I thought the ITS1 region is no more than 300 bp but my first PCR show fragments of about 500bp for different fungi!
Hi Jane,
I think that's extremely variable. I have experienced from around 500-600 bp for the entire ITS1, 5.8s, ITS2 region (using primers ITS1 and ITS4) up to ca. 1500bp in other fungi. These very long instances were due to very large ITS2 fragments, whereas ITS1 length was more stable. However, I would go ahead and sequence one of your 500 bp bands, as I believe that depending on what fungus you are amplifying it might be true that it has a 500bp ITS1 region.
Hi Jane,
I think that's extremely variable. I have experienced from around 500-600 bp for the entire ITS1, 5.8s, ITS2 region (using primers ITS1 and ITS4) up to ca. 1500bp in other fungi. These very long instances were due to very large ITS2 fragments, whereas ITS1 length was more stable. However, I would go ahead and sequence one of your 500 bp bands, as I believe that depending on what fungus you are amplifying it might be true that it has a 500bp ITS1 region.
Dear Jane,
Indeed, the length of ITS regions is very variable.
You can find some evidence of that in Toju et al, 2012, PLoS ONE.
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0040863
The Figure 3 of this paper shows differences in ITS length between different fungal phyla but also some variations within these phyla.
Best,
vincent
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