Comparative genomics analyses
The genome of every pressure was obtained querying RefSeq with the accession numbers in Supply Information 5. Genes had been mapped to COG phrases utilizing eggnog mapper and all strains had been then labelled as both auxotroph or prototroph iteratively for every of the next compounds: biotin, thiamine, pantothenate, niacin. The evaluation was restricted to COG phrases for which a pathway mapping is supplied (https://www.ncbi.nlm.nih.gov/research/cog/pathways/). A contingency desk was then constructed primarily based on the presence of every COG time period in auxotrophs and prototrophs respectively. A χ2 take a look at was carried out on the contingency desk, and p-values in addition to details about which group had the upper presence of every COG time period was saved. Ensuing p values had been subsequently corrected utilizing the Benjamini-Hochberg technique. For considerably totally different (q-value < 0.05) COG phrases, a purposeful annotation was retrieved from COG database API (https://www.ncbi.nlm.nih.gov/research/cog/api/cog/) and mapped to organic course of by way of KEGG (obtainable from Biopython). The effectiveness of a number of testing correction was confirmed by producing random fashions by shuffling the auxotrophy/prototrophy labels. No COG time period was considerably in another way considerable between randomly assigned auxotrophs and prototrophs.
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