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

Autoři: Andrew C. Read aff001;  Matthew J. Moscou aff002;  Aleksey V. Zimin aff003;  Geo Pertea aff003;  Rachel S. Meyer aff004;  Michael D. Purugganan aff004;  Jan E. Leach aff006;  Lindsay R. Triplett aff006;  Steven L. Salzberg aff003;  Adam J. Bogdanove aff001
Působiště autorů: Plant Pathology and Plant Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States of America aff001;  The Sainsbury Laboratory, University of East Anglia, Norwich, United Kingdom aff002;  Center for Computational Biology, Johns Hopkins University, Baltimore, MD, United States of America aff003;  Center for Genomics and Systems Biology, New York University, New York, NY, United States of America aff004;  Center for Genomics and Biology, New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, United Arab Emirates aff005;  Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, United States of America aff006;  Departments of Biomedical Engineering, Computer Science, and Biostatistics, Johns Hopkins University, Baltimore, MD, United States of America aff007
Vyšlo v časopise: Genome assembly and characterization of a complex zfBED-NLR gene-containing disease resistance locus in Carolina Gold Select rice with Nanopore sequencing. PLoS Genet 16(1): e1008571. doi:10.1371/journal.pgen.1008571
Kategorie: Research Article
doi: 10.1371/journal.pgen.1008571


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.

Klíčová slova:

Genetic loci – Genome sequencing – Phylogenetic analysis – Plant genomics – Protein domains – Rice – Sequence alignment – Sequence assembly tools


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