Evolutionary Genomics of Lactobacillales

This repository contains a pipeline to study the evolution of the order Lactobacillales using public genome data.

How to run?

Step 1: clone this repository:

git clone https://github.com/swittouck/legen.git

Step 2: install all dependencies.

Step 3: create folders for data and results:

cd legen
mkdir data results

Step 4: download type strain names of validly published species from the LPSN and put them in data.

Step 5: run all scripts in src in the order indicated by the file/folder names. Run each script directly from its parent directory. E.g.:

cd src/01_prepare_genomes
./01_download_metadata.R

Dependencies

Software:

R v4.2.3
ProClasp v1.0
Prodigal v2.6.3
SCARAP v0.4.0
trimAl 1.4.rev15
IQ-TREE v1.6.12

R packages:

tidyverse v2.0.0
tidygenomes v0.1.3
ape v5.7.1

The data

genomes_lactobacillales_gtdb-r207.tsv

metadata of all Lactobacillales genomes that are in release 207 of the GTDB
downloaded by the script src/lactobacillales/01_download_metadata.R

genomes_lactobacillales_gtdb-r207

a selection of one high-quality genome per species (for Carnobacteriaceae) or per genus (for non-Carnobacteriaceae) downloaded from the NCBI
downloaded by the script src/lactobacillales/02_download_genomes.sh

lpsn_gss_2023-03-23.csv

type strain names and other info for all validly published species, from LPSN
downloaded from https://lpsn.dsmz.de/downloads (PNU account required)

Data analyses based on this pipeline

Demonstration of SCARAP and analysis of the accessory tendency of gene families

This analysis was based on v4 of LEGEN and is available in the pangenome-toolkit repository. A manuscript describing the results has been submitted to an open access journal.

Genus-level taxonomy of Lactobacillaceae

This analysis was based on v3 of LEGEN and is available in the lacto_genus repository. The results have been published in IJSEM:

Zheng, J., Wittouck, S., Salvetti, E., Franz, C. M. A. P., Harris, H. M. B., Mattarelli, P., O’Toole, P. W., Pot, B., Vandamme, P., Walter, J., Watanabe, K., Wuyts, S., Felis, G. E., Gänzle, M. G., & Lebeer, S. (2020). A taxonomic note on the genus Lactobacillus: Description of 23 novel genera, emended description of the genus Lactobacillus Beijerinck 1901, and union of Lactobacillaceae and Leuconostocaceae. International Journal of Systematic and Evolutionary Microbiology.

Species-level taxonomy of Lactobacillaceae

This analysis was based on v3 of LEGEN and is available in the lacto_species repository. The results have been published in mSystems:

Wittouck, Stijn, Sander Wuyts, Conor J Meehan, Vera van Noort, and Sarah Lebeer. 2019. “A Genome-Based Species Taxonomy of the Lactobacillus Genus Complex.” MSystems 4 (5): e00264-19.

SWittouck/legen