Fig. 3

The classification, motif structure, evolutionary dynamics and selection force of the VQ gene family. a The phylogenetic analysis and classification of VQs among 12 species. The tree was constructed using the bootstrap method with a heuristic search of the PAUP 4.0b10 program as described in the Methods. The tree was verified by Bayesian analyses. Ancestral units were defined according to the description by Shiu et al. (2004) [21]. Black, green, red and blue filled circles represent MRCAs in eudicotyledons, monocotyledons, lycopodiophyta, and bryophyta, respectively. Pink filled stars indicate MRCAs of gymnosperm and angiosperm. Clade lines and VQ locus names from dicots, monocots, pine and moss were highlighted by black, green, red and blue colours, respectively. Enlarged phylogenetic tree is available in Additional file 5: Figure S1. b Conserved VQ motif structures of different groups of VQs. The VQ motifs were identified by HMM searched and were confirmed by the Pfam database searches. c The evolutionary dynamics of VQs. The estimated MRCAs were shown by filled circles/stars and the total numbers of VQs were indicated in the brackets following the species names