Figure 1
The origin of allelic specific and shared LTR retrotransposons. Case A: The origin of a specific element. Site t (grey triangles) in the common ancestor corresponds t1 and t2 in the two descendants. After two genomes diverge, an specific element e2 inserts at t2. This pair of alleles shows well-matched flanking sequences (white regions) with e2 being the alignment indel. Case B: The origin of a pair of shared elements. e inserts into the common ancestor and has e1 and e2 as its orthologous descendants. Case C: ISNR between a pair of shared elements. In recombination, loc2 is converted by loc1 and the sequence of loc2 become identical with that of loc1. Specifically, e2 is converted by e1.