DOI: 10.5061/dryad.xgxd254r4
title: The consolidated and reconciled annotations from all of the WGS strains used in this study

description: Pantoea agglomerans is one of four Pantoea species reported in the USA to
 cause bacterial rot of onion bulbs. However, not all P. agglomerans
 strains are pathogenic to onion. We characterized onion-associated strains
 of Pagg to elucidate the genetic and genomic signatures of
 onion-pathogenic P. agglomerans. We collected &gt;300 P. agglomerans
 strains associated with symptomatic onion plants and bulbs from public
 culture collections, research laboratories, and a multi-year survey in 11
 states in the USA. Combining the 87 genome assemblies with 100
 high-quality, public P. agglomerans genome assemblies we identified two
 well-supported P. agglomerans phylogroups. Strains causing severe symptoms
 on onion were only identified in Phylogroup II and encoded the HiVir
 pantaphos biosynthetic cluster, supporting the role of HiVir as a
 pathogenicity factor. The P. agglomerans HiVir cluster was encoded in two
 distinct plasmid contexts: 1) as an accessory gene cluster on a conserved
 P. agglomerans plasmid (pAggl), or 2) on a mosaic cluster of plasmids
 common among onion strains (pOnion). Analysis of closed genomes revealed
 that the pOnion plasmids harbored alt genes conferring tolerance to Allium
 thiosulfinate defensive chemistry and many harbored cop genes conferring
 resistance to copper. We demonstrated that the pOnion plasmid pCB1C can
 act as a natively mobilizable pathogenicity plasmid that transforms P.
 agglomerans Phylogroup I strains, including environmental strains, into
 virulent pathogens of onion. This work indicates a central role for
 plasmids and plasmid ecology in mediating P. agglomerans interactions with
 onion plants, with potential implications for onion bacterial disease
 management.
description: Eighty-one genomes assembled as part of this study were combined
 with 100 high-quality genome assemblies from NCBI Genbank (Table S3).
 Genomes were re-annotated with Prokka [@Seemann2014] for pangenome
 analysis with Roary [@Page2015] to identify core and accessory genes.
 Custom scripts were used to reconcile the CDS records of the Prokka,
 Genbank, and RefSeq annotations for each genome. For the process, CDS
 records were considered to be synonymous, if the coordinates for their
 stop codon were equal. If the coordinates of the start codon of synonymous
 CDS records were not equal, the records were marked as
 "interesting".
description: #### **`DatasetS1.zip`** This dataset contains the consolidated and
 reconciled annotations from all of the WGS strains of *Pantoea*
 *agglomerans* used in this study. In this study, Prokka was used,
 independently, by both the UGA and USDA authors to reannotate genomes for
 input to Roary
 ([https://dx.doi.org/10.1093/bioinformatics/btv421](https://dx.doi.org/10.1093/bioinformatics/btv421). For genomes available from NCBI, both GenBank and RefSeq annotations are available. Hence, for each genome, multiple sets of gene annotations are available. The ZIP file `DatasetS1.zip` contains 187 tab-separated values (`.tsv`) files, one for each of the 187 genomes analyzed by Roary in this study. For each WGS strain, we have provided a table (i.e., `.tsv` file) listing which CDS annotations are equivalent in the available annotation sets. That is, each row of each table lists the equivalent annotations for each CDS. Annotations are considered equivalent if they refer to CDS features whose amino acid sequences are equal. A number of attributes are reported for each set of equivalent CDS. For instance, below is the set (i.e., row) of results reported in `AR1a.tsv`. For ease of reading, this row and the corresponding column headers have been transposed (i.e., each row of this table corresponds to a row `AR1a.tsv`. | column | value | | :------------------------- | :------------------------------------------------------- | | `interesting` | | | `genbank_ncbi:locus_tag` | H0Z11\_03125 | | `genbank_ncbi:gene` | | | `genbank_ncbi:product` | aspartate aminotransferase family protein | | `prokka_plaster:locus_tag` | OFPLNBHF\_00389 | | `prokka_plaster:gene` | argD | | `prokka_plaster:product` | Acetylornithine/succinyldiaminopimelate aminotransferase | | `prokka_roary:locus_tag` | DBIDKNDH\_00633 | | `prokka_roary:gene` | argD | | `prokka_roary:product` | Acetylornithine/succinyldiaminopimelate aminotransferase | | `refseq:locus_tag` | H0Z11\_RS03125 | | `refseq:gene` | | | `refseq:product` | aspartate aminotransferase family protein | | `aa_seq` | MAAEKIAVTRETFDNV\[...] | Four sets of annotations are reported for each CDS: * `genbank_ncbi` - The annotations found in the GenBank version of the NCBI assembly * `refesq` - The annotations found in the RefSeq version of the NCBI assembly. * `prokka_roary` - The Prokka annotations generated for the whole-genome Roary pangenome analysis. * `prokka_plaster` - The Prokka annotations generated for the replicon-level, "plaster"-level Roary pangenome analysis. The whole-genome and replicon-level Roary pangenome analyses were performed separately in two different labs. By the time it was realized that both sets of results were to be reported in this study, it was not practical to rerun both analyses using a single set of Prokka annotations. For each set of annotations, the following values are reports: * `locus_tag` - the unique locus tag assigned by the respective annotation pipeline. * `gene` - the human-friendly gene name assigned by the respective annotation pipeline, if one exists. * `product` - a description of the protein predicted by the respective annotation pipeline, if one exists. In addition to these, there are two additional columns: * `interesting` - a `*` will appear in this column if the CDS is found to be "interested". This happens when annotations for the CDS are missing from one or more sets of annotations. * `aa` - the amino acid sequence of the CDS.