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correspondence: subbiah Parthasarathy Department of Bioinformatics, school of Life sciences, Bharathidasan University, Tiruchirappalli 620 024, Tamil nadu, india Tel +91 944 353 3095 Fax +91 431 240 7045 email bdupartha@gmail.com Abstract: Extensins are hydroxyproline-rich glycoproteins present in the plant cell wall. Accelerated evolution and the role of extensins involved in abiotic stresses, like gravitational stress and tension wood formation, and biotic stress, like pathogenic resistance, were investigated through computational internal sequence repeats analysis of their sequences. Multiple sequence alignment analysis of extensin-1 and extensin-2, present in both herbs and trees, was used to investigate their role in gravitational stress and tension wood formation. The role of extensins in pathogenic resistance was investigated by showing the existence of circular permutation in both extensin-1 and extensin-2 sequences between plants of Fabaceae. It was analyzed through Dot plots, and the study predicted that many partial circular permutations exist between sequences of different length. The clustering study of the internal sequence repeats of extensin family through phylogenetic analysis and reconstruction of patterns of repeat identities between sequences showed that unequal crossover exists in extensin-2. From the existence of unequal crossover nature in the circularly permuted extensin-2, accelerated evolution is indicated by the pattern of repeats in herbaceous plants of the Fabaceae family and trees of different taxa, in addition to pathogenic resistance.

Computational internal sequence repeats analysis of accelerated evolution and the role of extensins under abiotic and biotic stresses