Representative genes associated with the flagella in the transcriptome.

<p>The image shows the set of genes associated with the flagellar structure that are expressed by <i>P</i>. <i>salmonis</i> in all conditions tested. The green square represents genes expressed in the different media, whereas the orange square represents genes that did not show expression., in the different grown conditions analyzed.</p

Transcriptome Analysis of the Intracellular Facultative Pathogen <i>Piscirickettsia salmonis</i>: Expression of Putative Groups of Genes Associated with Virulence and Iron Metabolism

<div><p>The intracellular facultative bacteria <i>Piscirickettsia salmonis</i> is one of the most important pathogens of the Chilean aquaculture. However, there is a lack of information regarding the whole genomic transcriptional response according to different extracellular environments. We used next generation sequencing (NGS) of RNA (RNA-seq) to study the whole transcriptome of an isolate of <i>P</i>. <i>salmonis</i> (FAVET-INBIOGEN) using a cell line culture and a modified cell-free liquid medium, with or without iron supplementation. This was done in order to obtain information about the factors there are involved in virulence and iron acquisition. First, the isolate was grown in the Sf21 cell line; then, the bacteria were cultured into a cell-free liquid medium supplemented or not with iron. We identified in the transcriptome, genes associated with type IV secretion systems, genes related to flagellar structure assembly, several proteases and sigma factors, and genes related to the development of drug resistance. Additionally, we identified for the first time several iron-metabolism associated genes including at least two iron uptake pathways (ferrous iron and ferric iron uptake) that are actually expressed in the different conditions analyzed. We further describe putative genes that are related with the use and storage of iron in the bacteria, which have not been previously described. Several sets of genes related to virulence were expressed in both the cell line and cell-free culture media (for example those related to flagellar structure; such as basal body, MS-ring, C-ring, proximal and distal rod, and filament), which may play roles in other basic processes rather than been restricted to virulence.</p></div

Number of genes up and down regulated in the transcriptome from CFC-I medium compare to CFC-N medium.

<p>Number of genes up and down regulated in the transcriptome from CFC-I medium compare to CFC-N medium.</p

Correlation between RT-qPCR and RNA-seq data for six genes (<i>feoB</i>, <i>fur</i>, <i>bfr</i>, <i>fhuC</i>, <i>rpoS</i> and <i>hemH</i>) expressed by <i>P</i>. <i>salmonis</i> in both types of cultures.

<p>The tendency line and determination coefficient (R²) are showed for both cultures.</p

Number of genes up and down regulated in the transcriptome from CFC medium compare to CC medium.

<p>Number of genes up and down regulated in the transcriptome from CFC medium compare to CC medium.</p

Table containing differential expressed genes (result of edgeR)

This table contains data of list of genes that were < 0.01 FDR value and differed in their expression value at least 2 fold between two group

Information on SNPs identified from transcriptome data (vcf file)

The details of SNPs calling are described in Materials and method

GO term reduction table

Gene Ontology terms were summarized and redundant GO terms were removed by semantic similarity-based approach employed in REViGO

Sequences of S. lalandi transcriptome (fasta file)

Transcriptome contigs assembled from filtered paired end sequencing reads on Illumina HiSeq™ 2000 platform using Trinity. Only non-redundant (cluster in CAP3), more than 300bp contigs with open reading frame were kep

The mapping count table

This count table was used as an input for differential gene expression analysis in edge