ITS regions are used for identifications of bacterial species. But while observing bacterial genomes it is seen that tRNA sequences are present in the ITS regions present between 16S rRNA and 23S rRNA and there are 6-7 copies of sets of 16S-tRNA-23S-5S regions in genome (both strands). These sets differ among themselves in length as well as sequence. So how come ITS are reliable regions for identifications of organisms. Also the ITS regions between 23S and 5S which is quite short (approx 90 bp).
Are there any rules based on which a specific set of 16S-tRNAs-23S-5S regions is taken when comparing ITS regions? Is including the tRNA in the ITS regions justified? Should a short ITS region like the one between 23S and 5S be used for identification?
More reliable regions for identifications of Prokaryotes are 16s, rRNA, rpo and gyr gene regions so simply ignore ITS regions........
Yes, the regions between the 16S and 23S vary in length and sequence in bacteria. I found there were 2-3 different sequences in Enterobacter cloacae. 16S rRNA is the "standard" for a quick identification, but doing a more complete MLSA (MLST) is sometimes needed depending on the genus and species being studied.
The actual 16S rRNA coding sequence should be pretty much identical between all the copies. Occasionally there are a few bases that are different (sequencing error?). For bacteria, the "ITS" region is really not used. There is no database of those sequences. I would recommend using the full-length 16S rRNA for identification in general, but sometimes it is not the only thing needed for proper identification since some species in the same genera have quite identical 16S rRNA sequences. It also depends on how many representatives of that genus and species have been previously sequenced.
I have used ITS to identify cyanobacteria Genus Arthrospira in species level but i got a high similarity between them and it could not be able to differentiate them
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