Extended Data Fig. 9: Comparison of RPM1-like locus and Cytochrome P450  loci in LAB and QLD with other Solanaceae.

(a) Synteny of RPM1-like loci in tomato, N. attenuata, N.tabacum, LAB and QLD. (b) Synteny of a terpene biosynthesis pathway Cytochrome P450 locus in N. attenuata, LAB and QLD. Gene arrangement in cartoon form representing RPM1-like bacterial resistance genes  and CYP736A-like genes (functional - bright green), possibly functional (dark green), defective/pseudogenes (blue). In (A), distances between genes indicated (black text)< 15kbp; (red text) >15kbp and surrounding syntenic genes in are shown in orange, purple, yellow and brown. Orthology/homology relationships are indicated by coloured shading. In (B), distances between genes indicated (black text)< 50kbp; (red text) >50kbp. TE annotation tracks for LAB and QLD were prepared using annotation data from the EDTA TE annotation pipeline (see online Methods) and Geneious Prime software (Geneious Prime 2023.0.1; https://www.geneious.com). Only LTR-transposable elements are shown. Yellow blocks represent GYPSY elements and green blocks represent COPIA elements. The size of each block is proportional to the number of base-pairs annotated for that element. Red triangles represent LTR repeat regions that flank either a GYPSY or COPIA element. These elements are likely to be nearly complete and can be considered possible autonomous elements. The rectangular red blocks flank unknown LTR-TE elements. Unknown TEs are elements that are recognized as an LTR element but are not able to be classified as either a COPIA or GYPSY element due to irregularities in internal sequences for that element. These are likely to represent non-autonomous elements. Those elements not flanked by LTR sequences are highly fragmented nonfunctional elements. The blue rectangular boxes highlight the ___location of the genes annotated in the tracks above and below the TE annotation tracks.