Proteases distribute widely in organisms, their catalytic function is to hydrolyze peptide bonds, and they have many important physiological functions. Comparative genomic analysis of proteases between different categories may help us to understand them better. There are three categories of organisms in Platyhelminthes, including the free-living planaria and the parasitic trematode and tapeworm. Although the trematode and tapeworm are both helminths, their living environments and feeding ways are obviously different The differences may result in the proteases producing some corresponding biological characteristics, especially in parasites. We compared the proteases among different platyhelminthes for researching their diversity and respective traits. Then a further research with emphasis onSchistosome proteases for adaptive evolution was done. The followings were concluded: . We firstly perform homologous search on genomes of several platyhelminthes. Then multiple comparison of the functions of thier specific proteases among three categoryies of platyhelminthes was performed. The results of the comparison among planaria, trematode and tapeworm show that planaria have the most proteases, and those proteases have more functions and join more biological processes. Trematode and tapeworm possess of less specific proteases than planaria, their functions are approximately the same as planaria. Compare to trematode and tapeworm, the specific proteases of planaria are mainly have functions on movement, biological adhesion and so on. Those divergences are consistent with the different life styles and living environment between planaria and two parasitic worms. The free-living planaria develop better than trematode and tapeworm in locomotion, nervous system and so on, while the latter degenerate in those ssaspects because of autoeciousness, so planaria have more development protease system. The comparison between trematode and tapeworm found that their proteases are different in several functions, but this functions are mainly basal biological processes. The comparison between Schistosome and Clonorchis sinensis revealed similar numbers and kinds of proteases. This is related to their near evolutionary relationship and similar life styles. We also make a further analysis on proteases of Schistosome, the result revealed that Schistosome proteases have happenedwhich are related to the parasitic life. For example, the cercarlae elastases for degradation of skin are only possessed by trematode. It is beneficial for invasion. The M08 family of Metallo Proteases is expanded in Schistosome, which is also important for invasion. There are a kind of specific Cysteine Protease, Legumain, who play an important role in digestion. In addition, the cathepsin D also play it’s role in digestion. And it was subject to positive selection in history. a series of adaptive evolution
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