression between adult queens and workers in the ant Lasius niger. Mol Ecol 16(3): 675–683.
[24]
Wang XW, Luan JB, Li JM, Bao YY, Zhang CX, et al. (2010) De novo characterization of a whitefly transcriptome and analysis of its gene expression during development. BMC Genomics 11: 400.
[25]
Xue J, Bao YY, Li BL, Cheng YB, Peng ZY, et al. (2010) Transcriptome analysis of the brown planthopper Nilaparvata lugens. PLoS One 5(12): e14233.
[26]
Hao DC, Ge G, Xiao P, Zhang Y, Yang L (2011) The first insight into the tissue specific taxus transcriptome via Illumina second generation sequencing. PLoS One 6(6): e21220.
[27]
Xia Z, Xu H, Zhai J, Li D, Luo H, et al. (2011) RNA-Seq analysis and de novo transcriptome assembly of Hevea brasiliensis. Plant Mol Biol 77(3): 299–308.
[28]
Markovets AA, Herman D (2011) Analysis of cancer metabolism with high-throughput technologies. BMC Bioinformatics (Suppl 10):S8.
[29]
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(5): 511–515.
[30]
Mu Y, Ding F, Cui P, Ao J, Hu S, et al. (2010) Transcriptome and expression profiling analysis revealed changes of multiple signaling pathways involved in immunity in the large yellow croaker during Aeromonas hydrophila infection. BMC Genomics 11: 506.
[31]
Audic S, Claverie JM (1997) The significance of digital gene expression profiles. Genome Res 7(10): 986–995.
[32]
Guidugli KR, Nascimento AM, Amdam GV, Barchuk AR, Omholt S, et al. (2005) Vitellogenin regulates hormonal dynamics in the worker caste of a eusocial insect. FEBS Lett 579(22): 4961–4965.
[33]
Corona M, Velarde RA, Remolina S, Moran-Lauter A, Wang Y, et al. (2007) Vitellogenin, juvenile hormone, insulin signaling, and queen honey bee longevity. Proc Natl Acad Sci U S A 104(17): 7128–7133.
[34]
Martins JR, Nunes FM, Cristino AS, Sim?es ZL, Bitondi MM (2010) The four hexamerin genes in the honey bee: structure, molecular evolution and function deduced from expression patterns in queens, workers and drones. BMC Mol Biol 11: 23.
[35]
Martins JR, Anhezini L, Dallacqua RP, Sim?es ZL, Bitondi MM (2011) A honey bee hexamerin, HEX 70a, is likely to play an intranuclear role in developing and mature ovarioles and testioles. PLoS One 6(12): e29006.
[36]
Zhou X, Oi FM, Scharf ME (2006) Social exploitation of hexamerin: RNAi reveals a major caste-regulatory factor in termites. Proc Natl Acad Sci U S A 103(12): 4499–4504.
[37]
Zhou X, Tarver MR, Bennett GW, Oi FM, Scharf ME (2006) Two hexamerin genes from the termite Reticulitermes flavipes: Sequence, expression, and proposed functions in caste regulation. Gene 376(1): 47–58.
[38]
Willis LG, Winston ML, Honda BM (1992) Phylogenetic relationships in the honeybee (genus Apis) as determined by the sequence of the cytochrome oxidase II region of mitochondrial DNA. Mol Phylogenet Evol 1(3): 169–178.
[39]
Robertson HM, Wanner KW (2006) The chemoreceptor superfamily in the honey bee, Apis mellifera: expansion of the odorant, but not gustatory, receptor family. Genome Res 16: 1395–1403.
[40]
Zeng ZJ (2009) The biology of the honeybee. In: Wu XF, editor. Apiculture. Beijing: Chinese Agricultural Press. 36–38.
[41]
Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, et al. (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 29(7): 644–652.
[42]
Iseli C, Jongeneel CV, Bucher P (1999) ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences. Proc Int Conf Intell Syst Mol Biol 138–148.
[43]
Conesa A, G?tz S, García-Gómez JM, Terol J, Talón M, et al. (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21(18): 3674–3676.
[44]
Ye J, Fang L, Zheng H, Zhang Y, Chen J, et al.. (2006) WEGO: a web tool for plotting GO annotations. Nucleic Acids Res 34(Web Server issue):W293–297.
[45]
Louren?o AP, Mackert A, Cristino AS, Sim?es ZLP (2008) Validation of reference genes for gene expression studies in the honey bee, Apis mellifera, by quantitative real-time RT-PCR. Apidologie 39(3): 372–385.
[46]
Liu W, Saint DA (2002) A new quantitative method of real time reverse transcription polymerase chain reaction assay based on simulation of polymerase chain reaction kinetics. Anal Biochem 302(1): 52–59.