Independent variations in genome-wide expression, alternative splicing, and DNA methylation in brain tissues among castes of the buff-tailed bumblebee, Bombus terrestris

Dan Zhu; Jin Ge; Siyuan Guo; Li Hou; Rangjun Shi; Xian Zhou; Xin Nie; Xianhui Wang

doi:10.1016/j.jgg.2021.04.008

Volume 48 Issue 8

Aug. 2021

Turn off MathJax

Article Contents

Article Navigation > Journal of Genetics and Genomics > 2021 > 48(8): 681-694

PDF( 3388 KB)

Independent variations in genome-wide expression, alternative splicing, and DNA methylation in brain tissues among castes of the buff-tailed bumblebee, Bombus terrestris

doi: 10.1016/j.jgg.2021.04.008

Dan Zhu^a,b,
Jin Ge^a,b,
Siyuan Guo^a,b,
Li Hou^a,b,
Rangjun Shi^a,b,
Xian Zhou^a,b,
Xin Nie^a,
Xianhui Wang^a,b

a State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100080, China;
b CAS Centre for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China

Funds:

We gratefully thank Prof. Le Kang for the constructive advice on the framework of this study. We appreciate Li Feng for the assistance in analyzing the PacBio data. This study was supported by the National Natural Science Foundation of China (31930012, 31920103004, and 31772531), the Science and Technology Service Network Initiative of the Chinese Academy of Sciences (KFJ-STSZDTP-073), the Joint NSFC-ISF Research Grant (3201101042), and the State Key Laboratory of Integrated Management of Pest Insects and Rodents (Y852981203).

Received Date: 2021-02-03
Accepted Date: 2021-04-02
Rev Recd Date: 2021-03-26
Publish Date: 2021-08-20

Abstract

Abstract

Caste differentiation in social hymenopterans is an intriguing example of phenotypic plasticity. However, the co-ordination among gene regulatory factors to mediate caste differentiation remains inconclusive. In this study, we determined the role of gene regulation and related epigenetic processes in pre-imaginal caste differentiation in the primitively eusocial bumblebee Bombus terrestris. By combining RNA-Seq data from Illumina and PacBio and accurately quantifying methylation at whole-genomic base pair resolution, we found that queens, workers, and drones mainly differentiate in gene expression but not in alternative splicing and DNA methylation. Gynes are the most distinct with the lowest global level of whole-genomic methylation and with the largest number of caste-specific transcripts and alternative splicing events. By contrast, workers exhibit few uniquely expressed or alternatively spliced genes. Moreover, several genes involved in hormone and neurotransmitter metabolism are related to caste differentiation, whereas several neuropeptides are linked with sex differentiation. Despite little genome-wide association among differential gene expression, splicing, and differential DNA methylation, the overlapped gene ontology (GO) terms point to nutrition-related activity. Therefore, variations in gene regulation correlate with the behavioral differences among castes and highlight the specialization of toolkit genes in bumblebee gynes at the beginning of the adult stage.
- Social insects,
- Caste determination,
- PacBio,
- Epigenetics,
- Methylome,
- RNA-seq,
- WGBS-seq

These authors contributed equally to this work.

FullText(HTML)

References(75)

References

Alaux, C., Sinha, S., Hasadsri, L., Hunt, G.J., Guzmán-Novoa, E., DeGrandi-Hoffman, G., Uribe-Rubio, J.L., Southey, B.R., Rodriguez-Zas, S., Robinson, G.E., 2009. Honey bee aggression supports a link between gene regulation and behavioral evolution. Proc. Natl. Acad. Sci. U. S. A. 106, 15400.

Alford, D.V., 1969. Studies on the fat-body of adult bumble bees. J. Apicult. Res. 8, 37-48.

Amarasinghe, H.E., Clayton, C.I., Mallon, E.B., 2014. Methylation and worker reproduction in the bumble-bee (Bombus terrestris). Proc. R. Soc. B. 281, 20132502.

Amsalem, E., Grozinger, C.M., Padilla, M., Hefetz, A., 2015. The physiological and genomic bases of bumble bee social behaviour. In: Zayed, A., Kent, C.F. (Eds.), Adv. Insect Physiol. Academic Press, Massachusetts, pp. 37-93..

Anders, S., Reyes, A., Huber, W., 2012. Detecting differential usage of exons from RNA-seq data. Genome Res. 22, 2008-2017.

Andreatta, G., Broyart, C., Borghgraef, C., Vadiwala, K., Kozin, V., Polo, A., Bileck, A., Beets, I., Schoofs, L., Gerner, C., Raible, F., 2020. Corazonin signaling integrates energy homeostasis and lunar phase to regulate aspects of growth and sexual maturation in Platynereis. Proc. Natl. Acad. Sci. U. S. A. 117, 1097-1106.

Arsenault, S.V., Hunt, B.G., Rehan, S.M., 2018. The effect of maternal care on gene expression and DNA methylation in a subsocial bee. Nat. Commun. 9, 3468.

Bauer, J., Antosh, M., Chang, C., Schorl, C., Kolli, S., Neretti, N., Helfand, S.L., 2010. Comparative transcriptional profiling identifies takeout as a gene that regulates life span. Aging 2, 298-310.

Ben-Shahar, Y., Robichon, A., Sokolowski, M.B., Robinson, G.E., 2002. Influence of gene action across different time scales on behavior. Science 296, 741.

Berens, A.J., Hunt, J.H., Toth, A.L., 2015. Nourishment level affects caste-related gene expression in Polistes wasps. BMC Genom. 16, 235.

Bloch, G., Simon, T., Robinson, G.E., Hefetz, A., 2000. Brain biogenic amines and reproductive dominance in bumble bees (Bombus terrestris). J. Comp. Physiol. A. 186, 261-268.

Bonasio, R., Li, Q., Lian, J., Mutti, Navdeep, S., Jin, L., Zhao, H., Zhang, P., Wen, P., Xiang, H., Ding, Y., 2012. Genome-wide and caste-specific DNA methylomes of the ants Camponotus floridanus and Harpegnathos saltator. Curr. Biol. 22, 1755-1764.

Colgan, T.J., Carolan, J.C., Bridgett, S.J., Sumner, S., Blaxter, M.L., Brown, M.J.F., 2011. Polyphenism in social insects: insights from a transcriptome-wide analysis of gene expression in the life stages of the key pollinator, Bombus terrestris. BMC Genom. 12, 623.

Collins, D.H., Wirén, A., Labédan, M., Smith, M., Prince, D.C., Mohorianu, I., Dalmay, T., Bourke, A.F.G., 2021. Gene expression during larval caste determination and differentiation in intermediately eusocial bumblebees, and a comparative analysis with advanced eusocial honeybees. Mol. Ecol. 30, 718-735.

Crall, J.D., Gravish, N., Mountcastle, A.M., Kocher, S.D., Oppenheimer, R.L., Pierce, N.E., Combes, S.A., 2018. Spatial fidelity of workers predicts collective response to disturbance in a social insect. Nat. Commun. 9, 1201.

Cunningham, C.B., VanDenHeuvel, K., Khana, D.B., McKinney, E.C., Moore, A.J., 2016. The role of neuropeptide F in a transition to parental care. Biol. Lett. 12, 20160158.

Feng, H., Conneely, K.N., Wu, H., A Bayesian hierarchical model to detect differentially methylated loci from single nucleotide resolution sequencing data. Nucleic Acids Res. 42, e69-e69.

Fliszkiewicz, M., Wilkaniec, Z., 2007. Fatty acids and amino acids in the fat body of bumblebee Bombus terrestris (L.) in diapausing and non-diapausing queens. J. Apicult. Sci. 51, 55-63.

Foret, S., Kucharski, R., Pellegrini, M., Feng, S., Jacobsen, S.E., Robinson, G.E., Maleszka, R., 2012. DNA methylation dynamics, metabolic fluxes, gene splicing, and alternative phenotypes in honey bees. Proc. Natl. Acad. Sci. U. S. A. 109, 4968.

Friedman, D.A., Pilko, A., Skowronska-Krawczyk, D., Krasinska, K., Parker, J.W., Hirsh, J., Gordon, D.M., 2018. The role of dopamine in the collective regulation of foraging in harvester ants. iScience 8, 283-294.

Gadagkar, R., 1997. The evolution of caste polymorphism in social insects: 0 genetic release followed by diversifying evolution. J. Genet. 76, 167-179.

Gauthier, M., Grünewald, B., 2012. Neurotransmitter systems in the honey bee brain: functions in learning and memory. In: Galizia, C.G., Eisenhardt, D., Giurfa, M. (Eds.), Honeybee Neurobiology and Behavior: A Tribute to Randolf Menzel. Springer Netherlands..

Gilbert, S.F., Epel, D., 2009. Ecological Developmental Biology: Integrating Epigenetics, Medicine, and Evolution. Sinauer, Sunderland..

Glastad, K.M., Gokhale, K., Liebig, J., Goodisman, M.A.D., 2016. The caste- and sex-specific DNA methylome of the termite Zootermopsis nevadensis. Sci. Rep. 6, 37110.

Glastad, K.M., Hunt, B.G., Yi, S.V., Goodisman, M.A.D., 2014. Epigenetic inheritance and genome regulation: is DNA methylation linked to ploidy in haplodiploid insects?. Proc. R. Soc. 281, 20140411.

Gospocic, J., Shields, E.J., Glastad, K.M., Lin, Y., Penick, C.A., Yan, H., Mikheyev, A.S., Linksvayer, T.A., Garcia, B.A., Berger, S.L., 2017. The neuropeptide corazonin controls social behavior and caste identity in ants. Cell 170, 748-759.

Goulson, D., 2010. Bumblebees: Behaviour, Ecology, and Conservation. Oxford University Press, Demand..

Grover, C.D., Kay, A.D., Monson, J.A., Marsh, T.C., Holway, D.A., 2007. Linking nutrition and behavioural dominance: carbohydrate scarcity limits aggression and activity in argentine ants. Proc. R. Soc. 274, 2951-2957.

Harrison, M.C., Hammond, R.L., Mallon, E.B., 2015. Reproductive workers show queenlike gene expression in an intermediately eusocial insect, the buff-tailed bumble bee Bombus terrestris. Mol. Ecol. 24, 3043-3063.

Herb, B.R., Wolschin, F., Hansen, K.D., Aryee, M.J., Langmead, B., Irizarry, R., Amdam, G.V., Feinberg, A.P., 2012. Reversible switching between epigenetic states in honeybee behavioral subcastes. Nat. Neurosci. 15, 1371-1373.

Hou, J., Wang, X., McShane, E., Zauber, H., Sun, W., Selbach, M., Chen, W., 2015. Extensive allele-specific translational regulation in hybrid mice. Mol. Syst. Biol. 11, 825.

Jones, T.M., Durrant, J., Michaelides, E.B., Green, M.P., 2015. Melatonin: a possible link between the presence of artificial light at night and reductions in biological fitness. Philos. Trans. R. Soc., B 370, 20140122.

Krueger, F., Andrews, S.R., 2011. Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics 27, 1571-1572.

Kucharski, R., Maleszka, J., Foret, S., Maleszka, R., 2008. Nutritional control of reproductive status in honeybees via DNA methylation. Science 319, 1827.

Lee, G., Bahn, J.H., Park, J.H., 2006. Sex-and clock-controlled expression of the neuropeptide F gene in Drosophila. Proc. Natl. Acad. Sci. U. S. A. 103, 12580.

Li-Byarlay, H., Boncristiani, H., Howell, G., Herman, J., Clark, L., Strand, M.K., Tarpy, D., Rueppell, O., Transcriptomic and epigenomic dynamics of honey bees in response to lethal viral infection. Front. Genet. 11, 566320.

Li, B., Hou, L., Zhu, D., Xu, X., An, S., Wang, X., 2018. Identification and caste-dependent expression patterns of DNA methylation associated genes in Bombus terrestris. Sci. Rep. 8, 2332.

Libbrecht, R., Oxley, P.R., Keller, L., Kronauer, D.J.C., 2016. Robust DNA methylation in the clonal raider ant brain. Curr. Biol. 26, 391-395.

Lyko, F., Foret, S., Kucharski, R., Wolf, S., Falckenhayn, C., Maleszka, R., The honey bee epigenomes: differential methylation of brain DNA in queens and workers. PLoS Biol. e1000506.

Marshall, H., Lonsdale, Z.N., Mallon, E.B., 2019. Methylation and gene expression differences between reproductive and sterile bumblebee workers. Evol. Lett. 3, 485-499.

Michener, C.D., Michener, C.D., 1974. The Social Behavior of the Bees: A Comparative Study. Harvard University Press, Massachusetts..

Niu, J., Cappelle, K., de Miranda, J.R., Smagghe, G., Meeus, I., 2014. Analysis of reference gene stability after israeli acute paralysis virus infection in bumblebees Bombus terrestris. J. Invertebr. Pathol. 115, 76-79.

Nowak, M.A., Tarnita, C.E., Wilson, E.O., 2010. The evolution of eusociality. Nature 466, 1057-1062.

Opachaloemphan, C., Yan, H., Leibholz, A., Desplan, C., Reinberg, D., 2018. Recent advances in behavioral (epi)genetics in eusocial insects. Annu. Rev. Genet. 52, 489-510.

Park, Y., Wu, H., 2016. Differential methylation analysis for BS-seq data under general experimental design. Bioinformatics 32, 1446-1453.

Patalano, S., Vlasova, A., Wyatt, C., Ewels, P., Camara, F., Ferreira, P.G., Asher, C.L., Jurkowski, T.P., Segonds-Pichon, A., Bachman, M., 2015. Molecular signatures of plastic phenotypes in two eusocial insect species with simple societies. Proc. Natl. Acad. Sci. U. S. A. 112, 13970.

Patel, R.T., Soulages, J.L., Hariharasundaram, B., Arrese, E.L., 2005. Activation of the lipid droplet controls the rate of lipolysis of triglycerides in the insect fat body. J. Biol. Chem. 280, 22624-22631.

Porath, H.T., Hazan, E., Shpigler, H., Cohen, M., Band, M., Ben-Shahar, Y., Levanon, E.Y., Eisenberg, E., Bloch, G., 2019. RNA editing is abundant and correlates with task performance in a social bumblebee. Nat. Commun. 10, 1605.

Price, J., Harrison, M.C., Hammond, R.L., Adams, S., Gutierrez-Marcos, J.F., Mallon, E.B., 2018. Alternative splicing associated with phenotypic plasticity in the bumble bee Bombus terrestris. Mol. Ecol. 27, 1036-1043.

Qiu, B., Larsen, R.S., Chang, N.C., Wang, J., Boomsma, J.J., Zhang, G., 2018. Towards reconstructing the ancestral brain gene-network regulating caste differentiation in ants. Nat. Ecol. Evol. 2, 1782-1791.

Ristic, G., Tsou, W.L., Todi, S.V., An optimal ubiquitin-proteasome pathway in the nervous system: the role of deubiquitinating enzymes. Front. Mol. Neurosci. 7, 72..

Rittschof, C.C., Robinson, G.E., 2013. Manipulation of colony environment modulates honey bee aggression and brain gene expression. Gene Brain Behav. 12, 802-811.

Rittschof, C.C., Schirmeier, S., 2018. Insect models of central nervous system energy metabolism and its links to behavior. Glia 66, 1160-1175.

Röseler, P.F., Röseler, I., 1988. Influence of juvenile hormone on fat body metabolism in ovariolectomized queens of the bumblebee, Bombus terrestris. Insect Biochem. 18, 557-563.

Röseler, P.F., Van Honk, C.G., 1990. Castes and Reproduction in Bumblebees, Social Insects. Springer, Berlin.

Salmela, L., Rivals, E., 2014. LoRDEC: accurate and efficient long read error correction. Bioinformatics 30, 3506-3514.

Santos, C.G., Humann, F.C., Hartfelder, K., 2019. Juvenile hormone signaling in insect oogenesis. Curr. Opin. Insect Sci. 31, 43-48.

Shpigler, H.Y., Herb, B., Drnevich, J., Band, M., Robinson, G.E., Bloch, G., 2020. Juvenile hormone regulates brain-reproduction tradeoff in bumble bees but not in honey bees. Horm. Behav. 126, 104844.

Simola, D.F., Graham, R.J., Brady, C.M., Enzmann, B.L., Desplan, C., Ray, A., Zwiebel, L.J., Bonasio, R., Reinberg, D., Liebig, J., Berger, S.L., 2016. Epigenetic (re) programming of caste-specific behavior in the ant Camponotus floridanus. Science 351, aac6633.

Standage, D.S., Berens, A.J., Glastad, K.M., Severin, A.J., Brendel, V.P., Toth, A.L., 2016. Genome, transcriptome and methylome sequencing of a primitively eusocial wasp reveal a greatly reduced DNA methylation system in a social insect. Mol. Ecol. 25, 1769-1784.

Su, Z., Xia, J., Zhao, Z., 2011. Functional complementation between transcriptional methylation regulation and post-transcriptional microrna regulation in the human genome. BMC Genom. 12, S15.

Tedjakumala, S.R., Rouquette, J., Boizeau, M.L., Mesce, K.A., Hotier, L., Massou, I., Giurfa, M., A tyrosine-hydroxylase characterization of dopaminergic neurons in the honey bee brain. Front. Syst. Neurosci. 11, 47.

Terrapon, N., Li, C., Robertson, H.M., Ji, L., Meng, X., Booth, W., Chen, Z., Childers, C.P., Glastad, K.M., Gokhale, K., 2014. Molecular traces of alternative social organization in a termite genome. Nat. Commun. 5, 3636.

Toth, A.L., Tooker, J.F., Radhakrishnan, S., Minard, R., Henshaw, M.T., Grozinger, C.M., 2014. Shared genes related to aggression, rather than chemical communication, are associated with reproductive dominance in paper wasps (Polistes metricus). BMC Genom. 15, 75.

Trincado, J.L., Entizne, J.C., Hysenaj, G., Singh, B., Skalic, M., Elliott, D.J., Eyras, E., 2018. Suppa2: fast, accurate, and uncertainty-aware differential splicing analysis across multiple conditions. Genome Biol. 19, 40.

Tupec, M., Buček, A., Janoušek, V., Vogel, H., Prchalová, D., Kindl, J., Pavlíčková, T., Wenzelová, P., Jahn, U., Valterová, I., Expansion of the fatty acyl reductase gene family shaped pheromone communication in Hymenoptera. eLife e39231.

Via, S., Gomulkiewicz, R., De Jong, G., Scheiner, S.M., Schlichting, C.D., Van Tienderen, P.H., 1995. Adaptive phenotypic plasticity: consensus and controversy. Trends Ecol. Evol. 10, 212-217.

Vleurinck, C., Raub, S., Sturgill, D., Oliver, B., Beye, M., Linking genes and brain development of honeybee workers: a whole-transcriptome approach. PLoS One e0157980.

Wang, J., Rieder, S.A., Wu, J., Hayes, S., Halpin, R.A., de los Reyes, M., Shrestha, Y., Kolbeck, R., Raja, R., 2019. Evaluation of ultra-low input RNA sequencing for the study of human T cell transcriptome. Sci. Rep. 9, 8445.

Wilson, E.O., 2010. The evolution of eusociality. Nature 466, 1057-1062.

Woodard, S.H., Fischman, B.J., Venkat, A., Hudson, M.E., Varala, K., Cameron, S.A., Clark, A.G., Robinson, G.E., 2011. Genes involved in convergent evolution of eusociality in bees. Proc. Natl. Acad. Sci. U. S. A 108, 7472.

Wu, H., Xu, T., Feng, H., Chen, L., Li, B., Yao, B., Qin, Z., Jin, P., Conneely, K.N., Detection of differentially methylated regions from whole-genome bisulfite sequencing data without replicates. Nucleic Acids Res. 43 e141-e141.

Yerushalmi, S., Bodenhaimer, S., Bloch, G., 2006. Developmentally determined attenuation in circadian rhythms links chronobiology to social organization in bees. J. Exp. Biol. 209, 1044.

Yi, Y., Liu, Y., Barron, A.B., Zeng, Z., 2020. Transcriptomic, morphological, and developmental comparison of adult honey bee queens (Apis mellifera) reared from eggs or worker larvae of differing ages. J. Econ. Entomol. 113, 2581-2587.

Yu, G., Wang, L., Han, Y., He, Q., 2012. Cluster profiler: an R package for comparing biological themes among gene clusters. OMICS 16, 284-287.

Relative Articles

Supplements(0)

Cited By

Proportional views