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ARS Home » Southeast Area » Stoneville, Mississippi » Warmwater Aquaculture Research Unit » Research » Publications at this Location » Publication #343003

Research Project: Genetics, Breeding and Reproductive Physiology to Enhance Production of Catfish

Location: Warmwater Aquaculture Research Unit

Title: Comparative analysis of the Flavobacterium columnare genomovar I and II genomes

item KUMRU, SALIH - Mississippi State University
item TEKEDAR, HASAN - Mississippi State University
item GULSOY, NAGIHAN - Mississippi State University
item Waldbieser, Geoffrey - Geoff
item LAWRENCE, MARK - Mississippi State University
item KARSI, ATTILA - Mississippi State University

Submitted to: Frontiers in Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/6/2017
Publication Date: 7/25/2017
Citation: Kumru, S., Tekedar, H., Gulsoy, N., Waldbieser, G.C., Lawrence, M.L., Karsi, A. 2017. Comparative analysis of the Flavobacterium columnare genomovar I and II genomes. Frontiers in Microbiology. 8:1375.

Interpretive Summary: Flavobacterium columnare is a bacterial pathogen that is one of the most common diseases in farm raised catfish. However, not every strain of this bacteria is pathogenic. Scientists at Mississippi State University in Starkville, Mississippi, and ARS scientists at Stoneville, Mississippi, produced and compared the complete genomic DNA sequences of two F. columnare strains, one virulent and one non-virulent. The genomic DNA sequence differed by 10% between the two strains, which met criteria to be considered different species. Experimental mutagenesis of the pathogenic strain showed that mutations in specific genes significantly reduced its pathogenicity. This research provided important information on classification of F. columnare strains and the identification of potential virulence genes, and this information can be used to improve vaccines and diagnostics for this disease to reduce losses in commercial catfish production.

Technical Abstract: Columnaris disease caused by Gram-negative rod Flavobacterium columnare is one of the most common diseases of catfish. F. columnare is also a common problem in other cultured fish species worldwide. F. columnare has three major genomovars; we have sequenced a representative strain from genomovar I (ATCC 49512, which is avirulent in catfish) and genomovar II (94-081, which is highly pathogenic in catfish). Here we present a comparative analysis of the two genomes. Interestingly, F. columnare ATCC 49512 and 94-081 meet criteria to be considered different species based on the Average Nucleotide Identity (90.71% similar) and DNA-DNA Hybridization (42.6 % similar). Genome alignment indicated the two genomes have a large number of rearrangements. However, function-based comparative genomics analysis indicated that the two strains have similar functional capabilities with 2263 conserved orthologous clusters; strain ATCC 49512 has 290 unique orthologous clusters while strain 94-081 has 391. Both strains carry type I secretion system (T1SS), type VI secretion system (T6SSiii), and type IX secretion system (T9SS). The two genomes also have similar CRISPR capacities. The F. columnare strain ATCC 49512 genome contains a higher number of insertion sequence families and phage regions, while the F. columnare strain 94-081 genome has more genomic islands and more regulatory gene capacity. Transposon mutagenesis using Tn4351 in pathogenic strain 94-081 yielded six mutants, and experimental infections of fish showed hemolysin and glycine cleavage protein mutants had 15% and 10% mortalities, respectively, while the wild-type strain caused 100% mortalities. Our comparative and mutational analysis yielded important information on classification of genomovars I and II F. columnare as well as potential virulence genes in F. columnare strain 94-081.