No abstract
Background: Reciprocal gene loss (RGL) of duplicate genes is an important genetic resource of reproductive isolation, which is essential for speciation. In the past decades, various RGL patterns have been revealed, but RGL process is still poorly understood. 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, remains unclear. In this study, we investigated the evolutionary history of the duplicate genes for gaining insights into the 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 A- and B-genomic segments containing DPL1 and DPL2 respectively but not between DPL1 and DPL2 segments. Investigations of transposon elements indicated that DPL duplication is related to DNA transposons. Likelihood-based analyses with branch models showed a relaxation of selective constraint in DPL1 lineage but an enhancement in DPL2 lineage after DPL duplication. Sequence analysis also indicated that quite a few defective DPL1 can be found in 6 wild and cultivated species out of all 8 species of A-genome but only one defective DPL2 occurs in a cultivated rice subspecies. Conclusions: DPL duplication of rice originated in the 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 DPLs between two rice subspecies during the domestication.
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
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.
hi@scite.ai
10624 S. Eastern Ave., Ste. A-614
Henderson, NV 89052, USA
Copyright © 2024 scite LLC. All rights reserved.
Made with 💙 for researchers
Part of the Research Solutions Family.