Bioinformatic and statistical analysis of RNA-Seq data
Trimmed and demultiplexed reads were mapped back to transcripts using
Salmon (version 1.1.0) and quantification was imported into R using the
tximport package (version 1.10.1) as previously reported . Differential
abundance analysis was performed with the DESeq2 version 1.22.2 package
. For each S. meliloti strain, genes differentially expressed
(log2 fold change of >|2|; P value
<0.01) under at least one condition relative to the control
conditions were identified, and all fold change values for these genes
were extracted. Core and dispensable genome were computed with Roary
following annotation with Prokka and assignment to Clusters of
Orthologous Genes (COG) categories, as previously reported . Comparison
of expression values of genes in the core genome of strains and nested
likelihood ratio tests (LRTs) were performed as indicated in . All genes
of S. meliloti strains 1021, AK83, and BL225C were functionally
annotated using stand- alone version 2 of eggNOG-mapper with default
settings.