Iyer, L. M., Abhiman, S. & Aravind, L. Natural History of Eukaryotic DNA Methylation Systems, Vol. 101 (Elsevier, 2011).

Lyko, F. The DNA methyltransferase family: a versatile toolkit for epigenetic regulation. Nat. Rev. Genet. 19, 81–92 (2018).

Article 
CAS 
PubMed 

Google Scholar
 

Huff, J. T. & Zilberman, D. Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes. Cell 156, 1286–1297 (2014).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

De Mendoza, A., Lister, R. & Bogdanovic, O. Evolution of DNA methylome diversity in eukaryotes. J. Mol. Biol. 432, 1687–1705 (2020).

Article 
PubMed 

Google Scholar
 

Schmitz, R. J., Lewis, Z. A. & Goll, M. G. DNA methylation: shared and divergent features across eukaryotes. Trends Genet. 35, 818–827 (2019).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Sarkies, P. Encyclopaedia of eukaryotic DNA methylation: from patterns to mechanisms and functions. Biochem. Soc. Trans. 50, 1179–1190 (2022).

CAS 
PubMed 
PubMed Central 

Google Scholar
 

Rae, P. M. M. & Steele, R. E. Modified bases in the DNAs of unicellular eukaryotes: an examination of distributions and possible roles, with emphasis on hydroxymethyluracil in dinoflagellates. Biosystems 10, 37–53 (1978).

Article 
CAS 
PubMed 

Google Scholar
 

Borst, P. & Sabatini, R. Base J: discovery, biosynthesis, and possible functions. Annu. Rev. Microbiol. 62, 235–251 (2008).

Article 
CAS 
PubMed 

Google Scholar
 

Koziol, M. J. et al. Identification of methylated deoxyadenosines in vertebrates reveals diversity in DNA modifications. Nat. Struct. Mol. Biol. 23, 24–30 (2016).

Article 
CAS 
PubMed 

Google Scholar
 

Greer, E. L. et al. DNA methylation on N6-adenine in C. elegans. Cell 161, 868–878 (2015).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Wu, T. P. et al. DNA methylation on N(6)-adenine in mammalian embryonic stem cells. Nature 532, 329–333 (2016).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Zhang, G. et al. N6-methyladenine DNA modification in Drosophila. Cell 161, 893–906 (2015).

Article 
CAS 
PubMed 

Google Scholar
 

Liang, Z. et al. DNA N6-adenine methylation in Arabidopsis thaliana. Dev. Cell 45, 406–416 (2018).

Article 
CAS 
PubMed 

Google Scholar
 

Mondo, S. J. et al. Widespread adenine N6-methylation of active genes in fungi. Nat. Genet. 49, 964–968 (2017).

Article 
CAS 
PubMed 

Google Scholar
 

Lax, C. et al. Symmetric and asymmetric DNA N6-adenine methylation regulates different biological responses in Mucorales. Nat. Commun. 15, 6066 (2024).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Fu, Y. et al. N6-methyldeoxyadenosine marks active transcription start sites in Chlamydomonas. Cell 161, 879–892 (2015).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Wang, Y., Chen, X., Sheng, Y., Liu, Y. & Gao, S. N6-adenine DNA methylation is associated with the linker DNA of H2A.Z-containing well-positioned nucleosomes in Pol II-transcribed genes in Tetrahymena. Nucleic Acids Res. 45, 11594–11606 (2017).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Beh, L. Y. et al. Identification of a DNA N6-adenine methyltransferase complex and its impact on chromatin organization. Cell 177, 1781–1796 (2019).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Kong, Y. et al. Critical assessment of DNA adenine methylation in eukaryotes using quantitative deconvolution. Science 375, 515–522 (2022).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

O’Brown, Z. K. et al. Sources of artifact in measurements of 6mA and 4mC abundance in eukaryotic genomic DNA. BMC Genomics 20, 445 (2019).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Douvlataniotis, K., Bensberg, M., Lentini, A., Gylemo, B. & Nestor, C. E. No evidence for DNA N6-methyladenine in mammals. Sci. Adv. 6, eaay3335 (2020).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Boulias, K. & Greer, E. L. Means, mechanisms and consequences of adenine methylation in DNA. Nat. Rev. Genet. 23, 411–428 (2022).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Musheev, M. U., Baumgärtner, A., Krebs, L. & Niehrs, C. The origin of genomic N6-methyl-deoxyadenosine in mammalian cells. Nat. Chem. Biol. 16, 630–634 (2020).

Article 
CAS 
PubMed 

Google Scholar
 

Kong, Y., Mead, E. A. & Fang, G. Navigating the pitfalls of mapping DNA and RNA modifications. Nat. Rev. Genet. 24, 363–381 (2023).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Debo, B. M., Mallory, B. J. & Stergachis, A. B. Evaluation of N6-methyldeoxyadenosine antibody-based genomic profiling in eukaryotes. Genome Res. 33, 427–434 (2023).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Iyer, L. M., Zhang, D. & Aravind, L. Adenine methylation in eukaryotes: apprehending the complex evolutionary history and functional potential of an epigenetic modification. Bioessays 38, 27–40 (2016).

Article 
CAS 
PubMed 

Google Scholar
 

Bochtler, M. & Fernandes, H. DNA adenine methylation in eukaryotes: enzymatic mark or a form of DNA damage? Bioessays 43, e2000243 (2021).

Article 
PubMed 

Google Scholar
 

Wang, Y. et al. A distinct class of eukaryotic MT-A70 methyltransferases maintain symmetric DNA N6-adenine methylation at the ApT dinucleotides as an epigenetic mark associated with transcription. Nucleic Acids Res. 47, 11771–11789 (2019).

CAS 
PubMed 
PubMed Central 

Google Scholar
 

Chen, J. et al. Structural basis for MTA1c-mediated DNA N6-adenine methylation. Nat. Commun. 13, 3257 (2022).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Liu, J. et al. A METTL3-METTL14 complex mediates mammalian nuclear RNA N6-adenosine methylation. Nat. Chem. Biol. 10, 93–95 (2014).

Article 
CAS 
PubMed 

Google Scholar
 

Sheng, Y. et al. Semi-conservative transmission of DNA N6-adenine methylation in a unicellular eukaryote. Genome Res. 34, 740–756 (2024).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Luo, G.-Z. et al. N6-methyldeoxyadenosine directs nucleosome positioning in Tetrahymena DNA. Genome Biol. 19, 200 (2018).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Liu, Q. et al. Detection of DNA base modifications by deep recurrent neural network on Oxford Nanopore sequencing data. Nat. Commun. 10, 2449 (2019).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Hao, Z. et al. N6-deoxyadenosine methylation in mammalian mitochondrial DNA. Mol. Cell 78, 382–395 (2020).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Burki, F., Roger, A. J., Brown, M. W. & Simpson, A. G. B. The new tree of eukaryotes. Trends Ecol. Evol. 35, 43–55 (2020).

Article 
CAS 
PubMed 

Google Scholar
 

Thomy, J. et al. Combining nanopore and Illumina sequencing permits detailed analysis of insertion mutations and structural variations produced by PEG-mediated transformation in Ostreococcus tauri. Cells 10, 664 (2021).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Liechti, N., Schürch, N., Bruggmann, R. & Wittwer, M. Nanopore sequencing improves the draft genome of the human pathogenic amoeba Naegleria fowleri. Sci. Rep. 9, 16040 (2019).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Giguere, D. J. et al. Telomere-to-telomere genome assembly of Phaeodactylum tricornutum. PeerJ 10, e13607 (2022).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Lenhard, B., Sandelin, A. & Carninci, P. Metazoan promoters: emerging characteristics and insights into transcriptional regulation. Nat. Rev. Genet. 13, 233–245 (2012).

Article 
CAS 
PubMed 

Google Scholar
 

Bernard, C. et al. A time-resolved multi-omics atlas of Acanthamoeba castellanii encystment. Nat. Commun. 13, 4104 (2022).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

De Mendoza, A., Suga, H., Permanyer, J., Irimia, M. & Ruiz-Trillo, I. Complex transcriptional regulation and independent evolution of fungal-like traits in a relative of animals. eLife 4, e08904 (2015).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Olivetta, M., Bhickta, C., Chiaruttini, N., Burns, J. & Dudin, O. A multicellular developmental program in a close animal relative. Nature 635, 382–389 (2024).

Article 
CAS 
PubMed 

Google Scholar
 

Medina, E. M. et al. Genetic transformation of Spizellomyces punctatus, a resource for studying chytrid biology and evolutionary cell biology. eLife 9, e52741 (2020).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Drewell, R. A. et al. The Dictyostelium discoideum genome lacks significant DNA methylation and uncovers palindromic sequences as a source of false positives in bisulfite sequencing. NAR Genom. Bioinform 5, lqad035 (2023).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Sarre, L. A. et al. DNA methylation enables recurrent endogenization of giant viruses in an animal relative. Sci. Adv. 10, eado6406 (2024).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Pfeifer, G. P. Mutagenesis at methylated CpG sequences. Curr. Top. Microbiol. Immunol. 301, 259–281 (2006).

CAS 
PubMed 

Google Scholar
 

Shen, J. C., Rideout, W. M. 3rd & Jones, P. A. The rate of hydrolytic deamination of 5-methylcytosine in double-stranded DNA. Nucleic Acids Res. 22, 972–976 (1994).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Bird, A. P. DNA methylation and the frequency of CpG in animal DNA. Nucleic Acids Res. 8, 1499–1504 (1980).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Suzuki, M. M., Kerr, A. R. W., de Sousa, D. & Bird, A. CpG methylation is targeted to transcription units in an invertebrate genome. Genome Res. 17, 625–631 (2007).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

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, 1185–1197 (2018).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Bewick, A. J. et al. Diversity of cytosine methylation across the fungal tree of life. Nat. Ecol. Evol. 3, 479–490 (2019).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Bewick, A. J. & Schmitz, R. J. Gene body DNA methylation in plants. Curr. Opin. Plant Biol. 36, 103–110 (2017).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Zemach, A., McDaniel, I. E., Silva, P. & Zilberman, D. Genome-wide evolutionary analysis of eukaryotic DNA methylation. Science 328, 916–919 (2010).

Article 
CAS 
PubMed 

Google Scholar
 

Grau-Bové, X. et al. A phylogenetic and proteomic reconstruction of eukaryotic chromatin evolution. Nat. Ecol. Evol. 6, 1007–1023 (2022).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Ngan, C. Y. et al. Lineage-specific chromatin signatures reveal a regulator of lipid metabolism in microalgae. Nat. Plants 1, 15107 (2015).

Article 
CAS 
PubMed 

Google Scholar
 

Sebé-Pedrós, A. et al. The dynamic regulatory genome of Capsaspora and the origin of animal multicellularity. Cell 165, 1224–1237 (2016).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Navarrete, C., Montgomery, S. A., Mendieta, J., Lara-Astiaso, D. & Sebé-Pedrós, A. Diversity and evolution of chromatin regulatory states across eukaryotes. Preprint at bioRxiv https://doi.org/10.1101/2025.03.17.643675 (2025).

Sanchez, R. & Zhou, M.-M. The PHD finger: a versatile epigenome reader. Trends Biochem. Sci. 36, 364–372 (2011).

CAS 
PubMed 
PubMed Central 

Google Scholar
 

Grebien, F. et al. Pharmacological targeting of the Wdr5-MLL interaction in C/EBPα N-terminal leukemia. Nat. Chem. Biol. 11, 571–578 (2015).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Zhang, X. et al. Piribedil disrupts the MLL1-WDR5 interaction and sensitizes MLL-rearranged acute myeloid leukemia (AML) to doxorubicin-induced apoptosis. Cancer Lett. 431, 150–160 (2018).

Article 
CAS 
PubMed 

Google Scholar
 

Al Jewari, C. & Baldauf, S. L. An excavate root for the eukaryote tree of life. Sci. Adv. 9, eade4973 (2023).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Cerón-Romero, M. A., Fonseca, M. M., de Oliveira Martins, L., Posada, D. & Katz, L. A. Phylogenomic analyses of 2,786 genes in 158 lineages support a root of the eukaryotic tree of life between opisthokonts and all other lineages. Genome Biol. Evol. 14, evac119 (2022).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Williamson, K. et al. A robustly rooted tree of eukaryotes reveals their excavate ancestry. Nature 640, 974–981 (2025).

Article 
CAS 
PubMed 

Google Scholar
 

Jurkowski, T. P. & Jeltsch, A. On the evolutionary origin of eukaryotic DNA methyltransferases and Dnmt2. PLoS ONE 6, e28104 (2011).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Ponger, L. & Li, W.-H. Evolutionary diversification of DNA methyltransferases in eukaryotic genomes. Mol. Biol. Evol. 22, 1119–1128 (2005).

Article 
CAS 
PubMed 

Google Scholar
 

Tourancheau, A., Mead, E. A., Zhang, X.-S. & Fang, G. Discovering multiple types of DNA methylation from bacteria and microbiome using nanopore sequencing. Nat. Methods 18, 491–498 (2021).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Lizarraga, A. et al. Adenine DNA methylation, 3D genome organization, and gene expression in the parasite Trichomonas vaginalis. Proc. Natl Acad. Sci. USA 117, 13033–13043 (2020).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Pritham, E. J., Putliwala, T. & Feschotte, C. Mavericks, a novel class of giant transposable elements widespread in eukaryotes and related to DNA viruses. Gene 390, 3–17 (2007).

Article 
CAS 
PubMed 

Google Scholar
 

Lentini, A. et al. A reassessment of DNA-immunoprecipitation-based genomic profiling. Nat. Methods 15, 499–504 (2018).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Ma, C. et al. A novel N6-deoxyadenine methyltransferase METL-9 modulates C. elegans immunity via dichotomous mechanisms. Cell Res. 33, 628–639 (2023).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Zhang, J. et al. 6mA-Sniper: quantifying 6mA sites in eukaryotes at single-nucleotide resolution. Sci. Adv. 9, eadh7912 (2023).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Abakir, A. et al. N6-methyladenosine regulates the stability of RNA:DNA hybrids in human cells. Nat. Genet. 52, 48–55 (2020).

Article 
CAS 
PubMed 

Google Scholar
 

Febrimarsa et al. Randomly incorporated genomic N6-methyldeoxyadenosine delays zygotic transcription initiation in a cnidarian. EMBO J. 42, e112934 (2023).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Duan, L. et al. Methyl-dependent auto-regulation of the DNA N6-adenine methyltransferase AMT1 in the unicellular eukaryote Tetrahymena thermophila. Nucleic Acids Res. 53, gkaf022 (2025).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Zilberman, D. An evolutionary case for functional gene body methylation in plants and animals. Genome Biol. 18, 87 (2017).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Dixon, G. & Matz, M. Changes in gene body methylation do not correlate with changes in gene expression in Anthozoa or Hexapoda. BMC Genomics 23, 234 (2022).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Howe, F. S., Fischl, H., Murray, S. C. & Mellor, J. Is H3K4me3 instructive for transcription activation?. Bioessays 39, 1–12 (2017).

Article 
CAS 
PubMed 

Google Scholar
 

Wang, H. et al. H3K4me3 regulates RNA polymerase II promoter-proximal pause-release. Nature 615, 339–348 (2023).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

De Mendoza, A. et al. Convergent evolution of a vertebrate-like methylome in a marine sponge. Nat. Ecol. Evol. 3, 1464–1473 (2019).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Schwaiger, M. et al. Evolutionary conservation of the eumetazoan gene regulatory landscape. Genome Res. 24, 639–650 (2014).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Kaluscha, S. et al. Evidence that direct inhibition of transcription factor binding is the prevailing mode of gene and repeat repression by DNA methylation. Nat. Genet. 54, 1895–1906 (2022).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Torruella, G. et al. Phylogenomics reveals convergent evolution of lifestyles in close relatives of animals and fungi. Curr. Biol. 25, 2404–2410 (2015).

Article 
CAS 
PubMed 

Google Scholar
 

Eddy, S. R. Accelerated profile HMM searches. PLoS Comput. Biol. 7, e1002195 (2011).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Katoh, K. & Standley, D. M. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30, 772–780 (2013).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Capella-Gutiérrez, S., Silla-Martínez, J. M. & Gabaldón, T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25, 1972–1973 (2009).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Minh, B. Q. et al. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol. Biol. Evol. 37, 1530–1534 (2020).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Prescott, D. M. (ed.). Methods in Cell Biology Vol. 1, 55–83 (Academic, 1964).

Collier, J. L. et al. The protist Aurantiochytrium has universal subtelomeric rDNAs and is a host for mirusviruses. Curr. Biol. 33, 5199–5207 (2023).

Article 
CAS 
PubMed 

Google Scholar
 

Matthey-Doret, C. et al. Chromosome-scale assemblies of Acanthamoeba castellanii genomes provide insights into Legionella pneumophila infection-related chromatin reorganization. Genome Res. 32, 1698–1710 (2022).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Grau-Bové, X. et al. Dynamics of genomic innovation in the unicellular ancestry of animals. eLife 6, e26036 (2017).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Price, D. C. et al. Analysis of an improved Cyanophora paradoxa genome assembly. DNA Res. 26, 287–299 (2019).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Quinlan, A. R. & Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841–842 (2010).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Ramírez, F., Dündar, F., Diehl, S., Grüning, B. A. & Manke, T. deepTools: a flexible platform for exploring deep-sequencing data. Nucleic Acids Res. 42, W187–W191 (2014).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Hansen, K. D., Langmead, B. & Irizarry, R. A. BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions. Genome Biol. 13, R83 (2012).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Gao, F. et al. EasyCodeML: a visual tool for analysis of selection using CodeML. Ecol. Evol. 9, 3891–3898 (2019).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Sirén, J., Välimäki, N. & Mäkinen, V. HISAT2—fast and sensitive alignment against general human population. IEEE/ACM Trans. Comput. Biol. Bioinform. 11, 375–388 (2014).

PubMed 

Google Scholar
 

Pertea, M. et al. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat. Biotechnol. 33, 290–295 (2015).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Bray, N. L., Pimentel, H., Melsted, P. & Pachter, L. Near-optimal probabilistic RNA-seq quantification. Nat. Biotechnol. 34, 525–527 (2016).

Article 
CAS 
PubMed 

Google Scholar
 

Lara-Astiaso, D. et al. Immunogenetics. Chromatin state dynamics during blood formation. Science 345, 943–949 (2014).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Song, M.-J. et al. Epigenome mapping highlights chromatin-mediated gene regulation in the protozoan parasite Trichomonas vaginalis. Sci. Rep. 7, 45365 (2017).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Zhang, Y. et al. Model-based analysis of ChIP-seq (MACS). Genome Biol. 9, R137 (2008).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Kolmogorov, M., Yuan, J., Lin, Y. & Pevzner, P. A. Assembly of long, error-prone reads using repeat graphs. Nat. Biotechnol. 37, 540–546 (2019).

Article 
CAS 
PubMed 

Google Scholar
 

Kundu, R., Casey, J. & Sung, W.-K. HyPo: super fast & accurate polisher for long read genome assemblies. Preprint at bioRxiv https://doi.org/10.1101/2019.12.19.882506 (2019).

Joseph, S. J. et al. Comparative genomic and transcriptomic analysis of Naegleria fowleri clinical and environmental isolates. mSphere 6, e0063721 (2021).

Article 
PubMed 

Google Scholar
 

Alonge, M. et al. Automated assembly scaffolding using RagTag elevates a new tomato system for high-throughput genome editing. Genome Biol. 23, 258 (2022).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Grau-Bové, X., Ruiz-Trillo, I. & Irimia, M. Origin of exon skipping-rich transcriptomes in animals driven by evolution of gene architecture. Genome Biol. 19, 135 (2018).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Haas, B. J. et al. De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat. Protoc. 8, 1494–1512 (2013).

Article 
CAS 
PubMed 

Google Scholar
 

Venturini, L., Caim, S., Kaithakottil, G. G., Mapleson, D. L. & Swarbreck, D. Leveraging multiple transcriptome assembly methods for improved gene structure annotation. Gigascience 7, giy093 (2018).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Stanke, M., Diekhans, M., Baertsch, R. & Haussler, D. Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics 24, 637–644 (2008).

Article 
CAS 
PubMed 

Google Scholar
 

Shumate, A. & Salzberg, S. L. Liftoff: accurate mapping of gene annotations. Bioinformatics 37, 1639–1643 (2021).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Fritz-Laylin, L. K. et al. The genome of Naegleria gruberi illuminates early eukaryotic versatility. Cell 140, 631–642 (2010).

Article 
CAS 
PubMed 

Google Scholar
 

Haas, B. J. et al. Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments. Genome Biol. 9, R7 (2008).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Blanc, G. et al. Deep RNA sequencing reveals hidden features and dynamics of early gene transcription in Paramecium bursaria chlorella virus 1. PLoS ONE 9, e90989 (2014).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Flynn, J. M. et al. RepeatModeler2 for automated genomic discovery of transposable element families. Proc. Natl Acad. Sci. USA 117, 9451–9457 (2020).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

De Mendoza, A., Romero Charria, P., Shabardina, V. & Casacuberta, E. Adenine DNA methylation associated with transcriptionally permissive chromatin is widespread across eukaryotes. BioStudies https://doi.org/10.6019/S-BSST1363 (2025).

De Mendoza, A. & Romero Charria, P. AlexdeMendoza/6mA_evolution: 6mA_Evolution_publicationRelease (v1.0). Zenodo https://doi.org/10.5281/zenodo.17174913 (2025).