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Microb Genom. 2015 Oct;1(4). doi: 10.1099/mgen.0.000032. Epub 2015 Oct 13.

Single molecule real-time sequencing of Xanthomonas oryzae genomes reveals a dynamic structure and complex TAL (transcription activator-like) effector gene relationships.

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Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA.
Icahn Institute for Genomics and Multiscale Biology and Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Departments of Biomedical Engineering, Computer Science, and Biostatistics and Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21205, USA.
Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO 80523, USA.


Pathogen-injected, direct transcriptional activators of host genes, TAL (transcription activator-like) effectors play determinative roles in plant diseases caused by Xanthomonas spp. A large domain of nearly identical, 33-35 aa repeats in each protein mediates DNA recognition. This modularity makes TAL effectors customizable and thus important also in biotechnology. However, the repeats render TAL effector (tal) genes nearly impossible to assemble using next-generation, short reads. Here, we demonstrate that long-read, single molecule real-time (SMRT) sequencing solves this problem. Taking an ensemble approach to first generate local, tal gene contigs, we correctly assembled de novo the genomes of two strains of the rice pathogen X. oryzae completed previously using the Sanger method and even identified errors in those references. Sequencing two more strains revealed a dynamic genome structure and a striking plasticity in tal gene content. Our results pave the way for population-level studies to inform resistance breeding, improve biotechnology and probe TAL effector evolution.


PacBio; SMRT; TAL effectors; Xanthomonas; single molecule real-time sequencing; whole gene assembly

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