mgu FY2019 Annual Report 5.2 fig2

Figure 2 | Molecular phylogenetic analysis showing lineage-specific evolution of TALE class homeobox proteins in green plants and the ancient plant genomic structure. (a) The maximum-likelihood tree is constructed using multiple alignments of homeodomains. Green symbols show four members of the KNOX class and four of the BEL class in the Caulerpa genome. Nodes with more than 50 and 70% bootstrap support are marked with open and closed circles, respectively. Green, magenta and black lines correspond to chlorophyte, rhodophyte and Arabidopsis sequences, respectively. Ath, Arabidopsis thaliana. Cle, Caulerpa lentillifera. Cme, Cyanidioschyzon merolae. Cre, Chlamydomonas reinhardtii. Ota, Ostreococcus tauri. Vca, Volvox carteri. (b) Origin and evolution of the plant BEL/KNOX family and candidate genes for exploring the duplication mechanism of the ancestral gene. Simplified gene order in the Caulerpa genome is shown above. Scaffold numbers are indicated at the left side. Potential ancestral genomic structures are surrounded by dotted lines. Circles, rectangles and hexagonal boxes in diagrams of genomic sequences indicate protein domains contained in each locus. The synteny diagrams are not drawn to scale. (c) Expression levels of TALE homeobox genes. * indicates P-value <0.05 and false discovery rate <0.05. Two genes, g4802 of BEL, and g2165 of KNOX, show the difference of gene expression level between frond and stolon. Error bars and white circles show standard deviation and TMM-normalized CPM observed in each replicate, respectively.