DOI: 10.5061/dryad.v7h28
title: Data from: Horizontal gene acquisitions, mobile element proliferation, and genome decay in the host - restricted plant pathogen Erwinia tracheiphila

description: 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 to
 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 ~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 contributes 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 via 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.
description: HopV1-trimAligned and trimmed alignment of putative T3SS effector HopVI found in the E. tracheiphila genomeBHKY-assemblyE. tracheiphila strain BHKY hybrid mapping + deNovo assembly fasta fileMISpSq-assemblyE. tracheiphila strain MISpSq hybrid assembly from mapping + deNovo assembly of Illumina short readsNYZuch1-assemblyHybrid mapping and deNovo assembly file for E. tracheiphila strain NYZuch1ppHow2-assemblyE. tracheiphila genome assembly for strain ppHow2, from a hybrid mapping + deNovo assemblyGZ4-assemblyE. tracheiphila strain GZ4 assembly file in fasta format, generated by a hybrid mapping + deNovo strategycore_Enterobactericeae_alignmentCore Enterobacteriaceae alignment used to create figure 2. Relevant methods are in the 'Methods' section of the publicationcore_Erwinia_Pantoea_AlignmentsCore genome alignment of the Erwinia/Pantoea clade used to create figure 4. Relevant methods are in the 'methods' section of the publicationSupplemental_File_1File describing the exact parameters for the hybrid mapping + deNovo assembly using Mira 4.1, as described in the 'Methods' section of the accompanying publicationEt.Etrach_0.finalManual annotation of Contig 0, E. tracheiphila reference strain BuffGHEt.Etrach_1.finalManually corrected annotation of Contig 1, reference strain BuffGHEt.Etrach_2.finalManually corrected annotation of E. tracheiphila BuffGH contig 2Et.Etrach_3.finalManual corrections of annotations for E. tracheiphila BuffGH reference strain, contig 3Et.Etrach_4.finalManually corrected annotation file for contig 4 of E. tracheiphila reference genome BuffGHEt.Etrach_5.finalE. tracheiphila manual annotations of reference strain BuffGH, contig 5Et.Etrach_6.finalManual annotations of E. tracheiphila reference genome BuffGH, contig 6Etracheiphila_BuffGHErwinia tracheiphila embl file with four merged chromosomal contigs for viewing and editing as a single file in Artemis software from Sanger Institute.