title: Genomic plasticity enables phenotypic variation of Pseudomonas syringae pv. tomato DC3000.
abstract: Whole genome sequencing revealed the presence of a genomic anomaly in the region of 4.7 to 4.9 Mb of the Pseudomonas syringae pv. tomato (Pst) DC3000 genome. The average read depth coverage of Pst DC3000 whole genome sequencing results suggested that a 165 kb segment of the chromosome had doubled in copy number. Further analysis confirmed the 165 kb duplication and that the two copies were arranged as a direct tandem repeat. Examination of the corresponding locus in Pst NCPPB1106, the parent strain of Pst DC3000, suggested that the 165 kb duplication most likely formed after the two strains diverged via transposition of an ISPsy5 insertion sequence (IS) followed by unequal crossing over between ISPsy5 elements at each end of the duplicated region. Deletion of one copy of the 165 kb region demonstrated that the duplication facilitated enhanced growth in some culture conditions, but did not affect pathogenic growth in host tomato plants. These types of chromosomal structures are predicted to be unstable and we have observed resolution of the 165 kb duplication to single copy and its subsequent re-duplication. These data demonstrate the role of IS elements in recombination events that facilitate genomic reorganization in P. syringae.
authors: Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York, United States of America.
authors: Zhongmeng
authors: Z
authors: Bao
authors: United States Department of Agriculture-Agricultural Research Service, Ithaca, New York, United States of America.
authors: Paul V
authors: PV
authors: Stodghill
authors: Department of Physics, Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, New York, United States of America.
authors: Christopher R
authors: CR
authors: Myers
authors: Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York, United States of America.
authors: Hanh
authors: H
authors: Lam
authors: Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York, United States of America.
authors: Hai-Lei
authors: HL
authors: Wei
authors: Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York, United States of America.
authors: Suma
authors: S
authors: Chakravarthy
authors: MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan, United States of America.
authors: Brian H
authors: BH
authors: Kvitko
authors: Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York, United States of America.
authors: Alan
authors: A
authors: Collmer
authors: Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York, United States of America ; United States Department of Agriculture-Agricultural Research Service, Ithaca, New York, United States of America.
authors: Samuel W
authors: SW
authors: Cartinhour
authors: Biotechnology Resource Center, Cornell University, Ithaca, New York, United States of America.
authors: Peter
authors: P
authors: Schweitzer
authors: Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York, United States of America ; United States Department of Agriculture-Agricultural Research Service, Ithaca, New York, United States of America.
authors: Bryan
authors: B
authors: Swingle
mesh_terms: D000483:Alleles; D020029:Base Pairing / Q000235:genetics; D001483:Base Sequence; D020440:Gene Duplication / Q000235:genetics; D005798:Genes, Bacterial; D056426:Genetic Loci; D016680:Genome, Bacterial / Q000235:genetics*; D018551:Solanum lycopersicum / Q000382:microbiology; D008969:Molecular Sequence Data; D010641:Phenotype; D016133:Polymerase Chain Reaction; D044224:Pseudomonas syringae / Q000166:cytology* / Q000235:genetics* / Q000254:growth & development / Q000302:isolation & purification; D017422:Sequence Analysis, DNA