Relationship of diversity and the secondary structure in 16S-23S rDNA internal transcribed spacer: a case in Vibrio parahaemolyticus

Abstract

The 16S-23S rDNA internal transcribed spacer (ITS) sequence, located in the rrn operon, has been analyzed and evaluated for use in phylogenetic analysis and the detection target of bacteria. The ITS region displays a high level of diversity, being present in multiple copies and displaying variability in both length and sequence, and it carries more phylogenetic information than 16S rDNA. However, appropriately identifying ITS regions to use in analyses is challenging. To solve this problem, we analyzed the ITS regions in Vibrio parahaemolyticus and predicted the secondary structure of each analogous rrn transcript. The genomic DNA of V. parahaemolyticus contains approximately 8–14 rrns, making it more complex than the sequences of most other bacterial species. We analyzed 216 ITSs, of which 206 ITSs come from 18 complete genomes and 10 ITSs were identified in the present study. The subunits of each ITS were distinguished by their predicted secondary structures. We propose a refined backbone model of the V. parahaemolyticus ITS that can be applied to the sequences of other bacteria. The backbone includes C, V, tDNA, and linker blocks. These blocks, which may represent true functional units, may be used as potential targets for phylogenetic analysis or molecular detection.