- — Jenna Morgan Lang (@jennomics)Wed, May 21 2014 19:33:33
- — Jason Stajich (@hyphaltip)Wed, May 21 2014 19:52:35
- — Håvard Kauserud (@DrHyfe)Wed, May 21 2014 20:03:34
- — Anders Lanzen (@ambulanzen)Wed, May 21 2014 21:39:32
- — Jason Stajich (@hyphaltip)Thu, May 22 2014 01:42:25
- So, still two reasons to want a multiple sequence alignment of my "barcode" gene. 1) evolution! and 2) placement (even with uncertainty) of sequences that do not have an exact match in the database. It seems as though I won't be judged negatively should I switch to 28S (or LSU), but that I will have issues with taxonomic resolution and an inferior reference database, relative to ITS.
Pat brings up another concern. Isn't there a lot of intra-genomic size variation in ITS?
- — Pat Schloss (@PatSchloss)Wed, May 21 2014 20:30:41
- — Håvard Kauserud (@DrHyfe)Wed, May 21 2014 20:33:41@PatSchloss @jennomics Are a few examples, but intragenomic ITS variation seems not widespread in fungi, see e.g. http://www.mn.uio.no/ibv/english/people/aca/haavarka/lindner-et-al-2013.pdf …
- — Håvard Kauserud (@DrHyfe)Wed, May 21 2014 20:42:13
- — Pat Schloss (@PatSchloss)Wed, May 21 2014 20:47:56
- So, it seems like intragenomic ITS variation is no more of a concern with ITS than it is with 16S. So. maybe I will bring my ITS data to Pat's R workshop after all.
So, here's my final take on the issue:
- — Jenna Morgan Lang (@jennomics)Wed, May 21 2014 22:35:17
- We can't turn ITS into a good phylogenetic marker, but we can fill up the 28S database. Maybe taxonomic resolution isn't perfect, but what is?
What the fungi do I do with my ITS library? (Pt. 2)
Previously, I expressed some concern about size variation in my environmental fungal ITS PCR libraries. I'm still concerned about that, but I have an additional concern. The ITS region can't be aligned, and I'm partial to phylogenetic approaches to pretty much everything. So maybe ITS is not for me?
byJenna Morgan Lang60 Views