title: Single molecule real-time sequencing ofXanthomonas oryzaegenomes reveals a dynamic structure and complex TAL (transcription activator-like) effector gene relationships.
abstract: Pathogen-injected, direct transcriptional activators of host genes, TAL (transcription activator-like) effectors play determinative roles in plant diseases caused byXanthomonasspp. 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,talgene contigs, we correctly assembledde novothe genomes of two strains of the rice pathogenX. oryzaecompleted 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 intalgene content. Our results pave the way for population-level studies to inform resistance breeding, improve biotechnology and probe TAL effector evolution.
authors.affiliation: Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA.
authors.forename: Nicholas J
authors.initials: NJ
authors.lastname: Booher
authors.affiliation: Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA.
authors.forename: Sara C D
authors.initials: SCD
authors.lastname: Carpenter
authors.affiliation: 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.
authors.forename: Robert P
authors.initials: RP
authors.lastname: Sebra
authors.affiliation: Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA.
authors.forename: Li
authors.initials: L
authors.lastname: Wang
authors.affiliation: Departments of Biomedical Engineering, Computer Science, and Biostatistics and Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21205, USA.
authors.forename: Steven L
authors.initials: SL
authors.lastname: Salzberg
authors.affiliation: Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO 80523, USA.
authors.forename: Jan E
authors.initials: JE
authors.lastname: Leach
authors.affiliation: Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA.
authors.forename: Adam J
authors.initials: AJ
authors.lastname: Bogdanove
keywords: PacBio; SMRT; TAL effectors; Xanthomonas; single molecule real-time sequencing; whole gene assembly