Genome assembly and characterization of a complex zfBED-NLR gene-containing disease resistance locus in Carolina Gold Select rice with Nanopore sequencing
Year: 2020
Type: article
Abstract: Long-read sequencing facilitates assembly of complex genomic regions. In plants, loci containing nucleotide-binding, leucine-rich repeat (NLR) disease resistance genes are an important example of such regions. NLR genes constitute one of the largest gene families in plants and are often clustered, evolving via duplication, contraction, and transposition. We recently mapped the Xo1 locus for resistance to bacterial blight and bacterial leaf streak, found in the American heirloom rice variety Carolina Gold Select, to a region that in the Nipponbare reference genome is NLR gene-rich. Here, toward identification of the Xo1 gene, we combined Nanopore and Illumina reads and generated a high-quality Carolina Gold Select genome assembly. We identified 529 complete or partial NLR genes and discovered, relative to Nipponbare, an expansion of NLR genes at the Xo1 locus. One of these has high sequence similarity to the cloned, functionally similar Xa1 gene. Both harbor an integrated zfBED domain, and the repeats within each protein are nearly perfect. Across diverse Oryzeae, we identified two sub-clades of NLR genes with these features, varying in the presence of the zfBED domain and the number of repeats. The Carolina Gold Select genome assembly also uncovered at the Xo1 locus a rice blast resistance gene and a gene encoding a polyphenol oxidase (PPO). PPO activity has been used as a marker for blast resistance at the locus in some varieties; however, the Carolina Gold Select sequence revealed a loss-of-function mutation in the PPO gene that breaks this association. Our results demonstrate that whole genome sequencing combining Nanopore and Illumina reads effectively resolves NLR gene loci. Our identification of an Xo1 candidate is an important step toward mechanistic characterization, including the role(s) of the zfBED domain. Finally, the Carolina Gold Select genome assembly will facilitate identification of other useful traits in this historically important variety.
Source: PLoS Genetics
Language: English
Subfield: Plant Science
Domain: Life Sciences
SDG: Zero hunger
Open Access status: gold
Estimated APC paid: $2,500
Funders: National Science Foundation, Foundation for the National Institutes of Health, U.S. Department of Agriculture, Gatsby Charitable Foundation, National Institutes of Health, Directorate for Biological Sciences, National Institute of Food and Agriculture, Biotechnology and Biological Sciences Research Council, National Human Genome Research Institute, National Institute of General Medical Sciences
Awards: G2038832649, G3082350493, G4266696473, G4570290924, Quantitative Trait Locus Editing for Crop Improvement, G5832315372, G7808121326, Recognition, NSF NPGI Postdoctoral Fellowship in Biology FY 2012, Computational Methods for Gene Discovery, Genome Annotation, and Genome Assembly, Computational Methods for Microbial and Microbiome Sequence Analysis
OpenAlex ID: W3001465589