What makes the ITS sequencing one of the most valuable tool in the molecular identification of fungi? Then, is it reasonable for plants?, and what determine the suitable primer for amplification the ITS region, ITS1, ITS2....etc?
ITS is universal bar code marker, and you can get a lot of infos through this link:
http://www.pnas.org/content/109/16/6241
ITS permites to identify the fungi at the level o f the species because of its high variability and resolution at the species level.
Giorgia is correct; the ITS gene region shows just enough variability to make it the most effective indicator of identity at the species level.
Dear Colleagues...
I'm really appreciate for your sage statements.. and we may come out with this conclusion, which is the using of ITS for characterization refers to its distinctiveness, furthermore, this region is highly conservative and hard to be modified, therefore it will serve as an identity.
Kind Regards.
ITS are small sequences which facilitates sequencing, flanked by very conserved sequences which facilitates primers design, from repetitive genes which facilitates amplification, with sufficient variation to adequate recognition at the species level as mentioned by Giorgia. IGS may be more appropriate to find genetic diversity at the intraspecific level whereas ribosomal gene sequences (small or large subunit ribosomal RNA) on the contrary are better adapted to phylogenetic analysis at higher order taxon level (ie archaea vs bacteria vs eukaryota)
The fungal people chose ITS as a barcode based on its success in plants. It is a widely used marker for plants (although plant and fungal researchers read the locus in different directions [fungal SSU -> LSU, plant LSU -> SSU).
the spacer between SSU and LSU is the ITS (ITS1-5.8S-ITS2), the spacer between LSU and SSU is the IGS (IGS1-5S-IGS2 for fungi)
They're in a tandem repeat, so it just matters which direction you decide to go in. Since it is transcribed, the ITS is typically thought of as "within" the repeat, while the IGS (most of which is not transcribed) is thought of as "between" the repeats. Within the tandem repeats, both are sandwiched between an SSU and an LSU, which are the major features ("genes") of the tandem repeat.
Because operons have a very specific meaning in prokaryotes, in the literature I have read I don't find the eukaryotic rDNA tandem repeat commonly referred to as an operon (more commonly it is referred to as a repeat). This may not be an important distinction, but the products are not translated like mRNA but instead are cleaved and directly become the rRNA molecules that make up the ribosome. Because there are no protein-coding loci, it's not quite as clear which strand is "sense" and which "antisense." That being said, there is a strand of the DNA that has the same sequence as the rRNA molecules, and so this would be the most sensible direction. And that is indeed SSU -> 5.8S -> LSU. That is the direction that is commonly used for members of the Kingdom Fungi and Straminipila that I research, but not for Angiosperms, which (in my minimal experience) read the rDNA in the other direction.
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