Hey all,
Can anyone tell me why it is preferred to use sequencing of the ITS region of the 18s in fungi compared to shotgun sequencing? I would assume that shotgun would be preferred, based on the variability in the ITS size and PCR bias. But based on the literature, even in 2017, groups are using 18s.
I have shotgun data of the microbiome and I'm trying to determine the validity of my data in terms of the fungal community.
Thanks!
Hi Haley,
Shot gun will no doubt provide higher taxonomic resolution; it will also allow you to study the functional potential of the mycobiome. However, researchers like ITS because it is much cheaper and analysis pipelines are more established.
Regards
If you just want fungi, forget about the 18S. The taxonomic/phylogenetic resolution of the 18S in fungi is horrible unless you are only interested in quite high taxonomic rank resolution, e.g. order.
Shotgun seq of environmental samples for eukaryotes is simply not cost-effective, unless you are using your data for something else.
For a fine-grained profiling, use the ITS. You have well curated databases such UNITE and it was the marker used for fungal diversity by Earth Microbiome Project.
http://www.earthmicrobiome.org/protocols-and-standards/its/
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