Core non-coding RNAs of Piscirickettsia salmonis

PloS One
Cristopher SegoviaJavier Santander

Abstract

Piscirickettsia salmonis, a fastidious Gram-negative intracellular facultative bacterium, is the causative agent o Piscirickettsiosis. P. salmonis has broad host range with a nearly worldwide distribution, causing significant mortality. The molecular regulatory mechanisms of P. salmonis pathogenesis are relatively unknown, mainly due to its difficult in vitro culture and genomic differences between genogroups. Bacterial non-coding RNAs (ncRNAs) are important post-transcriptional regulators of bacterial physiology and virulence that are predominantly transcribed from intergenic regions (trans-acting) or antisense strand of open reading frames (cis-acting). The repertoire of ncRNAs present in the genome of P. salmonis and its possible role in bacterial physiology and pathogenesis are unknown. Here, we predicted and analyzed the core ncRNAs of P. salmonis base on structure and correlate this prediction to RNA sequencing data. We identified a total of 69 ncRNA classes related to tRNAs, rRNA, thermoregulators, antitoxins, ribozymes, riboswitches, miRNAs and antisense-RNAs. Among these ncRNAs, 29 classes of ncRNAs are shared between all P. salmonis genomes, constituting the core ncRNAs of P. salmonis. The ncRNA core of P. salmonis co...Continue Reading

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Citations

Jul 3, 2020·Frontiers in Molecular Biosciences·Juan José González Plaza
Apr 18, 2019·Biochimie·Maxence LejarsEliane Hajnsdorf

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Datasets Mentioned

BETA
AMFF02000000
PRJNA383157
PRJNA413085
PRJNA413083

Methods Mentioned

BETA
PCR
RNA-seq
RNAseq

Software Mentioned

gplots R package
Bowtie2
StructureRNAfinder
R package
Integrative Genomics Viewer ( IGV )
plots
sRNA
Infernal
intersectBED
SMS ( Sequence Manipulation Suite )

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