Characterizing Zebrafish Transcriptome Dynamics

To calculate codon optimality, zebrafish CDS sequences were downloaded from Ensembl Biomart and filtered to include only sequences starting with a start codon, ending with a stop codon, and sequence lengths being multiples of three. Codon optimality was calculated using icodon R package^{34 (link)}, keeping only the highest value per gene to keep only a single value per gene. Transcript translation efficiencies at different zebrafish developmental stages were taken from ref. ^{35 (link)}. A gene was considered m⁶A modified if evidence for m⁶A modification was measured by ref. ^{36 (link)} in either m6A-seq or m6A-CLIP-seq data. A gene was considered m⁵C modified if it contained a location with an m⁵C level >= 0.25, as measured by ref. ^{37 (link)}. Genes’ polyA lengths were taken as the mean length measured by ref. ^{33 (link)}. Independent maternal genes’ degradation rates (for maternal-only genes) were calculated from RNA sequencing measured by refs. ^{8 (link),14 (link),36 (link),51 (link)–53 (link)}. Only measurements until 6 hpf were used for the calculation.