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Characterization of a bacterial leaf streak of rice resistance locus aided by nanopore sequencing

Andrew Read: Cornell University

<div>Nanopore sequencing runs generate gigabases of data with average read-lengths limited only by the input DNA library (often well over 20 kb). This sequencing technology is suited for resolving challenging sequences including large, repetitive, and rapidly evolving gene families such as the plant nucleotide-binding leucine-rich repeat (NLR) defense genes. We utilized the Oxford Nanopore Technologies USB powered MinION sequencer to generate a draft genome of the American heirloom rice cultivar Carolina Gold Select. The long reads generated by this technology allow assembly of the multiple NLR-encoding ~1 Mb <em>Xo1</em> resistance locus. The <em>Xo1</em> locus is effective at controlling African strains of the bacterial leaf streak pathogen <em>Xanthomonas oryzae pv. oryzicola</em> (Xoc). Our group recently demonstrated that <em>Xo1</em> resistance can be overcome by a truncated TAL effector (truncTALE) from Asian Xoc strains, explaining why <em>Xo1</em> is not effective against these strains. Knowledge of the genes underlying the <em>Xo1</em> locus empowers our functional studies exploring how resistance is triggered by TAL effectors and suppressed by truncTALEs. We have cloned a candidate NLR from the <em>Xo1</em> locus and begun sub-cellular localization and interaction studies. We believe that nanopore sequencing is a powerful tool for rapid determination of the genes in mapped resistance loci and will accelerate the functional analysis of candidate genes.</div>