Aug 06, 2022
Phylogenomic analysis of Xanthomonas
- David J Studholme1
- 1University of Exeter
- Xanthomonas genomics
Protocol Citation: David J Studholme 2022. Phylogenomic analysis of Xanthomonas. protocols.io https://dx.doi.org/10.17504/protocols.io.261geny57g47/v1
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: August 04, 2022
Last Modified: August 06, 2022
Protocol Integer ID: 68154
Keywords: phylogenomic analysis of xanthomona, xanthomonas spp, xanthomona, phylogenomic tree, phylogenomic analysis, genome sequence, genome, using phame
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Abstract
This is a protocol for using PhaME to generate a phylogenomic tree from a set of Xanthomonas spp. genome sequences.
Troubleshooting
Create a directory for downloaded genome sequence data:
Command
Create directory (Ubuntu 22.04)
Enter the directory for downloaded genome sequence data:
Command
Enter directory (Ubuntu 22.04)
Ensure that NCBI Datasets command line tools are installed and executable (or a symbolic link to the executable) is in the current directory.
Software
NCBI Datasets command line tools
NAME
NCBI
DEVELOPER
Download the genome assemblies that will be included in the analysis:
Dataset
xanthomonas_assm_accs.txt
NAME
Command
Download assemblies from NCBI (Ubuntu 22.04 LTS)
Expected result
You should receive a message something like:
"Downloading: xanthomonas_genome_assemblies.zip197MB done"
Command
Unzip the assemblies download (Ubuntu 22.04 LTS)
Command
Make symbolic links to the downloaded assemblies (Ubuntu 22.04 LTS)
Command
List the symbolic links to assembly sequence files (Ubuntu 22.04 LTS)
Rename the symbolic links to more informative names. We will use the rename_files.pl script to effect this.
Software
rename_files.pl
NAME
Dataset
genomes.list.all.txt
NAME
Command
new command name
Expected result
This should generate a set of .fasta files and .contig symbolic links with informative filenames.
Come back out of the directory for downloaded genome sequence data:
Command
Change to previous directory (Ubuntu LTS 22.04)
Set-up the reference genome sequence data
Command
Create reference directory (Ubuntu 22.04 LTS)
Command
Enter the reference directory (Ubuntu 22.04 LTS)
Command
Make symbolic link to reference genome assembly (Ubuntu 22.04 LTS)
Command
Change back to the root directory (Ubuntu 22.04 LTS)
Set-up the working directory.
Command
Create working directory (Ubuntu 20.04 LTS)
Command
new command name
Command
Make symbolic links to all the genome assemblies (Ubuntu 22.04 LTS)
Optionally, at this point, we can delete the symbolic links for any genomes that we want to exclude from the final analysis. It is also an option to add any genome assemblies as .contig files (inf FASTA format).
Command
Return to previous directory (Ubuntu 22.04 LTS)
Install PhaME software into a Conda environment called 'phame', following instructions on the software's GitHub page:
The PhaME software is described in this paper:
Citation
LINK
Command
Activate Phame Conda environment (Ubuntu 22.04 LTS)
Dataset
phame.ctl
NAME
Execute PhaME:
Command
Execute PhaME (Ubuntu 22.04 LTS)
Expected result
This will generate output, including tree files, in directory:
./workdir/results/trees/
The tree file can now be visualised using any tree-viewing software, for example, iTOL.
Citation
LINK
Citations
Step 13
Letunic I, Bork P. Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation.
https://doi.org/10.1093/nar/gkab301Step 9
Shakya M, Ahmed SA, Davenport KW, Flynn MC, Lo CC, Chain PSG. Standardized phylogenetic and molecular evolutionary analysis applied to species across the microbial tree of life.
https://doi.org/10.1038/s41598-020-58356-1