Genomic Diversity and Evolution of the Fish Pathogen Flavobacterium psychrophilum

Frontiers in Microbiology
Eric DuchaudPierre Nicolas

Abstract

Flavobacterium psychrophilum, the etiological agent of rainbow trout fry syndrome and bacterial cold-water disease in salmonid fish, is currently one of the main bacterial pathogens hampering the productivity of salmonid farming worldwide. In this study, the genomic diversity of the F. psychrophilum species is analyzed using a set of 41 genomes, including 30 newly sequenced isolates. These were selected on the basis of available MLST data with the two-fold objective of maximizing the coverage of the species diversity and of allowing a focus on the main clonal complex (CC-ST10) infecting farmed rainbow trout (Oncorhynchus mykiss) worldwide. The results reveal a bacterial species harboring a limited genomic diversity both in terms of nucleotide diversity, with ~0.3% nucleotide divergence inside CDSs in pairwise genome comparisons, and in terms of gene repertoire, with the core genome accounting for ~80% of the genes in each genome. The pan-genome seems nevertheless "open" according to the scaling exponent of a power-law fitted on the rate of new gene discovery when genomes are added one-by-one. Recombination is a key component of the evolutionary process of the species as seen in the high level of apparent homoplasy in the core g...Continue Reading

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Citations

Jan 13, 2019·Applied and Environmental Microbiology·T RochatE Duchaud
Mar 30, 2018·Frontiers in Microbiology·Benjamin R LaFrentzSiow F Chang
Jan 19, 2020·Fish Physiology and Biochemistry·Felix K A KuebutornyeCai Xia Xie
Mar 18, 2020·Science Advances·Abhishek Shrivastava, Howard C Berg
Jun 15, 2018·Frontiers in Microbiology·Jana L Markley, Timothy A Wencewicz
Aug 10, 2019·Frontiers in Microbiology·Krister SundellTom Wiklund
May 15, 2021·Environmental Microbiology·Castillo DanielMiddelboe Mathias

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Methods Mentioned

BETA
electrophoresis
PCR

Software Mentioned

R library
yn00
Sickle
acctran
Muscle
- consed
phred
blastp
FastQC
MicroScope

Related Concepts

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