Journal Article

Genome assembly and characterization of a complex zfBED-NLR gene-containing disease resistance locus in Carolina Gold Select rice with Nanopore sequencing

Pertea, Geo, Meyer, Rachel S., Leach, Jan E., Purugganan, Michael D., Salzberg, Steven L., Triplett, Lindsay R., Moscou, Matthew J., Read, Andrew C., Zimin, Aleksey V., Bogdanove, Adam J.

2020

Overview

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.

• Publisher: Public Library of Science,Public Library of Science (PLoS)
• Subject: Biology / Biology and Life Sciences / Blight / Characterization / Computer and Information Sciences / Contraction / Deoxyribonucleic acid / Disease Resistance / Diseases / DNA / DNA sequencing / Engineering and Technology / Explosions / Funding / Gene families / Gene loci / Genes / Genetic aspects / Genomes / Genomics / Gold / Leaf streak / Leucine / Molecular Sequence Annotation / Nanopore Sequencing - methods / NLR Proteins - chemistry / NLR Proteins - genetics / NLR Proteins - metabolism / Oryza - genetics / Oryza - immunology / Oxidases / Pathogens / Plant diseases / Plant genetics / Plant pathology / Plant Proteins - chemistry / Plant Proteins - genetics / Plant Proteins - metabolism / Plant sciences / Polyphenol oxidase / Proteins / Research and Analysis Methods / Rice blast / Supervision / Transposition / Whole genome sequencing / Whole Genome Sequencing - methods / Zinc Fingers