LikeFokkens / FOSC_multi-speed-genome

FOSC_multi-speed-genome

This repo is a preliminary Suplemental Materials and Methods for the paper posted on [bioRxiv](doi: https://doi.org/10.1101/465070). Please raise an issue or contact me when you find something is not working properly or if something is not clear: this is highly appreciated.

Figure 1

1A

see LikeFokkens/whole_genome_alignments for pipelines to align genomes using nucmer, create coordinate files and sort these for plotting.

See LikeFokkens/genome-wide_plots for scripts used for plotting presence-absence plots and LikeFokkens/species_tree for scripts used to plot the species tree.

A species tree was inferred as described in van Dam et al. (doi: 10.1111/1462-2920.13445) and saved in newick format.

Plotting the species tree is described in plotSpeciesTree, plotting presence-absence, color-coded according to sequence similarity or synteny (length of the alignment) is described in presence-absencePlots. Figure 1 was made by cropping the png generated as described in presence-absencePlots and positioning this adjacent to the tree. The order of rows in a presence-absence plot can be specified in plot_presence_absence_wrt_referenceGenome_inTree_python3.py so that it matches the species tree.

1B

see map_reads_to_reference.py for mapping reads to the recipient genome, extracting unmapped reads and mapping those to the genome sequence of the donor strain. Bamfiles with extracted unmapped reads mapped tot he donor genome, with putative PCR duplicates removed can be downloaded from Zenodo (10.5281/zenodo.1479943), with duplications removed. Read densities were plotted on the genome using plot_read_density_withGnuplot.py (see --help for more detail on how to use this).

Figure 2

Similar to Figure 1A.

Figure 3

Up- and downregulated genes, see notebooks/DEGS.ipnb imports pandas, scipy, matplotlib.

Figure 4

see notebooks/Domains_of_enrichment_analyses

Figure 5

Is compased of parts of Supplemental Figures S4, S6, S8, S11, S13 and S14, using Gnuplot to combine files and Inkscape and Illustrator for further polishing the layout, adding legends, etc.)

Figure 6

see notebooks/correlations_sliding_windows