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Analysis of Sequence Polymorphism of LINEs and SINEs in Entamoeba histolytica

The goal of this dissertation is to study the sequence polymorphism in retrotransposable elements of Entamoeba histolytica. The Quasispecies theory, a concept of equilibrium (stationary), has been used to understand the behaviour of these elements. Two datasets of retrotransposons of Entamoeba histolytica have been used. We present results from both datasets of retrotransposons (SINE1s) of E. histolytica. We have calculated the mutation rate of EhSINE1s for both datasets and drawn a phylogenetic tree for newly determined EhSINE1s (dataset II). We have also discussed the variation in lengths of EhSINE1s for both datasets. Using the quasispecies model, we have shown how sequences of SINE1s vary within the population. The outputs of the quasispecies model are discussed in the presence and the absence of back mutation by taking different values of fitness. From our study of Non-long terminal repeat retrotransposons (LINEs and their non-autonomous partner's SINEs) of Entamoeba histolytica, we can conclude that an active EhSINE can generate very similar copies of itself by retrotransposition. Due to this reason, it increases mutations which give the result of sequence polymorphism. We have concluded that the mutation rate of SINE is very high. This high mutation rate provides an idea for the existence of SINEs, which may affect the genetic analysis of EhSINE1 ancestries, and calculation of phylogenetic distances.

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