Comparative Analysis of the Flavobacterium columnare Genomovar I and II Genomes

Abstract

Columnaris disease caused by Gram-negative rod <i>Flavobacterium columnare</i> is one of the most common diseases of catfish. <i>F. columnare</i> is also a common problem in other cultured fish species worldwide. <i>F. columnare</i> 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, <i>F. columnare</i> 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 2,263 conserved orthologous clusters; strain ATCC 49512 has 290 unique orthologous clusters while strain 94-081 has 391. Both strains carry type I secretion system, type VI secretion system, and type IX secretion system. The two genomes also have similar CRISPR capacities. The <i>F. columnare</i> strain ATCC 49512 genome contains a higher number of insertion sequence families and phage regions, while the <i>F. columnare</i> 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 <i>F. columnare</i> as well as potential virulence genes in <i>F. columnare</i> strain 94-081.