Figure 1.
A. Multi-dimensional topography of tomato chromosome 1 (chromosomes 2-12 are shown in Supplementary Figure 1).
(a) Left: contrast-reversed, DAPI-stained pachytene chromosome; centre and right: FISH signals for repeat sequences on diagrammatic pachytene chromosomes: TGR1 purple, TGR4 blue, telomere repeat red, Cot 100 DNA (including most repeats) green. (b) Frequency distribution of recombination nodules representing crossovers on 249 chromosomes. Red stars mark 5 cM intervals starting from the end of the short arm (top). Scale is in micrometers. (c) FISH-based locations of selected BACs (horizontal blue lines on left). (d) Kazusa F2-2000 linkage map. Blue lines to the left connect linkage map markers on the (c) BAC-FISH map, (e) heat maps and (f) DNA pseudomolecule. (e) From left to right: linkage map distance (cM/Mb, turquoise); repeated sequences (% nucleotides/500 kb, purple); genes (% nucleotides/500 kb, blue); chloroplast insertions; RNA-Seq reads from leaves and breaker fruits of S. lycopersicum and S. pimpinellifolium (number of reads/500 kb, green and red, respectively); microRNA genes (transcripts per million/500 kb, black); small RNAs (thin horizontal black lines, sum of hits-normalized abundances). Horizontal grey lines represent gaps in the pseudomolecule (f). (f) DNA pseudomolecule consisting of nine scaffolds. Unsequenced gaps (approximately 9.8 Mb, Supplementary Table 13) are indicated by white horizontal lines. Tomato genes identified by map-based cloning (Supplementary Table 14) are indicated on the right. For more details, see legend to Supplementary Figure 1.
B. Syntenic relationships in the Solanaceae.
COSII-based comparative maps of potato, eggplant, pepper and Nicotiana with respect to the tomato genome (Supplementary section 4.5, Supplementary Fig. 14). Each tomato chromosome is assigned a different colour and orthologous chromosome segment(s) in other species are shown in the same colour. White dots indicate approximate centromere locations. Each black arrow indicates an inversion relative to tomato and “+1”indicates a minimum of one inversion. Each black bar beside a chromosome indicates translocation breakpoints relative to tomato. Chromosome lengths are not to scale, but segments within chromosomes are.
C. Tomato-potato syntenic relationships.
Dot plot of tomato and potato genomic sequences based on collinear blocks Supplementary Section 4.1). Red and blue dots represent gene pairs with statistically significant high and low ω (Ka/Ks) in collinear blocks, which average Ks≤0.5, respectively. Green and magenta dots represent genes in collinear blocks which average 0.5<Ks≤1.5 and Ks>1.5, respectively. Yellow dots represent all other gene pairs. Blocks circled in red are examples of pan-eudicot triplication. Inserts represent schematic drawings of BAC-FISH patterns of cytologically demonstrated chromosome inversions (also in Supplementary Fig. 15).