Phylogenetic Analysis of Bacterial Species

We used PanACoTA⁴⁸ version 1.2.0 to build phylogenies for 15 bacterial species (Escherichia coli, Pseudomonas aeruginosa, Streptococcus pyogenes, Salmonella enterica, Listeria monocytogenes, Helicobacter pylori, Mycobacterium tuberculosis, Neisseria meningitidis, Staphylococcus aureus, Bacillus subtilis, Campylobacter jejuni, Klebsiella pneumoniae, Bacillus velezensis, Acinetobacter baumannii, Enterococcus faecium). PanACoTA allows phylogenetic tree reconstructions based on the core genomes. For each of the species, we took all genomes under a nucleic acid format in NCBI (fna) and annotated them using prodigal (PanACoTA annotate options–cutn 10000–l90 400 –prodigal). We then computed the pangenome and coregenome (PanACoTA pangenome; PanACoTA corepers; with default parameters). Finally, we aligned the coregenome (PanACoTA align, default parameters) and computed a phylogenetic tree (PanACoTA tree, -b 1000). For this step PanACoTA, uses IQTree^{49 (link)}, (version 2.1.4) and the following option (iqtree -m GTR -bb1000 -st DNA).

Free full text: Click here

Tesson F., Hervé A., Mordret E., Touchon M., d’Humières C., Cury J, & Bernheim A. (2022). Systematic and quantitative view of the antiviral arsenal of prokaryotes. Nature Communications, 13, 2561.

Publication 2022

Acinetobacter baumannii Bacillus subtilis Bacillus velezensis Bacterial Campylobacter jejuni Enterococcus faecium Escherichia coli Genomes Helicobacter pylori Klebsiella pneumoniae Listeria monocytogenes Mycobacterium tuberculosis Neisseria meningitidis Nucleic acid Pseudomonas aeruginosa Reconstructions Salmonella enterica Staphylococcus aureus Streptococcus pyogenes Tree

Corresponding Organization :

Other organizations : Université Paris Cité, Inserm, Institut Pasteur, Centre National de la Recherche Scientifique

Top 5 similar protocols

Protocol cited in 11 other protocols

Variable analysis

independent variables

Bacterial species used: Escherichia coli, Pseudomonas aeruginosa, Streptococcus pyogenes, Salmonella enterica, Listeria monocytogenes, Helicobacter pylori, Mycobacterium tuberculosis, Neisseria meningitidis, Staphylococcus aureus, Bacillus subtilis, Campylobacter jejuni, Klebsiella pneumoniae, Bacillus velezensis, Acinetobacter baumannii, Enterococcus faecium

dependent variables

Phylogenetic trees reconstructed for the 15 bacterial species

control variables

PanACoTA version 1.2.0 used for all steps
Nucleic acid (fna) format of genomes obtained from NCBI
Prodigal used for genome annotation with specific options (--cutn 10000 --l90 400 --prodigal)
Default parameters used for computing pangenome and coregenome
Default parameters used for aligning the coregenome
IQTree version 2.1.4 used for phylogenetic tree reconstruction with specific options (-m GTR -bb1000 -st DNA)

controls

No positive or negative controls were explicitly mentioned in the provided information.

Annotations

Based on most similar protocols

Etiam vel ipsum. Morbi facilisis vestibulum nisl. Praesent cursus laoreet felis. Integer adipiscing pretium orci. Nulla facilisi. Quisque posuere bibendum purus. Nulla quam mauris, cursus eget, convallis ac, molestie non, enim. Aliquam congue. Quisque sagittis nonummy sapien. Proin molestie sem vitae urna. Maecenas lorem.

As authors may omit details in methods from publication, our AI will look for missing critical information across the 5 most similar protocols.

About PubCompare

Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.

We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.

However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.

Ready to get started?

Revolutionizing how scientists
search and build protocols!