The emergence of bacterial blight pathogen followed the dispersal pattern of rice in Asia

The data and scripts that are stored here are part of the paper "The emergence of a bacterial pathogen followed the dispersal pattern of rice in Asia". The genomes used are Xanthomonas oryzae pv. oryzae (Xoo) strains that were collected in Asia.

The description of each data are as follows:

xoo_asia_genome.zip - all of the genomes in fasta file

xoo_asia_genbank.zip - all of the genomes in genbank format with gene annotations predicted by Prokka (1)

xoo_asia_gff.zip - all of the genomes with predicted gene annotation in gff3 format.

The description of the script used in this paper are as follows:

Figure1 folder - The scripts used to make all of the figures for Figure 1.

Figure2 folder - The scripts used to make all of the figures for Figure 2.

Figure3 folder - The scripts used to make all of the figures for Figure 3.

Figure4 folder - The scripts used to make all of the figures for Figure 4.

Figure5 folder - The scripts used to make all of the figures for Figure 5.

other_script - The scripts used to make the figures in supplementary data

    a. population_structure - The scripts stored are predicting the number of populations in Xoo using rheirbaps (2) and fastbaps (3), and the script for performing the principal component analysis for Supplementary Figure 1.

    b. pangenome - The scripts stored are the codes used to build Supplementary Figure 2.

    c. diversity - The script stored is for calculating different genetic analysis using PopGenome (4)

    d. tale - The script stored here are codes for producing the Transcription activator-like effectors (TALE) plots in Supplementary Figure 5.

     e. beast_phylogeny - The script stored is for the visualization of maximum clade credibility trees from BEAST (5) results

Reference:

1. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinforma Oxf Engl 2014; 30: 2068–2069. 

2.Tonkin-Hill G, Lees JA, Bentley SD, Frost SDW, Corander J. RhierBAPS: An R implementation of the population clustering algorithm hierBAPS. Wellcome Open Res 2018; 3: 93.

3. Tonkin-Hill G, Lees JA, Bentley SD, Frost SDW, Corander J. Fast hierarchical Bayesian analysis of population structure. Nucleic Acids Res 2019; 47: 5539–5549.

4. Pfeifer B, Wittelsbürger U, Ramos-Onsins SE, Lercher MJ. PopGenome: an efficient Swiss army knife for population genomic analyses in R. Mol Biol Evol 2014; 31: 1929–1936.

5. Suchard MA, Lemey P, Baele G, Ayres DL, Drummond AJ, Rambaut A. Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10. Virus Evol 2018; 4: vey016.