Fig. 2

The sd1 exon to exon gene diagrams of TN1, IR8 and Nipponbare. TN1 (2337 bp), IR8 (2335 bp), and Nipponbare (2,743 bp). a Nipponbare vs TN1 and b Nipponbare vs IR8. Os01t0883800-02 is from Nipponbare, OsTN1t004133.1 is from TN1, and OsIR8_01T0407900.1 is from IR8. These names are based on the transcript ids of their sd1 gene. Numbers indicate the exon boundaries of the genes. For TN1 position 1 is at 40,361,934 bp, while for IR8 position 1 is at 39,824,196 bp. In Nipponbare, position 1 is at 38,382,466. The gene diagrams were created by GenePainter (Hammesfahr et al. 2013) by using the protein alignments of sd1 and the information from their gff annotation (Nagano et al. 2005; Panibe et al. 2021). The range specified by the light blue arrow represents the sequences of sd1 in TN1 and IR8 that were validated by our Sanger sequencing. The 382 bp deletion in TN1 can be derived by computing the difference between 981 and 599, the latter of which represents the gene length of TN1 sd1 before its 2nd intron