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

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