Comparative Genomics and Transcriptional Analysis of Flavobacterium columnare Strain ATCC 49512

Abstract

<i>Flavobacterium columnare</i> is a Gram-negative fish pathogen causing columnaris disease in wild and cultured fish species. Although the pathogen is widespread in aquatic environments and fish worldwide, little is known about biology of <i>F. columnare</i> and mechanisms of columnaris disease pathogenesis. Previously we presented the complete genome sequence of <i>F. columnare</i> strain ATCC 49512. Here we present a comparison of the strain ATCC 49512 genome to four other <i>Flavobacterium</i> genomes. In this analysis, we identified predicted proteins whose functions indicate <i>F. columnare</i> is capable of denitrification, which would enable anaerobic growth in aquatic pond sediments. Anaerobic growth of <i>F. columnare</i> ATCC 49512 with nitrate supplementation was detected experimentally. <i>F. columnare</i> ATCC 49512 had a relatively high number of insertion sequences and genomic islands compared to the other <i>Flavobacterium</i> species, suggesting a larger degree of horizontal gene exchange and genome plasticity. A type VI subtype III secretion system was encoded in <i>F. columnare</i> along with <i>F. johnsoniae</i> and <i>F. branchiophilum</i>. RNA sequencing proved to be a valuable technique to improve annotation quality; 41 novel protein coding regions were identified, 16 of which had a non-traditional start site (TTG, GTG, and CTT). Candidate small noncoding RNAs were also identified. Our results improve our understanding of <i>F. columnare</i> ATCC 49512 biology, and our results support the use of RNA sequencing to improve annotation of bacterial genomes, particularly for type strains.