Fig. 1
Sequence characterization of the Fusarium wilt resistance I-3 flanking fruit size reducing region. A Dot plot comparison between the reference genome (horizontal) and contigs of Fla. 8814Long (vertical) (A and B). Numbers represent the tomato chromosomes. Sequence similarity is color coded from 0 to 1 (A and B; The summary of identity is placed next to B). B Zoomed in plots (a 14-Mbp interval) capturing the I-3 introgression on chromosome 7. Inferred I-3 introgression (approximately 3.5-Mbp) is depicted by dash arrows. Red arrows indicate the position of the I-3 gene. C: centromere. C Length distribution of 115 gaps found in a 4-Mbp interval of the wild tomato genome carrying the I-3 introgression (gray color) and 36 gaps overlapped by contigs (red color). D Common sequence variant density plot of the Fusarium wilt resistance I-3 introgression. Top and bottom panels show common sequence variants on the basis of alignment to a reference domesticated tomato (i.e., sequence variant found in both Fla. 8814Long and Fla. 8814Short, but not in Fla. 8814None) and to a reference wild tomato (i.e., found in both Fla. 8814Short and Fla. 8814None, but not in Fla. 8814Long), respectively. Inferred I-3 introgression (approximately 3.5-Mbp) is depicted in gray. The approximate locations of I-3 ortholog (Solyc07g055640 between 63,514,724 and 63,521,342 bp; top panel in D) and I-3 (Sopen07g029010 between 74,627,845 and 74,630,497 bp; bottom panel in D and E) are depicted by red lines. See Fig. S3 for the sequence variant density plot for each of Fla. 8814Long, Fla. 8814Short, and Fla. 8814None. Physical positions are based on individual reference genomes. E Locations of structural variants (SVs) (≥50 bp in length) found in Fla. 8814Long only as compared with orthologous DNA sequences (i.e., found in neither Fla. 8814Short nor Fla. 8814None) (orange vertical bars) and found in both Fla. 8814Short and Fla. 8814None, but not in Fla. 8814Long (blue vertical bars). Physical position is based on the reference genome of a wild tomato