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United States Department of Agriculture

Agricultural Research Service

Research Project: Integrated Aquatic Animal Health Strategies

Location: Aquatic Animal Health Research

Title: Intragenomic heterogeneity in the 16S rRNA genes of Flavobacterium columnare and relevance to genomovar assignment

Authors
item LAFRENTZ, BENJAMIN
item WALDBIESER, GEOFFREY
item WELCH, TIMOTHY
item SHOEMAKER, CRAIG

Submitted to: Annual Eastern Fish Health Workshop
Publication Type: Abstract Only
Publication Acceptance Date: April 8, 2013
Publication Date: May 1, 2013
Citation: Lafrentz, B.R., Waldbieser, G.C., Welch, T.J., Shoemaker, C.A. 2013. Intragenomic heterogeneity in the 16S rRNA genes of Flavobacterium columnare and relevance to genomovar assignment [abstract]. Annual Eastern Fish Health Workshop. p. 24.

Technical Abstract: Genetic variability in 16S rRNA gene sequences has been demonstrated among isolates of Flavobacterium columnare and a restriction fragment length polymorphism (RFLP) assay is available for genetic typing this important fish pathogen. Interpretation of restriction patterns can be difficult due to the lack of a formal description of the expected number and sizes of DNA fragments generated for each of the described genomovars. In this study, partial 16S rRNA gene sequences (ca. 1300 bp fragment) from isolates representing each described genomovar and isolates generating unique restriction patterns were cloned and sequenced. The results demonstrated that some isolates contained up to three different 16S rRNA genes whose sequences generate different RFLP patterns due to intragenomic heterogeneity within HaeIII restriction sites. The occurrence of HaeIII restriction sites within the portion of the 16S rRNA gene used for typing the F. columnare isolates and intragenomic heterogeneity within these sites explained the restriction patterns observed following RFLP analyses. This research provides a standard protocol for typing isolates of F. columnare by RFLP and a formal description of the expected restriction patterns for the previously described genomovars I, II, II-B, and III. Additionally, we describe two new genomovars, I-A and I/II.

Last Modified: 8/27/2014
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