Fig. 3.

Gene losses in C. australis. a The principally expressed tissues (PETs) of the respective orthologs of C. australis lost genes in S. lycopersicum and I. nil. The boxes represent different tissues. The respective PETs of the orthogroups, which have no C. australis members, were identified in S. lycopersicum and I. nil. The numbers of orthogroups, which have PETs in leaves, roots, flowers, and other tissues, are shown in the boxes, and the respective percentages (proportional to the areas of the boxes) indicate the ratios between these indicated numbers and the numbers of all orthogroups whose PETs were identified to be the corresponding tissues of I. nil and S. lycopersicum. b Simplified gene network controlling flowering time. Genes in green boxes are retained in C. australis, and the lost ones are in orange boxes. Arrows and T-ends represent promoting and inhibiting genetic interactions, respectively, and round dots at both ends symbolize genetic interactions with unknown directions. c Numbers of genes in the gene families of R genes, TPSs, P450s, and RLKs