Insights on the forming process of reciprocal gene loss in the duplicate DPL genes of rice

Abstract Background Reciprocal gene loss (RGL) of duplicate genes is an important genetic source of reproductive isolation, but the forming process of RGL remains poorly understood, particularly when concerning a single gene duplication. The RGL of the duplicate DOPPELGANGER1 ( DPL1 ) and DOPPELGANGER2 ( DPL2 ) gene can lead to BDM-type hybrid incompatibility between two rice subspecies. The evolutionary history of the duplicate genes, including their origin and mechanism of duplication as well as their evolutionary divergence after the duplication, is crucial for understanding the RGL process. Thus, we attempted to elucidate the evolutionary history of the duplicate genes for gaining insights into the forming process of RGL. Results We reconstructed phylogenetic relationships of DPL copies from all 15 diploid species representing six genome types of rice genus and then found that all the DPL copies from the latest diverged A- and B-genome gather into one monophyletic clade. Southern blot analysis also detected definitely two DPL copies only in A- and B-genome. High conserved collinearity can be observed between the DPL1 segments of A- and B-genome and between the DPL 2 segments of A- and B-genome respectively but not between DPL1 and DPL2 segments. Investigations of transposon elements indicated that DPL duplication is more likely to be produced by DNA transposons. Likelihood-based analyses with branch models showed a relaxation of selective strength on DPL1 lineage but an enhancement of selective constraint on DPL2 lineage after DPL duplication. Sequence analysis also indicated that defective DPL1 can be found in six wild and cultivated species out of the eight species of A-genome but only one defective DPL2 occurs in a cultivated rice subspecies. Conclusions DPL duplication of rice originated in the most recent common ancestor of A- and B-genome about 6.76 million years ago and the duplication was possibly caused by DNA transposons. The DPL1 is a redundant copy and has being in the process of pseudogenization, suggesting that artificial selection may play an important role in forming the RGL of DPL genes between two rice subspecies during the domestication. Keywords: Reciprocal gene loss, Gene duplication, Evolution history, DPL , Rice