| Summary: | <p>Abstract</p> <p>Background</p> <p>NOD26-like intrinsic proteins (NIPs) that belong to the aquaporin superfamily are plant-specific and exhibit a similar three-dimensional structure. Experimental evidences however revealed that functional divergence should have extensively occurred among NIP genes. It is therefore intriguing to further investigate the evolutionary mechanisms being responsible for the functional diversification of the NIP genes. To better understand this process, a comprehensive analysis including the phylogenetic, positive selection, functional divergence, and transcriptional analysis was carried out.</p> <p>Results</p> <p>The origination of NIPs could be dated back to the primitive land plants, and their diversification would be no younger than the emergence time of the moss <it>P. patens</it>. The rapid proliferation of NIPs in plants may be primarily attributed to the segmental chromosome duplication produced by polyploidy and tandem duplications. The maximum likelihood analysis revealed that <it>NIPs </it>should have experienced strong selective pressure for adaptive evolution after gene duplication and/or speciation, prompting the formation of distinct <it>NIP </it>groups. Functional divergence analysis at the amino acid level has provided strong statistical evidence for shifted evolutionary rate and/or radical change of the physiochemical properties of amino acids after gene duplication, and DIVERGE2 has identified the critical amino acid sites that are thought to be responsible for the divergence for further investigation. The expression of plant NIPs displays a distinct tissue-, cell-type-, and developmental specific pattern, and their responses to various stress treatments are quite different also. The differences in organization of <it>cis</it>-acting regulatory elements in the promoter regions may partially explain their distinction in expression.</p> <p>Conclusion</p> <p>A number of analyses both at the DNA and amino acid sequence levels have provided strong evidences that plant NIPs have suffered a high divergence in function and expression during evolution, which is primarily attributed to the strong positive selection or a rapid change of evolutionary rate and/or physiochemical properties of some critical amino acid sites.</p>
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