Fig. 1

Identification of novel transcripts using PacBio long-read sequencing in 21 stages of zebrafish embryos. A Schematic of the transcriptome reconstruction pipeline based on long-read sequencing. Stage-specific transcriptomes were reconstructed from 21 embryonic stages: unfertilized, 1-cell, 2-cell, 128-cell, 1 k-cell, oblong, dome, 50% epiboly, shield, 75% epiboly, 1–4 somites, 14–19 somites, 20–25 somites, prim-5, prim-15, prim-25, long pec, protruding mouth, day 4, day 5, and day 6. Long reads were mapped to the reference GRCz11 genome using GMAP and annotated against the reference transcriptome using Cuffcompare. The long-read transcripts were also compared and validated to the short RNA-seq data. B The ratios of high-quality transcripts of zebrafish embryo development to the reference GRCz11 were greater than 99%. C Annotation of identified long-read transcripts in the 21 stages. Transcripts from each stage were annotated into five categories, and the percentages of the five categories are shown. The red lines show the total number of transcripts in each stage. D Transcripts from 21 stages were merged using Cuffmerge, and the merged transcripts were annotated. The numbers and percentages show the transcripts of the five categories of transcripts after being merged. E According to the annotation of the reference GRCz11 and coding potential, annotated transcripts and novel transcripts were classified into protein-coding and lncRNA, respectively. F High-quality transcripts of 21 stages were identified in short-read RNA-seq data and their expression levels were calculated