2 questions reg. silva.nr_v123.align

Theory behind mothur
1

I understand that coordinates corresponding to 27f and 1492r priming sites are used in the generation of silva.nr_v123.align
from the silva.full_v123.fasta file ( http://blog.mothur.org/2015/12/03/SILVA-v123-reference-files/ ).

27f and 1492r priming sites would turn in the full length 16S gene.

When I do a grep for fungal sequences from silva.nr_v123.align, I do see a lot of Eukaryote / Fungal sequences in there.

grep “>” silva.nr_v123.align | grep “Eukaryota” | grep -c “Fungi”
4554

2 Questions

(1) So, does it imply presence of 16S molecule in eukaryotes / fungi as well ? --> Based on the above observation (i.e., grep outcomes)
(2) I understand that there are no ITS1/ITS2 portions in silva.nr_v123.align – based on the tests I did using
ITS1/ITS2 from S. cerevisea Chr12. Am I correct on this point ? Please tell me.

Please clarify. Thank you.

2

It’s 18S in Euk, slightly larger than the average bacterial.

There is no ITS in the SSU database. I can’t remember if there is ITS in LSU or not. If you are interested in fungal ITS, use unite. It is not aligned because it’s not possible to do a cross domain alignment of fungal ITS

3

To user: kmitchell
Thank you very much for confirming to me that there are no ITS sequences in the SSU database.