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The species Salmonella enterica is one of the most prevalent human and animal pathogens, it includes Non Typhoïdal Salmonella (NTS) serovars like Typhimurium and Enteridis, that are generalist pathogens with broad host specificity and Typhoïdal Salmonella (TS) serovars, like Typhi and Paratyphi A, that are specialized pathogens strictly adapted to the human host and the cause of an invasive, dangerous disease known as enteric (typhoid) fever [1,2,3]. The SalHostTrop project aims at identifying, characterizing and understanding the human-restricted tropism of Typhoidal Salmonella (TS) using comparative dual-RNAseq sequencing and other complementary approaches. We combine state of the art genome and transcriptome sequencing methods to decipher the molecular basis of host-tropism in clinical strains. We contrast the comparative genomics and differential expression analyses to explore and assess the variability and plasticity of pathogenesis routes among and between typhoidal and non-typhoidal serovars. We present our on-going work including the Pacbio long-read genomic sequencing, assembly and annotation [4] of a new S. Typhi strain (120130191) and the dual RNAseq data analysis of a pilot experiment of S. Typhimurium and S. Paratyphi A during human epithelial cells infection. The new S. Typhi strain includes one circularized complete chromosome and one plasmid of about 4.78 Mb with 4638 coding genes and 106.7 kb with 128 coding genes, respectively. The dual RNAseq pilot first analyses demonstrate the feasibility of the protocol to target both pathogen and host transcripts simultaneously during infection. We also built a S. enterica subsp. enterica reference phylogenetic tree from the super-alignment of Salmonella core genes in 214 complete genomes of various serotypes that is in agreement with previous studies and will be used to explore pseudogene content of serotypes according to their evolutionary history

Listeria sRNAs and coding genes coevolution groups. For each sRNA, the table includes the following informations on the corresponding co-evolving elements: the gene locus tag name (‘Element’ column), the type of element (CDS or 5’UTR, ‘Type’ column), the type of dependency model that highlighted the interaction: x = evolution of the sRNA depends on the state of the 5’UTR/CDS, y = evolution of 5’UTR/CDS depends on the state of the sRNA and xy = bidirectional dependency between evolution of the sRNA and the 5’UTR/CDS element (Model column), the distance between the sRNA and the element in nucleotides (Distance column) and the description of the gene/operon function according to Listeriomics database (‘Description’ column); ‘id’ = identical content. Coevolution groups that are included in the main network hub are highlighted in gray. (DOCX 142 kb)

Ancestral presence/absence patterns of L.m. EGD-e regulatory sRNAs. For all 52 L.m. EGD-e variable sRNAs, the table includes the following information according to the Listeria reference tree (see Fig. 2): root presence - absence information (Root state column), tree branches labels where gain (Gains column) and loss events (Losses column) were inferred (labels correspond to branch identifiers indicated in the cladogram of Fig. 2). The undefined column corresponds to tree branch labels with undefined state due to missing data in the corresponding genomes (draft genomes). The pattern_type column corresponds to the three different types of phyletic profiles inferred: monophyletic, polyphyletic or paraphyletic profiles. (DOCX 128 kb)

Multiple alignment of rli133. This figure represents the multiple alignment of rli133 sequences in strains where it is present. Red denotes a fully conserved position. The phylogenetic tree at the left corresponds to a Maximum Likelihood tree computed from the corresponding multiple alignment. (PDF 1413 kb)

Genomic distance between coevolving sRNAs and CDS. Plain curves show the distance density between sRNAs and 5’UTRs (red) or CDS (blue) engaged in coevolution relationships, considering genome circularity. They are compared to distances between sRNAs and all 5’UTRs or CDS (all) respectively represented by red and blue dotted curves. (PDF 117 kb)

Rli133 genomic context conservation in Listeria. 5′ and 3′ homolog genes are represented using red arrows. GFXXXX names correspond to PanOCT ortholog clusters identifiers. Blue arrows correspond to two genes inserted in several strains of Listeria lineages III and IV. (PDF 212 kb)

List of the 79 genomes used in this study. The table includes the list of 79 genomes obtained from Listeriomics and retrieved from the NCBI database. Several fields have been abbreviated for easier reading: ‘Se.’: strain serotype, ‘Li.’: Listeria lineage and ‘Co.’: country where the strain was first isolated. (DOCX 98 kb)

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Background Noncoding RNA (ncRNA) has been recognized as an important regulator of gene expression networks in Bacteria and Eucaryota. Little is known about ncRNA in thermococcal archaea except for the eukaryotic-like C/D and H/ACA modification guide RNAs. Results Using a combination of in silico and experimental approaches, we identified and characterized novel P. abyssi ncRNAs transcribed from 12 intergenic regions, ten of which are conserved throughout the Thermococcales. Several of them accumulate in the late-exponential phase of growth. Analysis of the genomic context and sequence conservation amongst related thermococcal species revealed two novel P. abyssi ncRNA families. The CRISPR family is comprised of crRNAs expressed from two of the four P. abyssi CRISPR cassettes. The 5'UTR derived family includes four conserved ncRNAs, two of which have features similar to known bacterial riboswitches. Several of the novel ncRNAs have sequence similarities to orphan OrfB transposase elements. Based on RNA secondary structure predictions and experimental results, we show that three of the twelve ncRNAs include Kink-turn RNA motifs, arguing for a biological role of these ncRNAs in the cell. Furthermore, our results show that several of the ncRNAs are subjected to processing events by enzymes that remain to be identified and characterized. Conclusions This work proposes a revised annotation of CRISPR loci in P. abyssi and expands our knowledge of ncRNAs in the Thermococcales, thus providing a starting point for studies needed to elucidate their biological function.