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

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

Submitted to: Genbank
Publication Type: Other
Publication Acceptance Date: 7/12/2013
Publication Date: 10/22/2013
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. Genbank. Accession Nos. KC912647-KC912684.

Interpretive Summary:

Technical Abstract: Flavobacterium columnare is the causative agent of columnaris disease which severely impacts channel catfish production in the USA and may be emerging as an important pathogen in the rainbow trout industry. The 16S rRNA gene is a housekeeping gene commonly used for bacterial taxonomy and genotyping. Genetic variability in the sequence of this gene has been demonstrated among isolates of F. columnare. A genetic typing system has been developed for F. columnare in which a portion of the 16S rRNA gene is amplified by PCR and then digested with an enzyme that will cut the DNA at specific sites. Based on the number and size of DNA fragments generated, isolates of the bacterium are assigned to a genomovar (i.e., genetic type). However, interpretation of results can be difficult due to the lack of a formal description of the expected number and sizes of DNA fragments generated. In this study, partial 16S rRNA gene sequences (ca. 1250 bp fragment) from isolates representing each described genomovar and isolates generating unique DNA fragment patterns were cloned and sequenced. Each unique sequence (n=38) was deposited in GenBank, and the results demonstrated that some isolates contained up to three different 16S rRNA genes whose sequences generate different patterns due to DNA nucleotide variability at the sites where the enzyme cuts the DNA. This research provides a standard protocol for the genetic typing of F. columnare and a formal description of the expected number and sizes of DNA fragments generated for each genomovar. The new knowledge obtained from these DNA sequences will allow for the proper assignment of an unknown isolate to a genetic type. Use of the standard protocol will allow for monitoring of the different genetic types in aquaculture reared fish species, which is important because research has demonstrated an association between genetic type of F. columnare and virulence.