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

Authors Jothi R, Parthasarathy S, Krishnamurthy K

Published 10 December 2010 Volume 2010:2 Pages 157—168

DOI https://doi.org/10.2147/OAB.S13631

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Ramalingam Jothi1,2, Subbiah Parthasarathy1, Kulithalai Viswanathan Krishnamurthy1
1Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli; 2Department of Zoology, Dharmapuram Gnanambigai Government Arts College (Women), Mayiladuthurai, Tamil Nadu, India

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.

Keywords: extensin, abiotic and biotic stresses, tension wood, circular permutation, unequal crossover, pathogenic resistance

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