Fig. 3.

Phylogenetic trees of some plant and tomato TPL proteins. (A) Representative phylogenetic tree of TPL proteins from land plants: moss (P. patens, PHYPADRAFT_xxx), lycophyte (Selaginella moellendorffii, SELMODRAFT_xxx), rice (LOC_Os-xxx), tomato (red boxes) and Arabidopsis (green boxes). The coloured brackets emphasize the main branches conserved among angiosperms. The present tree was obtained after alignment of full-length TPL sequences using ClustalW and clustering with the neighbour-joining method. The percentages of replicate trees in which the associated taxa clustered together in the bootstrap test (500 replicates) are shown next to the branches. Phylogenetic analyses including additional genome sets (Z. mays, Sorghum bicolor, Populus trichocarpa, G. max, V. vinifera and M. guttatus) or using the maximum-likelihood clustering method displayed similar topologies, the majority of the nodes being conserved (blue circles) while only few nodes (yellow crosses) were unstable. (B) Phylogenetic tree of TPL proteins among Asterid and Solanaceaous species. The tree was built using sequences from four genomes: Solanum lycopersicon, Solanum tuberosum, N. benthamiana and M. guttatus. (This figure is available in colour at JXB online.)