title: Horizontal Gene Acquisitions, Mobile Element Proliferation, and Genome Decay in the Host-Restricted Plant Pathogen Erwinia Tracheiphila.
abstract: Modern industrial agriculture depends on high-density cultivation of genetically similar crop plants, creating favorable conditions for the emergence of novel pathogens with increased fitness in managed compared with ecologically intact settings. Here, we present the genome sequence of six strains of the cucurbit bacterial wilt pathogen Erwinia tracheiphila (Enterobacteriaceae) isolated from infected squash plants in New York, Pennsylvania, Kentucky, and Michigan. These genomes exhibit a high proportion of recent horizontal gene acquisitions, invasion and remarkable amplification of mobile genetic elements, and pseudogenization of approximately 20% of the coding sequences. These genome attributes indicate that E. tracheiphila recently emerged as a host-restricted pathogen. Furthermore, chromosomal rearrangements associated with phage and transposable element proliferation contribute to substantial differences in gene content and genetic architecture between the six E. tracheiphila strains and other Erwinia species. Together, these data lead us to hypothesize that E. tracheiphila has undergone recent evolution through both genome decay (pseudogenization) and genome expansion (horizontal gene transfer and mobile element amplification). Despite evidence of dramatic genomic changes, the six strains are genetically monomorphic, suggesting a recent population bottleneck and emergence into E. tracheiphila's current ecological niche.
authors.affiliation: Department of Organismic and Evolutionary Biology, Harvard University lori.r.shapiro@gmail.com olgazh@dartmouth.edu.
authors.forename: Lori R
authors.initials: LR
authors.lastname: Shapiro
authors.affiliation: Grain, Forage, and Bioenergy Research Unit, USDA-ARS, Lincoln, Nebraska and Department of Agronomy and Horticulture, University of Nebraska-Lincoln.
authors.forename: Erin D
authors.initials: ED
authors.lastname: Scully
authors.affiliation: Department of Biological Sciences, Dartmouth College.
authors.forename: Timothy J
authors.initials: TJ
authors.lastname: Straub
authors.affiliation: Graduate Program in Bioinformatics and Genomics, Pennsylvania State University Present address: Department of Pediatrics, Massachusetts General Hospital, Boston, Massachusetts.
authors.forename: Jihye
authors.initials: J
authors.lastname: Park
authors.affiliation: Department of Biology, Pennsylvania State University.
authors.forename: Andrew G
authors.initials: AG
authors.lastname: Stephenson
authors.affiliation: Department of Plant Pathology and Microbiology, Iowa State University.
authors.forename: Gwyn A
authors.initials: GA
authors.lastname: Beattie
authors.affiliation: Department of Plant Pathology and Microbiology, Iowa State University.
authors.forename: Mark L
authors.initials: ML
authors.lastname: Gleason
authors.affiliation: Department of Microbiology and Immunology, Harvard Medical School, Boston, Massachusetts.
authors.forename: Roberto
authors.initials: R
authors.lastname: Kolter
authors.affiliation: Department of Molecular and Cellular Biology, Harvard University.
authors.forename: Miguel C
authors.initials: MC
authors.lastname: Coelho
authors.affiliation: Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland.
authors.forename: Consuelo M
authors.initials: CM
authors.lastname: De Moraes
authors.affiliation: Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland.
authors.forename: Mark C
authors.initials: MC
authors.lastname: Mescher
authors.affiliation: Department of Biological Sciences, Dartmouth College Department of Computer Science, Dartmouth College lori.r.shapiro@gmail.com olgazh@dartmouth.edu.
authors.forename: Olga
authors.initials: O
authors.lastname: Zhaxybayeva
mesh_terms: D028464:Cucurbita / Q000235:genetics*; D004885:Erwinia / Q000235:genetics* / Q000472:pathogenicity; D019143:Evolution, Molecular; D022761:Gene Transfer, Horizontal; D018745:Genome, Plant / Q000235:genetics; D054884:Host-Pathogen Interactions / Q000235:genetics; D020071:Interspersed Repetitive Sequences / Q000235:genetics; D010935:Plant Diseases / Q000235:genetics* / Q000469:parasitology
keywords: Cucurbita, Cucumis; Erwinia, mobile DNA; cucumber; host specialization; insertion sequence; monomorphic; phage; pseudogene; pumpkin; squash; transposase; vector