Fig. 1: Identification of novel transcripts using PacBio SMRT sequencing in seven stages of preimplantation mouse embryos.

a Workflow for transcriptome reconstruction based on PacBio SMRT sequencing data. The Iso-seq3 pipeline was used to assemble transcripts from long-read data, and these transcripts were then mapped to the reference genome with GMAP and compared with the GENCODE (vM20) annotation using Cuffcompare. Zygotes and in vitro cultured embryos from female C57BL/6J and male DBA/2 inbred mice were collected. For a batch of samples, 150 oocytes (Oo), 150 1-cell embryos (1C), 100 2-cell embryos (2C), 50 4-cell embryos (4C), 25 8-cell embryos (8C), 20 blastocysts (BL, 32-64C), and bulk sperms, were collected for experiments. Long-read transcripts were also validated and compared to short-read data. b Annotation of identified long-read transcripts in the seven stages. By comparison with the GENCODE annotation, the transcripts for each stage were divided into the five indicated categories, and the percentages of transcripts in each category are shown. The red line represents the total number of transcripts in each stage. c Annotation of merged long-read transcripts that were the combination of transcripts identified across seven stages. The numbers and percentages of merged transcripts in the five categories are presented. d, e Classification of annotated (d) and novel (e) merged transcripts according to the GENCODE annotation or protein-coding potential and the length of transcripts. f The expression of transcripts identified from long-read data in the seven stages quantified by using short-read data. The bar plot presents the number of annotated (left) and novel (right) transcripts classified by TPM.