Journal
NATURE PLANTS
Volume 4, Issue 10, Pages 762-765Publisher
NATURE PUBLISHING GROUP
DOI: 10.1038/s41477-018-0264-0
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Funding
- Pawsey Supercomputing Centre
- Australian Government
- Government of Western Australia
- Australian Government through the Australian Research Council [FT130100604, DP1601004497, LP140100537, LP160100030]
- Forrest Research Foundation
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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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