Fig. 3: Examples of known genes with improved annotations or newly identified genes.

a IGV view of the RNA-seq reads for the two adjacent genes (FvH4_1g14650 and FvH4_1g14660) with changed gene models in v4.0.a2 vs v4.0.a1 in the tissue “SAM”. b Gene models of two MYB genes that were specifically expressed in roots. c Gene models of three newly identified genes encoding FAR1 family proteins in the tissue “SAM”. Gray peaks indicate read coverage. Pink bars indicate the aligned reads. Blue bars indicate exons in v4.0.a1. Orange bars indicate exons in v4.0.a2. The thinner orange bars indicate UTRs. “t1”–“t7” under each gene model indicate different isoforms. d, Gel image showing the amplified products of the seven genes. The sizes of the products are 924 bp, 1,473 bp, 1,050 bp, 846 bp, 2,685 bp, 2,505 bp, and 2,601 bp, respectively