Pubblicazione scientifica

Genomic Diversity and Evolution of the Fish Pathogen Flavobacterium psychrophilum

FILONE TECNOLOGICO	TEMA
produzione e raccolta	applicazione delle biotecnologie in acquacoltura metodi di allevamento: specie ittiche da allevamento metodi di allevamento: tipologia in funzione della specie ittica metodi di riproduzione (micro alghe, molluschi, ecc.)
trasformazione e commercializzazione	certificazione e marchi di qualità macchinari di ausilio alla lavorazione e trasformazione del pesce sistemi di packaging, etichettatura e conservazione dei prodotti sistemi di trasporto, logistica e catena del freddo

RIASSUNTO

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 genome. Using a Hidden Markov Model to delineate recombination tracts in pairs of closely related genomes, the average recombination tract length was estimated to ~4.0 Kbp and the typical ratio of the contributions of recombination and mutations to nucleotide-level differentiation (r/m) was estimated to ~13. Within CC-ST10, evolutionary distances computed on non-recombined regions and comparisons between 22 isolates sampled up to 27 years apart suggest a most recent common ancestor in the second half of the nineteenth century in North America with subsequent diversification and transmission of this clonal complex coinciding with the worldwide expansion of rainbow trout farming. With the goal to promote the development of tools for the genetic manipulation of F. psychrophilum, a particular attention was also paid to plasmids. Their extraction and sequencing to completion revealed plasmid diversity that remained hidden to classical plasmid profiling due to size similarities.

DATA

Data di pubblicazione: 07/02/2018

AUTORI

DUCHAUD ERIC
ROCHAT TATIANA
HABIB CHRISTOPHE
BARBIER PAUL
LOUX VALENTIN
GUERIN CYPRIEN
DALSGAARD INGER
MADSEN LONE
NILSEN HANNE
SUNDELL KRISTER
WIKLUND TOM
STREPPARAVA NICOLE
WAHLI THOMAS
CABURLOTTO GRETA
MANFRIN AMEDEO
WIENS GREGORY D
FUJIWARA-NAGATA ERINA
AVENDANO-HERRERA RUBEN
BERNARDET JEAN-FRANCOIS
NICOLAS PIERRE

ENTE DI AFFERENZA

UNITE DE VIROLOGIE & IMMUNOLOGIE MOLECULAIRES VIM INST NATL RECHERCHE AGRONOMIQUE UNIV PARIS SACLAY JOUY EN JOSAS FRANCE
UNITE MATHEMATIQUES & INFORMATIQUE APPLIQUEES DU GENOME A L ENVIRONNEMENT MAIAGE INST NATL RECHERCHE AGRONOMIQUE UNIV PARIS SACLAY JOUY EN JOSAS FRANCE
SECTION FOR BACTERIOLOGY & PATHOLOGY NATL VETERINARY INST TECH UNIV DENMARK KGS LYNGBY DENMARK
DEPT AQUATIC ANIMAL HEALTH NORWEGIAN VETERINARY INST BERGEN NORWAY
LAB OF AQUATIC PATHOBIOLOGY ENVIRONMENTAL & MARINE BIOLOGY FACULTY OF SCIENCE & ENG ABO AKAD UNIV TURKU FINLAND
LAB OF APPLIED MICROBIOLOGY DEPT ENVIRONMENT CONSTRC & DESIGN UNIV APPLIED SCIENCES & ARTS OF SOUTHERN SWITZERLAND SUPSI BELLINZONA SWITZERLAND
CTR FISH & WILDLIFE HEALTH FIWI UNIV BERN BERN SWITZERLAND
DEPT FISH PATHOLOGY INST ZOOPROFILATTICO SPERIMENTALE DELLE VENEZIE LEGNARO ITALY
NATL CTR COOL & COLD WATER AQUACULTURE AGRICULTURAL RSCH SRVC US DEPT AGRICULTURE KEARNEYSVILLE WV US
DEPT FISHERIES KINDAI UNIV NARA JAPAN
DEPARTAMENTO FACULTAD DE CIENCIAS BIOLOGICAS UNIV ANDRES BELLO UNIV ANDRES BELLOVINA DEL MAR INTERDISCIPLINARY CTR AQUACULTURE RSCH CONCEPCION CHILE

RIVISTA

Frontiers in Microbiology, 9, 138

IMPACT FACTOR

4,190

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