Identification, characterization and evolutionary origin of LTR retro-elements in pea aphid and human

Mobile genetic elements are DNA sequences that have the ability to move around the genome using unique mechanisms of inserting in a random manner which can bring deleterious effects to the host. The process by which they operate is called transposition and based on the way they transpose, they are classified into two categories. The sequences that ‘copy and paste’ themselves by reverse transcribing within the genome are called retrotransposons. These elements include LTR and non LTRs like LINEs and SINEs. The types of sequences that cut and paste simply by inserting themselves are called DNA transposons. Mobile genetic elements (MGEs) are abundant selfish components of living organisms that can eventually supply functional substrate to the host genome in order to generate new functions through a process called domestication. This process occurs when MGE genes or domains become co-opted into functional host proteins(Volff, 2006). Although the conventional belief of evolution is by offspring or lineage specific, there are increasing evidences of reticulate mechanism of gene transfer, which is one of the main discussions in this project. In this study I focused on DNA transposons and LTR retroelements from the pea aphid and human. The pea aphid was annotated with respect to LTRs, such as the Ty1/Copia, Ty3/Gypsy and Bel/Pao elements. I examined the evolutionary relationships of GIN/GINGER integrases (INTs) and transposases (TRs), which are briefly described in introductory section. Multiple alignments and phylogenetic analysis reveal that GINGER2 transposons of A. pisum are closely related to the SCAN/KRAB cellular integrases of mammals, suggesting a horizontal gene transfer from insects to mammals, a transfer that is believed to have occurred prior to the metatherian-eutherian spilt. We also discovered that the C-terminal region of SCAND3, the hATd domain, is related to another set of transposons, SPIN/Buster. We also hypothesize here that the SCAND3 transposon is not only a GINGER2 domesticated transposon but also a hybrid between GINGER2 and SPIN/Buster. The annotation of the human genome is improved with respect to LTRs, with the help of Repbase, RepeatMasker and BLAST. Analysis of these results revealed two previously uncharacterized families of LTRs. Each of these novel sequences may be classified in either of two different structural variants. One of these variants contains a zinc finger domain that is characterized as a conserved GVQW motif of genus Homo