Abstract：In this paper, to study the molecular evolution patterns of polygalacturonases and the feasibility of using polygalacturonases gene to study species phylogeny, we collected 88 polygalacturonases sequences of bacteria, fungi, and plants from GenBank、EMBL and DDBJ database and constructed the phylogenetic tree. All sequence alignments were performed using the program CLUSTAL W, and the methods used for building the evolutionary trees was the neighboring-joining (N-J) method. The amino acid sequence alignment of all polygalacturonases sequences confirmed that there were four strictly conserved sequence segments (175NTD, 197DD, 218GHG, 250RIK). And conserved cysteines were also found. However, the conservation of cysteines reflects taxonomy, and the corresponding sites could be conserved only in the frames of the respective bacterial, fungal and plant groups. There is no one cysteine residue conserved out all the polygalacturonases. The evolutionary tree reflects both the taxonomy and specificity so that bacterial, fungal and plant enzymes form their own clusters, the endo- and the exo-mode of action being respected, too.
