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ARS Home » Southeast Area » Auburn, Alabama » Aquatic Animal Health Research » Research » Publications at this Location » Publication #305850
Title: Intragenomic heterogeneity in the 16S rRNA genes of Flavobacterium columnare and standard protocol for genomovar assignment

Author
item Lafrentz, Benjamin
item Waldbieser, Geoffrey - Geoff
item Welch, Timothy - Tim
item Shoemaker, Craig

Submitted to: International Aquaculture Meeting
Publication Type: Abstract Only
Publication Acceptance Date: 6/30/2014
Publication Date: 8/31/2014
Citation: Lafrentz, B.R., Waldbieser, G.C., Welch, T.J., Shoemaker, C.A. 2014. Intragenomic heterogeneity in the 16S rRNA genes of Flavobacterium columnare and standard protocol for genomovar assignment [abstract]. International Symposium on Aquatic Animal Health. p.92.

Interpretive Summary:

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. 1250 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 a new genomovar, I/II.