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Bias in resistance gene prediction due to repeat masking

Abstract

Several recently published Brassicaceae genome annotations show strong differences in resistance (R)-gene content. We believe that this is caused by different approaches to repeat masking. Here we show that some of the repeats stored in public databases used for repeat masking carry pieces of predicted R-gene-related domains, and demonstrate that at least some of the variance in R-gene content in recent genome annotations is caused by using these repeats for repeat masking. We also show that other classes of genes are less affected by this phenomenon, and estimate a false positive rate of R genes (0 to 4.6%) that are in reality transposons carrying the R-gene domains. These results may partially explain why there has been a decrease in published novel R genes in recent years, which has implications for plant breeding, especially in the face of pathogens changing as a response to climate change.

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Data availability

Raw data used in this study are available from RepBase and publicly available annotations8,9,10,13. Additional tables listing Repbase repeats containing R-gene-related repeats, and listing the R-gene candidates for the B. napus and the B. rapa annotations are available at https://doi.org/10.5281/zenodo.1172258.

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Acknowledgements

This work was supported by resources provided by The Pawsey Supercomputing Centre with funding from the Australian Government and the Government of Western Australia. This work was supported by computational resources provided by the Australian Government through FlashLite under the National Computational Merit Allocation Scheme. This research was funded by the Australian Government through the Australian Research Council (FT130100604, DP1601004497, LP140100537, LP160100030). P.E.B. acknowledges the support of the Forrest Research Foundation. The authors would like to thank B. Greshake Tzovaras for his valuable suggestions.

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P.E.B. carried out analysis; P.E.B., D.E. and J.B. wrote the manuscript.

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Correspondence to Jacqueline Batley.

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Bayer, P.E., Edwards, D. & Batley, J. Bias in resistance gene prediction due to repeat masking. Nature Plants 4, 762–765 (2018). https://doi.org/10.1038/s41477-018-0264-0

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