Fungal diversity surveys not using ITS amplicons


I was at a meeting a few weeks ago where the topic of fungal diversity surveys was discussed and many people there commented on how ITS based surveys (one of the main approaches for culture independent studies of fungi) had some limitations. ITS stands for the “internal transcribed sequence” and it is a region in between two rRNA genes that is highly variable and has become used as a means to identify fungi from sequence data. One limitation of ITS is that it is so variable that one cannot align many ITS regions to each other and this in turn means that to identify an organism from its ITS sequence the best way to do it is to have a reference database that has information on which ITS sequences map to which taxa. Unfortunately such reference DBS are not available for many fungi of interest. There are also other limitations of ITS approaches. There are benefits to using ITS too, but that is not the issue here – the issue is that there are some disadvantages and thus people are looking for other approaches.

In my lab we have been looking into fungal diversity studies using approaches other than ITS surveys but were not convinced we had found all the examples out there of such work. So I posted to Twitter and Facebook asking for help and got some useful responses. I have collated them together into a Storify. See below:

If you know of any other approaches, please share.

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Jonathan Eisen

I am an evolutionary biologist and a Professor at U. C. Davis. My lab is in the UC Davis Genome Center and I hold appointments in the Department of Medical Microbiology and Immunology in the School of Medicine and the Department of Evolution and Ecology in the College of Biological Sciences. My research focuses on the origin of novelty (how new processes and functions originate). To study this I focus on sequencing and analyzing genomes of organisms, especially microbes and using phylogenomic analysis (see my lab site here which has more information on lab activities).  In addition to research, I am heavily involved in the Open Access publishing and Open Science movements.