Fig. 3

Unrooted phylogeny of individual LysM-RLK domains. Phylogeny of amino acid sequences of each of the three LysM-RLK protein domains from each of the canonical LysM-RLKs of Solanum lycopersicum (Sl), Arabidopsis thaliana (At), Lotus japonicus (Lj), Oryza sativa (Os), and Medicago truncatula (Mt). Each gene is represented three times in the tree, once for each individual LysM domain (see emphasis on SlLYK3 in phylogeny), with color-coding by domain position. The phylogeny and 500 bootstrap replicates were inferred using RAxML under the WAG model with empirical frequencies and seed values of 100. The Log-likelihood was −13,081. The scale bar indicates amino acid substitutions per site. Sequences from the first, second, and third LysM domains generally cluster in clades with others of the corresponding LysM domain, but the first and third domains do not form separate clades. Especially long branches subtend the groups of the first and second domains of genes of interest, referred to as the red clade and the black clade. Domain sequences from the red clade are highlighted in red: AtLYK3, SlLYK3, LjLYS4, and LjLYS5. Those from the black clade are highlighted in black: OsLYK1, MtLYK10, SlLYK14, and LjLYS3. The third domain of OsLYK1 and first domain of LjLYS3 are separated from the corresponding domains of the second group