DOI: 10.5061/dryad.59zw3r2nw
title: Data from: Genome resources of <em>Xanthomonas vasicola</em> strains from various hosts: Reference-guided chromosome and plasmid assemblies for enhanced pathogen genomics

description: This dataset comprises eleven whole-genome assemblies of Xanthomonas
 vasicola strains isolated from four economically important hosts:
 Eucalyptus spp., maize, sorghum, and sugarcane. Included in this dataset
 are FASTA files of the assembled chromosome and plasmid sequences for each
 strain. All the assemblies are chromosome-level, with the contigs
 assembled into a single chromosome using reference-guided scaffolding. The
 assemblies were generated from Illumina short-read data using a pipeline
 that included an initial de novo assembly performed with Unicycler,
 reference-guided scaffolding of chromosomes using Ragout, and iterative
 plasmid discovery and assembly using BLAST against the PLSDB database and
 Ragtag.
description: # Genome assemblies of *Xanthomonas vasicola* strains from multiple host
 plants ##### Chromosome-scale and plasmid genome assemblies of eleven
 *Xanthomonas vasicola* strains isolated from *Eucalyptus*, maize, sorghum
 and sugarcane ## Overview This dataset contains the whole-genome
 assemblies for eleven strains of the plant pathogen *Xanthomonas
 vasicola*, isolated from four different host plants: *Eucalyptus* spp.,
 maize, sorghum, and sugarcane. These chromosome-scale and plasmid
 assemblies provide a resource for comparative genomics, host adaptation
 studies, virulence gene analysis, and evolutionary research. These are the
 **final, revised assemblies** associated with the accepted manuscript. ##
 Corresponding Manuscript **Genome resources of** ***Xanthomonas
 vasicola*** **strains from various hosts: reference-guided chromosome and
 plasmid assemblies for enhanced pathogen genomics**\ Nomakula Y. Zim, Anna
 E. J. Yssel, and Teresa A. Coutinho\ *Journal of Plant Pathology* (2025,
 Accepted) ## Data and Code Availability * **Genome Assemblies (this
 dataset):**\ This repository contains the final FASTA files for all
 chromosome and plasmid assemblies. * **NCBI GenBank:**\ Assemblies have
 been submitted to GenBank under BioProject **PRJNA1195417**.\ At the time
 of Dryad data submission, the public release on GenBank is pending;
 therefore, the Dryad files indicate the authoritative versions associated
 with the publication. * **Analysis Code:**\ All scripts, environments, and
 workflow materials are permanently archived on Zenodo:\
 [https://doi.org/10.5281/zenodo.17634337](https://doi.org/10.5281/zenodo.17634337) ## File Manifest and Structure This dataset includes the chromosome and plasmid assemblies for 11 *Xanthomonas vasicola* strains.\ All sequences are in FASTA format. Filenames correspond to the strain name and plasmid identifier. ### Included Files **Chromosome assemblies** * `BCC42.fasta` * `BCC169.fasta` * `BCC448.fasta` * `BCC510.fasta` * `BCC516.fasta` * `BCC777.fasta` * `BCC931.fasta` * `BCC932.fasta` * `BCC1689.fasta` * `J5.fasta` * `J12.fasta` **Plasmid assemblies** * `BCC42_pLMG911.2.fasta` * `BCC42_pXvvA1.fasta` * `BCC42_pXvvB1.fasta` * `BCC169_pXvvC.fasta` * `BCC448_pXvvD.fasta` * `BCC510_pXvvA2.fasta` * `BCC510_pXvvE.fasta` * `BCC510_pXvvF.fasta` * `BCC510_pXvvG.fasta` * `BCC516_pXvhA.fasta` * `BCC516_pXvhB.fasta` * `BCC777_pXvhA.fasta` * `BCC777_pXvhB.fasta` * `BCC931_pLMG911.2.fasta` * `BCC931_pXvvB2.fasta` * `BCC932_pLMG911.2.fasta` * `BCC932_pXvvB3.fasta` * `BCC1689_pXvvH.fasta` * `J5_pLMG911.2.fasta` * `J5_pXvvA3.fasta` * `J5_pXvvB4_.fasta` * `J5_pXvvF.fasta` * `J12_pLMG911.2.fasta` * `J12_pXvvA4.fasta` * `J12_pXvvB5.fasta` * `J12_pXvvF.fasta` **Metadata file** * `metadata.csv` Each FASTA file represents a completed, circularised assembly. The plasmid filenames indicate the corresponding plasmid names (e.g., `pXvvA1`, `pLMG911.2`).\ The `metadata.csv` file links strain names to host species, genome sizes, N50 values,and plasmid counts. ## Column Descriptions for `metadata.csv` This file contains key information for each assembled strain: * `Strain_name`: Strain identifier (matches FASTA prefix). * `Host_of_isolation`: Host plant (*Eucalyptus*, maize, sorghum, or sugarcane). * `Genome_size_Mbp`: Total length of the assembly in base pairs. * `GC_mol%`: GC content of the assembly, expressed as a percentage. * `Contig_N50`: N50 of the initial Unicycler contigs (before scaffolding). * `Number_of_plasmids`: Number of plasmids identified and assembled. ## Methods Summary Assemblies were generated from Illumina paired-end reads using the following workflow: 1. **Initial Assembly:**\ *De novo* assembly was performed using **Unicycler v0.5.1**. 2. **Chromosome Scaffolding:**\ Linear contigs were ordered and oriented with **Ragout v2.2** using a reference-guided approach. 3. **Plasmid Discovery & Assembly:**\ Unplaced contigs were searched against **PLSDB** with BLASTN.\ Significant hits (≥90% identity and ≥500 bp) guided plasmid scaffolding using **RagTag v2.1.0**. 4. **Circularisation:**\ Chromosome and plasmid assemblies were circularised and start positions standardised using **Circlator** (`fixstart`). ## Definitions and Notes * **Chromosome-scale:** Assemblies represent a full-length chromosome reconstructed via reference-guided scaffolding. * **Reuse Potential:** The datasets support comparative genomics, pangenomics, phylogenetics, and virulence gene discovery. ## Contact Information For questions regarding this dataset, please contact: **Prof. Teresa A. Coutinho**\ Email: [teresa.coutinho@up.ac.za](mailto:teresa.coutinho@up.ac.za)