Theses and Dissertations

Issuing Body

Mississippi State University

Advisor

Hanson, A. Larry

Committee Member

Petrie-Hanson, Lora

Committee Member

Greenway, Terrence

Date of Degree

8-9-2008

Document Type

Graduate Thesis - Open Access

Major

Veterinary Medical Science

Degree Name

Master of Science

College

College of Veterinary Medicine

Department

Department of Basic Sciences

Abstract

The 16S, 23S, and 5S ribosomal RNA (rRNA) genes are highly conserved sequences in bacteria. For this reason, rRNA genes are often used for phylogenetic classification. On the other hand, the regions between the structural sequences, known as intergenic spacer regions (ITS), are under less evolutionary pressure to be conserved. Because they are not as highly conserved, they can be used to differentiate strains of the same bacterial specie. The purpose of this study was to evaluate the 16S-23S ITS of Flavobacterium columnare, an important pathogen of cultured fish, by comparing the 16S-23S ITS sequences from 70 isolates. We developed two PCR assays that amplify overlapping regions of one large previously identified ITS. The primers targeted the 16S sequence and isoleucine tRNA encoding sequences and the 23S sequence and alanine tRNA encoding sequences. The PCR products were cloned and sequenced. We also targeted I-CeuI restriction fragments from the ATCC type strain that were separated by pulse field gel electrophoresis and analyzed the 16S-23S ITS regions. We found that the genome of this species harbors at least 6 intergenic spacer regions that are very similar and contain the same tRNA encoding sequences. This suggests that earlier studies that used the ITS for distinguishing between strains of Flavobacterium columnare may be comparing sequences from different structural RNA operons and thus have misleading data.

URI

https://hdl.handle.net/11668/15350

Comments

molecular diagnostics||channel catfish||16S-23S intergenic spacer region||Flavobacterium columnare

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