Figure 1.
The copy number of PME and PMEI families in the collected species.
The ultrametric tree was modified from Jiao et al. [23], Popper et al. [4] and Lee et al. [35]. The grey boxes (ζ, ε), diamonds (γ, T) and ellipses (α, β, σ, ρ) show the whole genome duplication events in the species, the red dot indicates when pectins appeared in the cell wall of organisms. -Indicates not detected.
Figure 2.
The intra- and inter-genomic comparison analyses showed gene synteny of the PME and PMEI families in A. thaliana (At), V. vinifera (Vv), O. sativa (Os) and S. bicolor (Sb).
The synteny gene pairs were parsed from the Plant Genome Duplication Database (PGDD). The gray lines indicate whole genome duplication blocks between species, the green lines indicate the synteny of PME genes, the purple lines indicate the synteny of proPME genes, and the red lines indicate the synteny of PMEI genes. (A) gene synteny of PME and PMEI families in A. thaliana (At) and O. sativa (Os), (B) gene synteny of PME and PMEI families in A. thaliana (At) and V. vinifera (Vv), and (C) gene synteny of PME and PMEI families in O. sativa (Os) and S. bicolor (Sb).
Figure 3.
The exon-intron structural analysis of the 23 PME genes in Arabidopsis.
The gene structures were drawn using the online tool GSDS. The legend shows that the blue boxes are UTR regions, the green boxes are exons, the black lines are introns, the red boxes are the PME domains, and numbers at the exon-intron joints are intron phases.
Figure 4.
The molecular phylogenetic analysis of the orthologous PME genes, and pro and PMEI domains.
(A) The phylogenetic analysis of the pro and PMEI domains in 10 species using the neighbor joining method. The blue lines represent the pro domain, and the red lines represent the PMEI domain. (B) The consensus sequence alignment shows the conserved motifs of the pro and PMEI domains in the representative species. The MEME program was then used to verify the conserved motifs.
Figure 5.
The Ka/Ks value distributions of the PME, pro and PMEI domains in 10 species.
The red broken line indicates that genes are under positive selection (more than one) or negative selection (less than one). The short species names are P. patens (Pp), S. moellendorffii (Sm), A. trichopoda (Am), S. bicolor (Sb), O. sativa (Os), S. lycopersicum (Sl), V. vinifera (Vv), P. trichocarpa (Pt), C. papaya (Cp) and A. thaliana (At). The Ka and Ks values were computed using the PAML program.
Figure 6.
The Arabidopsis PME gene network.
Twenty-six PME genes in Arabidopsis were mapped to the ANAP database. This network involves 257 unique genes exhibiting 514 interactions. The red nodes represent the PME genes.