Functional and Structural Divergence of an Unusual LTR Retrotransposon Family in Plants

<div><p>Retrotransposons with long terminal repeats (LTRs) more than 3 kb are not frequent in most eukaryotic genomes. Rice LTR retrotransposon, <em>Retrosat2</em>, has LTRs greater than 3.2 kb and two open reading frames (ORF): ORF1 encodes enzymes for retrotransposition whereas no function can be assigned to ORF0 as it is not found in any other organism. A variety of experimental and <em>in silico</em> approaches were used to determine the origin of <em>Retrosat2</em> and putative function of ORF0. Our data show that not only is <em>Retrosat2</em> highly abundant in the <em>Oryza</em> genus, it may yet be active in rice. Homologs of <em>Retrosat2</em> were identified in maize, sorghum, Arabidopsis and other plant genomes suggesting that the <em>Retrosat2</em> family is of ancient origin. Several putatively cis-acting elements, some multicopy, that regulate retrotransposon replication or responsiveness to environmental factors were found in the LTRs of <em>Retrosat2</em>. Unlike the ORF1, the ORF0 sequences from <em>Retrosat2</em> and homologs are divergent at the sequence level, 3D-structures and predicted biological functions. In contrast to other retrotransposon families, <em>Retrosat2</em> and its homologs are dispersed throughout genomes and not concentrated in the specific chromosomal regions, such as centromeres. The genomic distribution of <em>Retrosat2</em> homologs varies across species which likely reflects the differing evolutionary trajectories of this retrotransposon family across diverse species.</p>