Figure 1.

The phylogeny of LBD proteins in 18 genome-available plant species. The phylogenetic tree was reconstructed using aligned amino acid sequences of LOB domains. We reconstructed the hidden Markov model (HMM) of LBD domain using hmmbuild (HMMer package) with 163 seed sequences belonging to the LBD gene family (PF03195) in the Pfam database. All collected protein sequences of LBD candidates were aligned to the above HMM LBD domain by hmmalign (HMMer package). A maximum likelihood (ML) tree was constructed using the PhyML program with JTT model and 100 times of bootstrap replicates. Colored taxon names indicate the presence of Class IA1 (IA1-1, IA1-2) (blue), Class IA2 (orange), Class IB (yellow), Class IC1/D (IC1/D-1, IC1/D-2, and IC1/D-4)(cyan) without IC1/D-3 (black), Class IC2 (purple), Class IE (green), Class IIA (black) and Class IIB (red).