Bioinformatic analysis of Arabidopsis reverse transcriptases with a zinc-finger domain

Plants, as most eukaryotic organisms, harbor several genes encoding a reverse transcriptase domain. The majority of them are part of transposable elements (TEs) and/or retroviral genomes that have been inserted into their genomes. However, there are some examples of RT domain-containing genes that have been endogenized during plant evolution; these genes appear to display functions other than “selfish” maintenance and replication of TEs, and subjected to host gene regulation. In the present work we have analyzed a subset of genes in Arabidopsis with an RT domain (RVT) containing a zinc finger motif (Znf), termed RVT-Znf domain, with structural characteristics of endogenous genes i.e., contain potential upstream regions as well as 5’UTR, and 3’UTR, and are not flanked by retroelement features. Phylogenetic analysis of these genes, based on the RVT-Znf domain, indicates that there are three clades, the members of which having additional domains. When compared to additional sequences, RVT-Znf formed a cluster that is more closely related to non-LTR retrotransposons and group II introns. Extant data from microarray databases indicate that several Arabidopsis genes are expressed. These data indicate that these RTs may have been endogenized. Possible roles for these genes are discussed.