Akalin A, Kormaksson M, Li S, Garrett-Bakelman FE, Figueroa ME, Melnick A, Mason CE. 2012. MethylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles. Genome Biol. 13.
Arsenault S V., Hunt BG, Rehan SM. 2018. The effect of maternal care on gene expression and DNA methylation in a subsocial bee. Nat. Commun. 9:3468.
Baumgarten S, Simakov O, Esherick LY, Liew YJ, Lehnert EM, Michell CT, Li Y, Hambleton EA, Guse A, Oates ME, et al. 2015. The genome of Aiptasia , a sea anemone model for coral symbiosis. Proc. Natl. Acad. Sci. 112:201513318.
Bewick AJ, Ji L, Niederhuth CE, Willing E-M, Hofmeister BT, Shi X, Wang L, Lu Z, Rohr NA, Hartwig B, et al. 2016. On the origin and evolutionary consequences of gene body DNA methylation. Proc. Natl. Acad. Sci. U. S. A. 113:9111–9116.
Bewick Adam J., Sanchez Z, McKinney EC, Moore AJ, Moore PJ, Schmitz RJ. 2019. Dnmt1 is essential for egg production and embryo viability in the large milkweed bug, Oncopeltus fasciatus. Epigenetics and Chromatin 12:1–14.
Bewick Adam J, Zhang Y, Wendte JM, Zhang X, Schmitz RJ. 2019. Evolutionary and Experimental Loss of Gene Body Methylation and Its Consequence to Gene Expression. G3 Genes Genomes Genet. 9:2441–2445.
Bogan, Samuel N, Strader, Marie E, Hofmann GE. 2021. Gene regulation by DNA methylation is contingent on chromatin accessibility during transgenerational plasticity in the purple sea urchin. bioRxiv Prepr.
Broad Institute. 2019. Picard Toolkit.
Choi J, Lyons DB, Kim MY, Moore JD, Choi J, Lyons DB, Kim MY, Moore JD, Zilberman D. 2020. DNA Methylation and Histone H1 Jointly Repress Transposable Elements and Aberrant Intragenic DNA Methylation and Histone H1 Jointly Repress Transposable Elements and Aberrant Intragenic Transcripts. Mol. Cell:1–14.
Dixon G. 2020. invert_meth_and_transcription GitHub Page. https://github.com/grovesdixon/invert_meth_and_transcription.
Dixon G, Bay LK, Matz M V. 2016. Evolutionary consequences of DNA methylation in a basal metazoan. Mol. Biol. Evol. 33:2285–2293.
Dixon G, Liao Y, Bay LK, Matz M V. 2018. Role of gene body methylation in acclimatization and adaptation in a basal metazoan. Proc. Natl. Acad. Sci. U. S. A. 115:13342–13346.
Dixon G, Matz M V. 2020. Benchmarking DNA methylation assays in a reef-building coral. Mol. Ecol. Resour. 21:464–477.
Fuller ZL, Mocellin VJL, Morris LA, Cantin N, Shepherd J, Sarre L, Peng J, Liao Y, Pickrell J, Andolfatto P, et al. 2020. Population genetics of the coroal Acropora millepora: Toward genomic prediction of bleaching. Science. 369.
Gatzmann F, Falckenhayn C, Gutekunst J, Hanna K, Raddatz G, Carneiro VC, Lyko F. 2018. The methylome of the marbled crayfish links gene body methylation to stable expression of poorly accessible genes. Epigenetics and Chromatin 11:1–12.
Glastad KM, Gokhale K, Liebig J, Goodisman MAD. 2016. The caste- and sex-specific DNA methylome of the termite Zootermopsis nevadensis. Sci. Rep. 6.
Harris KD, Lloyd JPB, Domb K, Zilberman D, Zemach A. 2019. DNA methylation is maintained with high fidelity in the honey bee germline and exhibits global non-functional fluctuations during somatic development. Epigenetics and Chromatin 12:1–18.
Herb BR, Wolschin F, Hansen KD, Aryee MJ, Langmead B, Irizarry R, Amdam G V, Feinberg AP. 2012. Reversible switching between epigenetic states in honeybee behavioral subcastes. Nat. Neurosci. 15:1371–1373.
Krueger F, Andrews SR. 2011. Bismark: A flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics 27:1571–1572.
Langmead B, Salzberg SL. 2012. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9:357–359.
Li B, Hu P, Zhu LB, You LL, Cao HH, Wang J, Zhang SZ, Liu MH, Toufeeq S, Huang SJ, et al. 2020. DNA methylation is correlated with gene expression during diapause termination of early embryonic development in the silkworm (Bombyx mori). Int. J. Mol. Sci. 21.
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R. 2009. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25:2078–2079.
Li Y, Liew YJ, Cui G, Cziesielski MJ, Zahran N, Michell CT, Voolstra CR, Aranda M. 2018. DNA methylation regulates transcriptional homeostasis of algal endosymbiosis in the coral model Aiptasia. Sci. Adv. 4:eaat2142.
Liao Y, Smyth GK, Shi W. 2014. FeatureCounts: An efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30:923–930.
Libbrecht R, Oxley PR, Keller L, Kronauer DJC. 2016. Robust DNA methylation in the clonal raider ant brain. Curr. Biol. 26:391–395.
Liew YJ, Zoccola D, Li Y, Tambutte E, Venn AA, Michell CT, Cui G, Deutekom ES, Kaandorp JA, Voolstra CR, et al. 2018. Epigenome-associated phenotypic acclimatization to ocean acidification in a reef-building coral. Sci. Adv. 4.
Love MI, Huber W, Anders S. 2014. Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2. Genome Biol. 15:1–21.
Marshall H, Lonsdale ZN, Mallon EB. 2019. Methylation and gene expression differences between reproductive and sterile bumblebee workers. Evol. Lett. 3:485–499.
Martin M. 2011. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnetjournal 17:10–12.
McKenzie SK, Kronauer DJC. 2018. The genomic architecture and molecular evolution of ant odorant receptors. Genome Res. 28:1757–1765.
de Mendoza A, Lister R, Bogdanovic O. 2019. Evolution of DNA Methylome Diversity in Eukaryotes. J. Mol. Biol. 432:1687–1705.
Meyer E, Aglyamova G V, Matz M V. 2011. Profiling gene expression responses of coral larvae (Acropora millepora) to elevated temperature and settlement inducers using a novel RNA-Seq procedure. Mol. Ecol. 20:3599–3616.
Rehan SM, Glastad KM, Lawson SP, Hunt BG. 2016. The genome and methylome of a subsocial small carpenter bee, ceratina calcarata. Genome Biol. Evol. 8:1401–1410.
Sadd BM, Barribeau SM, Bloch G, de Graaf DC, Dearden P, Elsik CG, Gadau J, Grimmelikhuijzen CJP, Hasselmann M, Lozier JD, et al. 2015. The genomes of two key bumblebee species with primitive eusocial organization. Genome Biol. 16.
Voolstra CR, Li Y, Liew YJ, Baumgarten S, Zoccola D, Flot JF, Tambutté S, Allemand D, Aranda M. 2017. Comparative analysis of the genomes of Stylophora pistillata and Acropora digitifera provides evidence for extensive differences between species of corals. Sci. Rep. 7:1–14.
Xia Q, Wang J, Zhou Z, Li R, Fan W, Cheng D, Cheng T, Qin J, Duan J, Xu H, et al. 2008. The genome of a lepidopteran model insect, the silkworm Bombyx mori. Insect Biochem. Mol. Biol. 38:1036–1045.
Xu X, Li G, Li C, Zhang J, Wang Q, Simmons DK, Chen X, Wijesena N, Zhu W, Wang Zhanyang, et al. 2019. Evolutionary transition between invertebrates and vertebrates via methylation reprogramming in embryogenesis. Natl. Sci. Rev. 6:993–1003.
Zemach A, McDaniel IE, Silva P, Zilberman D. 2010. Genome-wide evolutionary analysis of eukaryotic DNA methylation. Science. 328:916–919.