Retrotransposon insertions in rice gene pairs associated with reduced conservation of gene pairs in grass genomes

Small-scale changes in gene order and orientation are common in plant genomes, even across relatively short evolutionary distances. We investigated the association of retrotransposons in and near rice gene pairs with gene pair conservation, inversion, rearrangement, and deletion in sorghum, maize, and Brachypodium. Copia and Gypsy LTR-retrotransposon insertions were found to be primarily associated with reduced frequency of gene pair conservation and an increase in both gene pair rearrangement and gene deletions. SINEs are associated with gene pair rearrangement, while LINEs are associated with gene deletions. Despite being more frequently associated with retrotransposons than convergent and tandem pairs, divergent gene pairs showed the least effects from that association. In contrast, convergent pairs were least frequently associated with retrotransposons yet showed the greatest effects. Insertions between genes were associated with the greatest effects on gene pair arrangement, while insertions flanking gene pairs had significant effects only on divergent pairs.

► We investigated the effect of retrotransposon insertions on gene pair conservation.
► LTR-retros are associated with lower gene pair conservation & higher rearrangement.
► Intergenic insertions show highest correlation with reduced gene pair conservation.
► Insertions flanking gene pairs correlate with reduced divergent pair conservation.