{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,2]],"date-time":"2026-05-02T11:31:58Z","timestamp":1777721518266,"version":"3.51.4"},"reference-count":73,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2025,10,13]],"date-time":"2025-10-13T00:00:00Z","timestamp":1760313600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"},{"start":{"date-parts":[[2025,10,13]],"date-time":"2025-10-13T00:00:00Z","timestamp":1760313600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"}],"funder":[{"name":"Portuguese Science Funding Agency","award":["grant PTDC\/BIA-EVL\/0321\/2021"],"award-info":[{"award-number":["grant PTDC\/BIA-EVL\/0321\/2021"]}]},{"name":"Brighton Integrative Genomics"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Sci Rep"],"DOI":"10.1038\/s41598-025-18794-1","type":"journal-article","created":{"date-parts":[[2025,10,13]],"date-time":"2025-10-13T13:18:29Z","timestamp":1760361509000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Whole organism integrated DNA methylation and transcriptomics analysis of butterfly metamorphosis"],"prefix":"10.1038","volume":"15","author":[{"given":"Andrew","family":"Hesketh","sequence":"first","affiliation":[]},{"given":"Juned","family":"Kadiwala","sequence":"additional","affiliation":[]},{"given":"Ana Rita","family":"Garizo","sequence":"additional","affiliation":[]},{"given":"Patr\u00edcia","family":"Beldade","sequence":"additional","affiliation":[]},{"given":"Rameen","family":"Shakur","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2025,10,13]]},"reference":[{"key":"18794_CR1","doi-asserted-by":"publisher","first-page":"20190063","DOI":"10.1098\/rstb.2019.0063","volume":"374","author":"J Rolff","year":"2019","unstructured":"Rolff, J., Johnston, P. R. & Reynolds, S. Complete metamorphosis of insects. Philos. Trans. R Soc. Lond B Biol. Sci. 374, 20190063. https:\/\/doi.org\/10.1098\/rstb.2019.0063 (2019).","journal-title":"Philos. Trans. R Soc. Lond B Biol. Sci."},{"key":"18794_CR2","doi-asserted-by":"publisher","first-page":"R1252","DOI":"10.1016\/j.cub.2019.10.009","volume":"29","author":"JW Truman","year":"2019","unstructured":"Truman, J. W. The evolution of insect metamorphosis. Curr. Biol. 29, R1252\u2013R1268. https:\/\/doi.org\/10.1016\/j.cub.2019.10.009 (2019).","journal-title":"Curr. Biol."},{"key":"18794_CR3","doi-asserted-by":"publisher","first-page":"2270","DOI":"10.1126\/science.1072152","volume":"297","author":"MN Arbeitman","year":"2002","unstructured":"Arbeitman, M. N. et al. Gene expression during the life cycle of Drosophila melanogaster. Science 297, 2270\u20132275. https:\/\/doi.org\/10.1126\/science.1072152 (2002).","journal-title":"Science"},{"key":"18794_CR4","doi-asserted-by":"publisher","first-page":"1787","DOI":"10.1126\/science.1198374","volume":"330","author":"EC Mod","year":"2010","unstructured":"Mod, E. C. et al. Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science 330, 1787\u20131797. https:\/\/doi.org\/10.1126\/science.1198374 (2010).","journal-title":"Science"},{"key":"18794_CR5","doi-asserted-by":"publisher","first-page":"473","DOI":"10.1038\/nature09715","volume":"471","author":"BR Graveley","year":"2011","unstructured":"Graveley, B. R. et al. The developmental transcriptome of Drosophila melanogaster. Nature 471, 473\u2013479. https:\/\/doi.org\/10.1038\/nature09715 (2011).","journal-title":"Nature"},{"key":"18794_CR6","doi-asserted-by":"publisher","first-page":"393","DOI":"10.1038\/nature12962","volume":"512","author":"JB Brown","year":"2014","unstructured":"Brown, J. B. et al. Diversity and dynamics of the Drosophila transcriptome. Nature 512, 393\u2013399. https:\/\/doi.org\/10.1038\/nature12962 (2014).","journal-title":"Nature"},{"key":"18794_CR7","doi-asserted-by":"publisher","first-page":"3513","DOI":"10.1111\/mec.16957","volume":"32","author":"J Boman","year":"2023","unstructured":"Boman, J. et al. Environmental stress during larval development induces DNA methylation shifts in the migratory painted lady butterfly (Vanessa cardui). Mol. Ecol. 32, 3513\u20133523. https:\/\/doi.org\/10.1111\/mec.16957 (2023).","journal-title":"Mol. Ecol."},{"key":"18794_CR8","doi-asserted-by":"publisher","first-page":"646281","DOI":"10.3389\/fevo.2021.646281","volume":"9","author":"J Gegner","year":"2021","unstructured":"Gegner, J., Vogel, H., Billion, A., F\u00f6rster, F. & Vilcinskas, A. Complete metamorphosis in manduca sexta involves specific changes in DNA methylation patterns. Front. Ecol. Evol. 9, 646281. https:\/\/doi.org\/10.3389\/fevo.2021.646281 (2021).","journal-title":"Front. Ecol. Evol."},{"key":"18794_CR9","doi-asserted-by":"publisher","first-page":"126","DOI":"10.1093\/molbev\/msac126","volume":"39","author":"S Tian","year":"2022","unstructured":"Tian, S. & Monteiro, A. A transcriptomic atlas underlying developmental plasticity of seasonal forms of Bicyclus anynana butterflies. Mol. Biol. Evol. 39, 126. https:\/\/doi.org\/10.1093\/molbev\/msac126 (2022).","journal-title":"Mol. Biol. Evol."},{"key":"18794_CR10","doi-asserted-by":"publisher","first-page":"1269","DOI":"10.1111\/mec.16304","volume":"31","author":"P Pruisscher","year":"2022","unstructured":"Pruisscher, P., Lehmann, P., Nylin, S., Gotthard, K. & Wheat, C. W. Extensive transcriptomic profiling of pupal diapause in a butterfly reveals a dynamic phenotype. Mol. Ecol. 31, 1269\u20131280. https:\/\/doi.org\/10.1111\/mec.16304 (2022).","journal-title":"Mol. Ecol."},{"key":"18794_CR11","doi-asserted-by":"publisher","first-page":"pdb emo122","DOI":"10.1101\/pdb.emo122","volume":"2009","author":"PM Brakefield","year":"2009","unstructured":"Brakefield, P. M., Beldade, P. & Zwaan, B. J. The African butterfly Bicyclus anynana: a model for evolutionary genetics and evolutionary developmental biology. Cold Spring Harb Protoc. 2009, pdb emo122. https:\/\/doi.org\/10.1101\/pdb.emo122 (2009).","journal-title":"Cold Spring Harb Protoc."},{"key":"18794_CR12","doi-asserted-by":"publisher","first-page":"D672","DOI":"10.1093\/nar\/gkae909","volume":"53","author":"M Kanehisa","year":"2025","unstructured":"Kanehisa, M., Furumichi, M., Sato, Y., Matsuura, Y. & Ishiguro-Watanabe, M. KEGG: biological systems database as a model of the real world. Nucleic Acids Re.s 53, D672\u2013D677. https:\/\/doi.org\/10.1093\/nar\/gkae909 (2025).","journal-title":"Nucleic Acids Re.s"},{"key":"18794_CR13","doi-asserted-by":"publisher","first-page":"5825","DOI":"10.1093\/molbev\/msab293","volume":"38","author":"CP Cantalapiedra","year":"2021","unstructured":"Cantalapiedra, C. P., Hernandez-Plaza, A., Letunic, I., Bork, P. & Huerta-Cepas, J. eggNOG-mapper v2: functional annotation, orthology assignments, and domain prediction at the metagenomic scale. Mol. Biol. Evol. 38, 5825\u20135829. https:\/\/doi.org\/10.1093\/molbev\/msab293 (2021).","journal-title":"Mol. Biol. Evol."},{"key":"18794_CR14","doi-asserted-by":"publisher","first-page":"964","DOI":"10.1161\/HYPERTENSIONAHA.123.21364","volume":"81","author":"M Bader","year":"2024","unstructured":"Bader, M., Steckelings, U. M., Alenina, N., Santos, R. A. S. & Ferrario, C. M. Alternative renin-angiotensin system. Hypertension 81, 964\u2013976. https:\/\/doi.org\/10.1161\/HYPERTENSIONAHA.123.21364 (2024).","journal-title":"Hypertension"},{"key":"18794_CR15","doi-asserted-by":"publisher","first-page":"353","DOI":"10.1016\/s0896-6273(00)80166-x","volume":"17","author":"T Araki","year":"1996","unstructured":"Araki, T. & Milbrandt, J. Ninjurin, a novel adhesion molecule, is induced by nerve injury and promotes axonal growth. Neuron 17, 353\u2013361. https:\/\/doi.org\/10.1016\/s0896-6273(00)80166-x (1996).","journal-title":"Neuron"},{"key":"18794_CR16","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0216987","volume":"14","author":"M Kny","year":"2019","unstructured":"Kny, M. et al. Ninjurin1 regulates striated muscle growth and differentiation. PLoS ONE 14, e0216987. https:\/\/doi.org\/10.1371\/journal.pone.0216987 (2019).","journal-title":"PLoS ONE"},{"key":"18794_CR17","doi-asserted-by":"publisher","first-page":"159","DOI":"10.1159\/000512222","volume":"42","author":"K Liu","year":"2020","unstructured":"Liu, K., Wang, Y. & Li, H. The role of Ninjurin1 and its impact beyond the nervous system. Dev. Neurosci. 42, 159\u2013169. https:\/\/doi.org\/10.1159\/000512222 (2020).","journal-title":"Dev. Neurosci."},{"key":"18794_CR18","doi-asserted-by":"publisher","first-page":"462","DOI":"10.1016\/j.bbrc.2019.09.007","volume":"519","author":"Y Tomita","year":"2019","unstructured":"Tomita, Y. et al. Ninjurin 1 mediates peripheral nerve regeneration through Schwann cell maturation of NG2-positive cells. Biochem. Biophys. Res. Commun. 519, 462\u2013468. https:\/\/doi.org\/10.1016\/j.bbrc.2019.09.007 (2019).","journal-title":"Biochem. Biophys. Res. Commun."},{"key":"18794_CR19","doi-asserted-by":"publisher","first-page":"1899","DOI":"10.1101\/gad.1426906","volume":"20","author":"S Zhang","year":"2006","unstructured":"Zhang, S. et al. An MMP liberates the Ninjurin A ectodomain to signal a loss of cell adhesion. Genes Dev. 20, 1899\u20131910. https:\/\/doi.org\/10.1101\/gad.1426906 (2006).","journal-title":"Genes Dev."},{"key":"18794_CR20","doi-asserted-by":"publisher","first-page":"6357","DOI":"10.1038\/s41467-024-50725-y","volume":"15","author":"JR Occean","year":"2024","unstructured":"Occean, J. R. et al. Gene body DNA hydroxymethylation restricts the magnitude of transcriptional changes during aging. Nat. Commun. 15, 6357. https:\/\/doi.org\/10.1038\/s41467-024-50725-y (2024).","journal-title":"Nat. Commun."},{"key":"18794_CR21","doi-asserted-by":"publisher","first-page":"4249","DOI":"10.1038\/s41467-021-24425-w","volume":"12","author":"B He","year":"2021","unstructured":"He, B. et al. Tissue-specific 5-hydroxymethylcytosine landscape of the human genome. Nat. Commun. 12, 4249. https:\/\/doi.org\/10.1038\/s41467-021-24425-w (2021).","journal-title":"Nat. Commun."},{"key":"18794_CR22","doi-asserted-by":"publisher","first-page":"20190071","DOI":"10.1098\/rstb.2019.0071","volume":"374","author":"MJR Hall","year":"2019","unstructured":"Hall, M. J. R. & Martin-Vega, D. Visualization of insect metamorphosis. Philos. Trans. R Soc. Lond B Biol. Sci. 374, 20190071. https:\/\/doi.org\/10.1098\/rstb.2019.0071 (2019).","journal-title":"Philos. Trans. R Soc. Lond B Biol. Sci."},{"key":"18794_CR23","doi-asserted-by":"publisher","first-page":"315","DOI":"10.1146\/annurev-ento-011118-112007","volume":"64","author":"S Li","year":"2019","unstructured":"Li, S., Yu, X. & Feng, Q. Fat body biology in the last decade. Annu. Rev. Entomol. 64, 315\u2013333. https:\/\/doi.org\/10.1146\/annurev-ento-011118-112007 (2019).","journal-title":"Annu. Rev. Entomol."},{"key":"18794_CR24","doi-asserted-by":"publisher","first-page":"20190070","DOI":"10.1098\/rstb.2019.0070","volume":"374","author":"JW Truman","year":"2019","unstructured":"Truman, J. W. & Riddiford, L. M. The evolution of insect metamorphosis: a developmental and endocrine view. Philos. Trans. R Soc. Lond B Biol. Sci. 374, 20190070. https:\/\/doi.org\/10.1098\/rstb.2019.0070 (2019).","journal-title":"Philos. Trans. R Soc. Lond B Biol. Sci."},{"key":"18794_CR25","doi-asserted-by":"publisher","first-page":"4302","DOI":"10.1111\/bph.14431","volume":"176","author":"BY Nguyen","year":"2019","unstructured":"Nguyen, B. Y. et al. Mitochondrial function in the heart: the insight into mechanisms and therapeutic potentials. Br. J. Pharmacol. 176, 4302\u20134318. https:\/\/doi.org\/10.1111\/bph.14431 (2019).","journal-title":"Br. J. Pharmacol."},{"key":"18794_CR26","doi-asserted-by":"publisher","first-page":"293","DOI":"10.1242\/jeb.115.1.293","volume":"115","author":"CP Ellington","year":"1985","unstructured":"Ellington, C. P. Power and efficiency of insect flight muscle. J. Exp. Biol. 115, 293\u2013304. https:\/\/doi.org\/10.1242\/jeb.115.1.293 (1985).","journal-title":"J. Exp. Biol."},{"key":"18794_CR27","doi-asserted-by":"publisher","first-page":"241","DOI":"10.1006\/dbio.2002.0812","volume":"251","author":"H Amthor","year":"2002","unstructured":"Amthor, H. et al. The regulation and action of myostatin as a negative regulator of muscle development during avian embryogenesis. Dev. Biol. 251, 241\u2013257. https:\/\/doi.org\/10.1006\/dbio.2002.0812 (2002).","journal-title":"Dev. Biol."},{"key":"18794_CR28","first-page":"56","volume":"10","author":"MN Elkasrawy","year":"2010","unstructured":"Elkasrawy, M. N. & Hamrick, M. W. Myostatin (GDF-8) as a key factor linking muscle mass and bone structure. J. Musculoskelet. Neuronal Interact. 10, 56\u201363 (2010).","journal-title":"J. Musculoskelet. Neuronal Interact."},{"key":"18794_CR29","doi-asserted-by":"publisher","unstructured":"Tarantino, U. et al. Effects of Simulated Microgravity on Muscle Stem Cells Activity. Cell Physiol Biochem 54, 736\u2013747 (2020). https:\/\/doi.org\/10.33594\/000000252","DOI":"10.33594\/000000252"},{"issue":"Suppl 1","key":"18794_CR30","doi-asserted-by":"publisher","first-page":"S51","DOI":"10.1007\/s40520-015-0427-z","volume":"27","author":"U Tarantino","year":"2015","unstructured":"Tarantino, U. et al. Sarcopenia: a histological and immunohistochemical study on age-related muscle impairment. Aging Clin. Exp. Res. 27(Suppl 1), S51-60. https:\/\/doi.org\/10.1007\/s40520-015-0427-z (2015).","journal-title":"Aging Clin. Exp. Res."},{"key":"18794_CR31","doi-asserted-by":"publisher","first-page":"1287972","DOI":"10.3389\/fendo.2023.1287972","volume":"14","author":"Z Zhao","year":"2023","unstructured":"Zhao, Z., Yan, K., Guan, Q., Guo, Q. & Zhao, C. Mechanism and physical activities in bone-skeletal muscle crosstalk. Front Endocrinol (Lausanne) 14, 1287972. https:\/\/doi.org\/10.3389\/fendo.2023.1287972 (2023).","journal-title":"Front Endocrinol (Lausanne)"},{"key":"18794_CR32","doi-asserted-by":"publisher","first-page":"488","DOI":"10.1016\/j.cub.2014.12.029","volume":"25","author":"C Schaub","year":"2015","unstructured":"Schaub, C., Marz, J., Reim, I. & Frasch, M. Org-1-dependent lineage reprogramming generates the ventral longitudinal musculature of the Drosophila heart. Curr. Biol. 25, 488\u2013494. https:\/\/doi.org\/10.1016\/j.cub.2014.12.029 (2015).","journal-title":"Curr. Biol."},{"key":"18794_CR33","doi-asserted-by":"publisher","first-page":"51","DOI":"10.1016\/s0925-4773(01)00509-3","volume":"109","author":"MR Molina","year":"2001","unstructured":"Molina, M. R. & Cripps, R. M. Ostia, the inflow tracts of the Drosophila heart, develop from a genetically distinct subset of cardial cells. Mech. Dev. 109, 51\u201359. https:\/\/doi.org\/10.1016\/s0925-4773(01)00509-3 (2001).","journal-title":"Mech. Dev."},{"key":"18794_CR34","doi-asserted-by":"publisher","first-page":"494","DOI":"10.3390\/jcdd10120494","volume":"10","author":"C Bileckyj","year":"2023","unstructured":"Bileckyj, C., Blotz, B. & Cripps, R. M. Drosophila as a model to understand second heart field development. J. Cardiovasc. Dev. Dis. 10, 494. https:\/\/doi.org\/10.3390\/jcdd10120494 (2023).","journal-title":"J. Cardiovasc. Dev. Dis."},{"key":"18794_CR35","doi-asserted-by":"publisher","first-page":"e85752","DOI":"10.7554\/eLife.85752","volume":"12","author":"S Rey","year":"2023","unstructured":"Rey, S. et al. Glial-dependent clustering of voltage-gated ion channels in Drosophila precedes myelin formation. Elife 12, e85752. https:\/\/doi.org\/10.7554\/eLife.85752 (2023).","journal-title":"Elife"},{"key":"18794_CR36","doi-asserted-by":"publisher","first-page":"207","DOI":"10.1146\/annurev-ento-112408-085356","volume":"55","author":"EL Arrese","year":"2010","unstructured":"Arrese, E. L. & Soulages, J. L. Insect fat body: energy, metabolism, and regulation. Annu. Rev. Entomol. 55, 207\u2013225. https:\/\/doi.org\/10.1146\/annurev-ento-112408-085356 (2010).","journal-title":"Annu. Rev. Entomol."},{"key":"18794_CR37","doi-asserted-by":"publisher","first-page":"9064","DOI":"10.3390\/ijms23169064","volume":"23","author":"Y Song","year":"2022","unstructured":"Song, Y. et al. The key role of fatty acid synthase in lipid metabolism and metamorphic development in a destructive insect pest, spodoptera litura (Lepidoptera: Noctuidae). Int. J. Mol. Sci. 23, 9064. https:\/\/doi.org\/10.3390\/ijms23169064 (2022).","journal-title":"Int. J. Mol. Sci."},{"key":"18794_CR38","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0044567","volume":"7","author":"S Broderick","year":"2012","unstructured":"Broderick, S., Wang, X., Simms, N. & Page-McCaw, A. Drosophila Ninjurin A induces nonapoptotic cell death. PLoS ONE 7, e44567. https:\/\/doi.org\/10.1371\/journal.pone.0044567 (2012).","journal-title":"PLoS ONE"},{"key":"18794_CR39","doi-asserted-by":"publisher","first-page":"11140","DOI":"10.1016\/S0021-9258(17)39158-5","volume":"260","author":"TA Cooper","year":"1985","unstructured":"Cooper, T. A. & Ordahl, C. P. A single cardiac troponin T gene generates embryonic and adult isoforms via developmentally regulated alternate splicing. J. Biol. Chem. 260, 11140\u201311148 (1985).","journal-title":"J. Biol. Chem."},{"key":"18794_CR40","doi-asserted-by":"publisher","first-page":"165","DOI":"10.3389\/fphys.2014.00165","volume":"5","author":"JJ Sheng","year":"2014","unstructured":"Sheng, J. J. & Jin, J. P. Gene regulation, alternative splicing, and posttranslational modification of troponin subunits in cardiac development and adaptation: a focused review. Front. Physiol. 5, 165. https:\/\/doi.org\/10.3389\/fphys.2014.00165 (2014).","journal-title":"Front. Physiol."},{"key":"18794_CR41","doi-asserted-by":"publisher","first-page":"67","DOI":"10.3390\/ijms21010067","volume":"21","author":"N Fili","year":"2019","unstructured":"Fili, N. & Toseland, C. P. Unconventional myosins: how regulation meets function. Int. J. Mol. Sci. 21, 67. https:\/\/doi.org\/10.3390\/ijms21010067 (2019).","journal-title":"Int. J. Mol. Sci."},{"key":"18794_CR42","doi-asserted-by":"publisher","first-page":"408","DOI":"10.3389\/fonc.2018.00408","volume":"8","author":"G Biamonti","year":"2018","unstructured":"Biamonti, G., Maita, L. & Montecucco, A. The krebs cycle connection: reciprocal influence between alternative splicing programs and cell metabolism. Front. Oncol. 8, 408. https:\/\/doi.org\/10.3389\/fonc.2018.00408 (2018).","journal-title":"Front. Oncol."},{"key":"18794_CR43","doi-asserted-by":"publisher","first-page":"16","DOI":"10.3390\/cancers16010016","volume":"16","author":"M Campos","year":"2023","unstructured":"Campos, M. & Albrecht, L. V. Hitting the sweet spot: how glucose metabolism is orchestrated in space and time by phosphofructokinase-1. Cancers (Basel) 16, 16. https:\/\/doi.org\/10.3390\/cancers16010016 (2023).","journal-title":"Cancers (Basel)"},{"key":"18794_CR44","doi-asserted-by":"publisher","first-page":"evaf100","DOI":"10.1093\/gbe\/evaf100","volume":"17","author":"AM Ozerova","year":"2025","unstructured":"Ozerova, A. M., Kulikova, D. A., Evgen\u2019ev, M. B. & Gelfand, M. S. Temporal dynamics of gene expression during metamorphosis in two distant drosophila species. Genome Biol. Evol. 17, evaf100. https:\/\/doi.org\/10.1093\/gbe\/evaf100 (2025).","journal-title":"Genome Biol. Evol."},{"key":"18794_CR45","doi-asserted-by":"publisher","first-page":"274","DOI":"10.1016\/j.tig.2015.03.002","volume":"31","author":"G Lev Maor","year":"2015","unstructured":"Lev Maor, G., Yearim, A. & Ast, G. The alternative role of DNA methylation in splicing regulation. Trends Genet. 31, 274\u2013280. https:\/\/doi.org\/10.1016\/j.tig.2015.03.002 (2015).","journal-title":"Trends Genet."},{"key":"18794_CR46","doi-asserted-by":"publisher","first-page":"754","DOI":"10.1093\/bib\/bbx019","volume":"19","author":"S Li","year":"2018","unstructured":"Li, S., Zhang, J., Huang, S. & He, X. Genome-wide analysis reveals that exon methylation facilitates its selective usage in the human transcriptome. Brief. Bioinform. 19, 754\u2013764. https:\/\/doi.org\/10.1093\/bib\/bbx019 (2018).","journal-title":"Brief. Bioinform."},{"key":"18794_CR47","doi-asserted-by":"publisher","first-page":"321","DOI":"10.1038\/nature14192","volume":"517","author":"D Schubeler","year":"2015","unstructured":"Schubeler, D. Function and information content of DNA methylation. Nature 517, 321\u2013326. https:\/\/doi.org\/10.1038\/nature14192 (2015).","journal-title":"Nature"},{"key":"18794_CR48","doi-asserted-by":"publisher","first-page":"62","DOI":"10.1186\/s13072-019-0307-4","volume":"12","author":"KD Harris","year":"2019","unstructured":"Harris, K. D., Lloyd, J. P. B., Domb, K., Zilberman, D. & Zemach, A. DNA methylation is maintained with high fidelity in the honey bee germline and exhibits global non-functional fluctuations during somatic development. Epigenetics Chromatin 12, 62. https:\/\/doi.org\/10.1186\/s13072-019-0307-4 (2019).","journal-title":"Epigenetics Chromatin"},{"key":"18794_CR49","doi-asserted-by":"publisher","first-page":"516","DOI":"10.1038\/nbt.1626","volume":"28","author":"H Xiang","year":"2010","unstructured":"Xiang, H. et al. Single base-resolution methylome of the silkworm reveals a sparse epigenomic map. Nat. Biotechnol. 28, 516\u2013520. https:\/\/doi.org\/10.1038\/nbt.1626 (2010).","journal-title":"Nat. Biotechnol."},{"key":"18794_CR50","doi-asserted-by":"publisher","first-page":"691","DOI":"10.1007\/s00427-008-0247-7","volume":"218","author":"R Albalat","year":"2008","unstructured":"Albalat, R. Evolution of DNA-methylation machinery: DNA methyltransferases and methyl-DNA binding proteins in the amphioxus Branchiostoma floridae. Dev. Genes. Evol. 218, 691\u2013701. https:\/\/doi.org\/10.1007\/s00427-008-0247-7 (2008).","journal-title":"Dev. Genes. Evol."},{"key":"18794_CR51","doi-asserted-by":"publisher","first-page":"534","DOI":"10.1111\/imb.12936","volume":"33","author":"K Yoon","year":"2024","unstructured":"Yoon, K., Williams, S. & Duncan, E. J. DNA methylation machinery is involved in development and reproduction in the viviparous pea aphid (Acyrthosiphon pisum). Insect Mol. Biol. 33, 534\u2013549. https:\/\/doi.org\/10.1111\/imb.12936 (2024).","journal-title":"Insect Mol. Biol."},{"key":"18794_CR52","doi-asserted-by":"publisher","first-page":"1185","DOI":"10.1093\/gbe\/evy066","volume":"10","author":"P Provataris","year":"2018","unstructured":"Provataris, P., Meusemann, K., Niehuis, O., Grath, S. & Misof, B. Signatures of DNA Methylation across Insects suggest reduced DNA methylation levels in holometabola. Genome Biol. Evol. 10, 1185\u20131197. https:\/\/doi.org\/10.1093\/gbe\/evy066 (2018).","journal-title":"Genome Biol. Evol."},{"key":"18794_CR53","doi-asserted-by":"publisher","first-page":"591","DOI":"10.1093\/gbe\/evt030","volume":"5","author":"BG Hunt","year":"2013","unstructured":"Hunt, B. G., Glastad, K. M., Yi, S. V. & Goodisman, M. A. Patterning and regulatory associations of DNA methylation are mirrored by histone modifications in insects. Genome Biol. Evol. 5, 591\u2013598. https:\/\/doi.org\/10.1093\/gbe\/evt030 (2013).","journal-title":"Genome Biol. Evol."},{"key":"18794_CR54","doi-asserted-by":"publisher","first-page":"319","DOI":"10.1093\/icb\/ict003","volume":"53","author":"BG Hunt","year":"2013","unstructured":"Hunt, B. G., Glastad, K. M., Yi, S. V. & Goodisman, M. A. The function of intragenic DNA methylation: insights from insect epigenomes. Integr. Comp. Biol. 53, 319\u2013328. https:\/\/doi.org\/10.1093\/icb\/ict003 (2013).","journal-title":"Integr. Comp. Biol."},{"key":"18794_CR55","doi-asserted-by":"publisher","first-page":"102040","DOI":"10.1016\/j.isci.2021.102040","volume":"24","author":"G Xu","year":"2021","unstructured":"Xu, G. et al. Intragenic DNA methylation regulates insect gene expression and reproduction through the MBD\/Tip60 complex. iScience 24, 102040. https:\/\/doi.org\/10.1016\/j.isci.2021.102040 (2021).","journal-title":"iScience"},{"key":"18794_CR56","doi-asserted-by":"publisher","first-page":"779","DOI":"10.1534\/g3.117.1112","volume":"8","author":"CM Jones","year":"2018","unstructured":"Jones, C. M., Lim, K. S., Chapman, J. W. & Bass, C. Genome-wide characterization of DNA methylation in an invasive lepidopteran pest, the cotton bollworm helicoverpa armigera. G3 (Bethesda) 8, 779\u2013787. https:\/\/doi.org\/10.1534\/g3.117.1112 (2018).","journal-title":"G3 (Bethesda)"},{"key":"18794_CR57","doi-asserted-by":"publisher","first-page":"154","DOI":"10.1186\/s13148-022-01382-9","volume":"14","author":"Q Wang","year":"2022","unstructured":"Wang, Q. et al. Gene body methylation in cancer: molecular mechanisms and clinical applications. Clin. Epigenetics 14, 154. https:\/\/doi.org\/10.1186\/s13148-022-01382-9 (2022).","journal-title":"Clin. Epigenetics"},{"key":"18794_CR58","doi-asserted-by":"publisher","first-page":"111","DOI":"10.1146\/annurev-ento-031616-034925","volume":"62","author":"X Belles","year":"2017","unstructured":"Belles, X. MicroRNAs and the evolution of insect metamorphosis. Annu. Rev. Entomol. 62, 111\u2013125. https:\/\/doi.org\/10.1146\/annurev-ento-031616-034925 (2017).","journal-title":"Annu. Rev. Entomol."},{"key":"18794_CR59","doi-asserted-by":"publisher","DOI":"10.1016\/j.ygcen.2020.113507","volume":"295","author":"WG Bendena","year":"2020","unstructured":"Bendena, W. G., Hui, J. H. L., Chin-Sang, I. & Tobe, S. S. Neuropeptide and microRNA regulators of juvenile hormone production. Gen. Comp. Endocrinol. 295, 113507. https:\/\/doi.org\/10.1016\/j.ygcen.2020.113507 (2020).","journal-title":"Gen. Comp. Endocrinol."},{"key":"18794_CR60","doi-asserted-by":"publisher","DOI":"10.1002\/arch.21657","volume":"104","author":"K Mukherjee","year":"2020","unstructured":"Mukherjee, K., Baudach, A., Vogel, H. & Vilcinskas, A. Seasonal phenotype-specific expression of microRNAs during metamorphosis in the European map butterfly Araschnia Levana. Arch. Insect Biochem. Physiol. 104, e21657. https:\/\/doi.org\/10.1002\/arch.21657 (2020).","journal-title":"Arch. Insect Biochem. Physiol."},{"key":"18794_CR61","doi-asserted-by":"publisher","first-page":"69","DOI":"10.1016\/j.jsbmb.2018.01.013","volume":"184","author":"Z Qu","year":"2018","unstructured":"Qu, Z., Bendena, W. G., Tobe, S. S. & Hui, J. H. L. Juvenile hormone and sesquiterpenoids in arthropods: biosynthesis, signaling, and role of MicroRNA. J. Steroid. Biochem. Mol. Biol. 184, 69\u201376. https:\/\/doi.org\/10.1016\/j.jsbmb.2018.01.013 (2018).","journal-title":"J. Steroid. Biochem. Mol. Biol."},{"key":"18794_CR62","doi-asserted-by":"publisher","first-page":"e17348","DOI":"10.1111\/mec.17348","volume":"34","author":"KT Roberts","year":"2024","unstructured":"Roberts, K. T., Steward, R. A., Suess, P., Lehmann, P. & Wheat, C. W. A time course analysis through diapause reveals dynamic temporal patterns of microRNAs associated with endocrine regulation in the butterfly Pieris napi. Mol. Ecol. 34, e17348. https:\/\/doi.org\/10.1111\/mec.17348 (2024).","journal-title":"Mol. Ecol."},{"issue":"6726","key":"18794_CR63","doi-asserted-by":"publisher","first-page":"1135","DOI":"10.1101\/2024.02.09.579741","volume":"386","author":"S Tian","year":"2024","unstructured":"Tian, S. et al. A micro-RNA is the effector gene of a classic evolutionary hotspot locus. Science 386(6726), 1135\u20131141. https:\/\/doi.org\/10.1101\/2024.02.09.579741 (2024).","journal-title":"Science"},{"key":"18794_CR64","doi-asserted-by":"publisher","unstructured":"Saccheri, I. J., Wellcome Sanger Institute Tree of Life, p., Wellcome Sanger Institute Scientific Operations, D. N. A. P. c., Tree of Life Core Informatics, c. & Darwin Tree of Life, C. The genome sequence of the Squinting Bush Brown, Bicyclus anynana (Butler, 1879). Wellcome Open Res 8, 280 (2023). https:\/\/doi.org\/10.12688\/wellcomeopenres.19432.1","DOI":"10.12688\/wellcomeopenres.19432.1"},{"key":"18794_CR65","doi-asserted-by":"publisher","first-page":"1650","DOI":"10.1038\/nprot.2016.095","volume":"11","author":"M Pertea","year":"2016","unstructured":"Pertea, M., Kim, D., Pertea, G. M., Leek, J. T. & Salzberg, S. L. Transcript-level expression analysis of RNA-seq experiments with HISAT StringTie Ballgown. Nat. Protoc. 11, 1650\u20131667. https:\/\/doi.org\/10.1038\/nprot.2016.095 (2016).","journal-title":"Nat. Protoc."},{"key":"18794_CR66","doi-asserted-by":"publisher","unstructured":"Pertea, G. & Pertea, M. GFF Utilities: GffRead and GffCompare. F1000Res 9 (2020). https:\/\/doi.org\/10.12688\/f1000research.23297.2","DOI":"10.12688\/f1000research.23297.2"},{"key":"18794_CR67","doi-asserted-by":"publisher","first-page":"417","DOI":"10.1038\/nmeth.4197","volume":"14","author":"R Patro","year":"2017","unstructured":"Patro, R., Duggal, G., Love, M. I., Irizarry, R. A. & Kingsford, C. Salmon provides fast and bias-aware quantification of transcript expression. Nat. Methods 14, 417\u2013419 (2017).","journal-title":"Nat. Methods"},{"key":"18794_CR68","doi-asserted-by":"publisher","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","volume":"15","author":"MI Love","year":"2014","unstructured":"Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550. https:\/\/doi.org\/10.1186\/s13059-014-0550-8 (2014).","journal-title":"Genome Biol."},{"key":"18794_CR69","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gku154","volume":"42","author":"H Feng","year":"2014","unstructured":"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. https:\/\/doi.org\/10.1093\/nar\/gku154 (2014).","journal-title":"Nucleic. Acids Res."},{"key":"18794_CR70","doi-asserted-by":"publisher","first-page":"R87","DOI":"10.1186\/gb-2012-13-10-r87","volume":"13","author":"A Akalin","year":"2012","unstructured":"Akalin, A. et al. methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles. Genome Biol. 13, R87. https:\/\/doi.org\/10.1186\/gb-2012-13-10-r87 (2012).","journal-title":"Genome Biol."},{"key":"18794_CR71","doi-asserted-by":"publisher","first-page":"W187","DOI":"10.1093\/nar\/gku365","volume":"42","author":"F Ramirez","year":"2014","unstructured":"Ramirez, F., Dundar, F., Diehl, S., Gruning, B. A. & Manke, T. deepTools: a flexible platform for exploring deep-sequencing data. Nucleic. Acids Res. 42, W187-191. https:\/\/doi.org\/10.1093\/nar\/gku365 (2014).","journal-title":"Nucleic. Acids Res."},{"key":"18794_CR72","doi-asserted-by":"publisher","first-page":"100141","DOI":"10.1016\/j.xinn.2021.100141","volume":"2","author":"T Wu","year":"2021","unstructured":"Wu, T. et al. clusterProfiler 4.0: a universal enrichment tool for interpreting omics data. Innovation (Camb) 2, 100141. https:\/\/doi.org\/10.1016\/j.xinn.2021.100141 (2021).","journal-title":"Innovation (Camb)"},{"key":"18794_CR73","unstructured":"Kolde, R. Pheatmap: Pretty Heatmaps R package version 1.0.12. https:\/\/CRAN.R-project.org\/package=pheatmap (2019)."}],"container-title":["Scientific Reports"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41598-025-18794-1.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41598-025-18794-1","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41598-025-18794-1.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,13]],"date-time":"2025-10-13T13:18:31Z","timestamp":1760361511000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41598-025-18794-1"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,10,13]]},"references-count":73,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2025,12]]}},"alternative-id":["18794"],"URL":"https:\/\/doi.org\/10.1038\/s41598-025-18794-1","relation":{},"ISSN":["2045-2322"],"issn-type":[{"value":"2045-2322","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,10,13]]},"assertion":[{"value":"22 April 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"3 September 2025","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"13 October 2025","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"The authors declare no competing interests.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"35612"}}