Fig. 3

IsoSeq full-length cDNA reads (a) and CAGE data (b) validate fine structures of PTs in the integrated transcriptome assembly. a An example showing one assembled PT shadowed gray in the “Assembly” panel was validated by one IsoSeq full-length cDNA read shadowed gray in the “IsoSeq” panel in terms of intron arrangement. For references, from top to bottom displayed are genomic coordinates, genome coverage by the normalized RNA-seq reads, aligned RNA-seq reads, pig RefSeq mRNAs, SSC10.2 transcripts and IsoSeq read alignments. In the panel labeled as “RNA-seq Cov”, heights of the gray or colored bars represent CPB by the RNA-seq reads. In the “RNA-seq” panel, purple and blue boxes represent reads mapped to the forward and reverse strands of the chromosome; while the thin segments represent introns spanned by spliced reads. In the panels labeled as “Assembly”, “RefSeq”, “SSC10.2” or “IsoSeq”, red boxes represent exons, and thin segments stand for introns, with arrows indicating the orientation of the sense strand. The “Assembly” panel shows PTs mapped to this genomic window. b An example showing a conserved proximal promoter among pigs, humans and mice, determined by CAGE, overlaps the 5′ termini of several assembled isoforms of a gene, indicating completeness of the 5′ termini of those PTs. Meaning of the symbols is the same as those in (a); in addition, the blue boxes stand for proximal promoters determined by CAGE in porcine macrophage, human and mouse cells in the three panels labeled with “Pig CAGE”, “Human CAGE” or “Mouse CAGE”