REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
α-6mA	Synaptic Systems	Cat#202003; RRID:AB_2279214
Goat anti-Rabbit IgG (H+L)	Invitrogen	Cat#A-21428; RRID:AB_2535849
Bacterial and virus strains
Klebsiella pneumonia	repository	N/A
Escherichia coli	repository	HST04
Deposited data
MNase-seq, RNA-seq, 6mA-IP-seq and Oxford Nanopore Technologies (ONT) data of P. bursaria	This paper	NCBI: PRJNA673334
SMRT-seq and RNA-seq data of P. bursaria	He et al.41	BIGD: PRJCA001086
RNA-seq dataset of P. bursaria	Kodama and Fujishima76	NCBI: DRP000940
SMRT-seq of Tetrahymena	Wang et al.57	NCBI: SRX5993111
SMRT-seq of Oxytricha	Beh et al.11	NCBI: SRX5944401
SMRT-seq of P. tetraurelia	Hardy et al.34	ENA: PRJEB40264
RNA-seq of P. tetraurelia	Hardy et al.34	ENA: ERR1827399
Customized scripts	This paper	https://github.com/Bryan0425/Paramecium-6mA-related
Software and algorithms
RepeatMasker v4.0.9	Tarailo-Graovac and Chen77	http://www.repeatmasker.org/RMDownload.html
Trimmomatic v0.39	Bolger et al.78	http://www.usadellab.org/cms/?page = trimmomatic
Augustus v3.3.3	Stanke et al.79	https://github.com/Gaius-Augustus/Augustus
SMRT link v7.0	Pacific Biosciences	https://www.pacb.com/support/software-downloads/
R package circlize v0.4.4	Gu et al.80	https://jokergoo.github.io/circlize_book/book/
R package ggplot2	Wickham81	http://had.co.nz/ggplot2/
WebLogo3	Crooks et al.82	https://weblogo.threeplusone.com/
RNAmmer v1.2	Lagesen et al.83	https://services.healthtech.dtu.dk/service.php?RNAmmer-1.2
tRNAscan-SE v2.0.5	Lowe and Eddy84	http://lowelab.ucsc.edu/tRNAscan-SE/
Rfam v11.0	Griffiths-Jones et al.85	ftp://ftp.ebi.ac.uk/pub/databases/Rfam/12.2/Rfam.cm.gz
guppy v3.2.10	Oxford Nanopore Technologies	https://github.com/metagenomics/denbi-nanopore-training/blob/master/docs/basecalling/basecalling.rst
Nanofilt v2.5.0	De Coster et al.86	https://pypi.org/project/NanoFilt/
Pychopper	Oxford Nanopore Technologies	https://github.com/nanoporetech/pychopper
minimap2 v2.16	Li87	https://github.com/lh3/minimap2
Pinfish	Oxford Nanopore Technologies	https://github.com/nanoporetech/pinfish
Gffcompare	Pertea and Pertea88	https://github.com/gpertea/gffcompare
Tophat2 v2.1.1	Trapnell et al.89	http://ccb.jhu.edu/software/tophat/index.shtml
cufflinks v2.2.1	Trapnell et al.89	https://cole-trapnell-lab.github.io/cufflinks/
ASprofile v1.0.4	Florea et al.90	https://ccb.jhu.edu/software/ASprofile/
SQANTI3 v3.0	Tardaguila et al.91	https://github.com/ConesaLab/SQANTI3
Cupcake v24.3.0	Elizabeth Tseng	https://github.com/Magdoll/cDNA_Cupcake
FLAIR v1.5	Tang et al.92	https://github.com/BrooksLabUCSC/FLAIR
eggNOG-mapper	Huerta-Cepas et al.93	http://eggnog-mapper.embl.de/
GSEA v4.1.0	Mootha et al.94; Subramanian et al.95	http://www.gsea-msigdb.org/gsea/index.jsp
PSI-BLAST v2.9.0+	Altschul et al.96	https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/
CD-HIT	Huang et al.97	http://cd-hit.org
MUSCLE v3.8	Edgar98	http://www.drive5.com/muscle/
FastTree v2.1	Price et al.99	http://www.microbesonline.org/fasttree/
NCBI Conserved Domain Search	Lu et al.100	https://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml
Phylostratigraphic analysis v0.0.5	Drost et al.101; Domazet-Loso et al.102	https://github.com/AlexGa/Phylostratigraphy