Question: Chloroplast 16S sequences - any fun to be had?
gravatar for beegrackle
3 months ago by
United States
beegrackle90 wrote:

I am working with some 16S sequences (V4 region) from soils. I am looking at bacterial diversity and so of course removed chloroplast sequences, but I took a look at them and I am very curious about some of the patterns I am seeing in the phylogenetic tree in correlation with environmental variables.

I know nothing about plant phylogenetics, but is there any sort of taxonomic assignment I can do with my tiny bits of chloroplast sequences? At least to figure out if they are from green algae or land plants? I can only seem to find papers about removing chloroplast contamination or using the 18S region, but I figured it can't hurt to ask if anyone's ever tried it...or at least finding out if this is a really stupid question before I put in any effort.

sequencing taxonomy 16s • 176 views
ADD COMMENTlink modified 3 months ago by 5heikki7.3k • written 3 months ago by beegrackle90
gravatar for 5heikki
3 months ago by
5heikki7.3k wrote:

I think SILVA includes chloroplast SSU sequences

ADD COMMENTlink written 3 months ago by 5heikki7.3k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1060 users visited in the last hour