I have 16S data from ~270 plant samples, and most of them have a significant degree of chloroplast “contamination.” One of my projects originally sought to combine this data with RADseq data from the host plants in order to assess the influence of host phylogeny and geography on endophytic bacterial communities.
Due to COVID and time/budget issues, it is looking like it won’t be feasible for me to generate this RADseq data. I am a Ph.D. student trying to complete my dissertation, and cannot afford to delay graduation forever.
My advisor and I were talking, and he asked if I could do anything with the chloroplast sequences. In a sense, I already have host genetic data, though I’m not sure how useful these 16s chloroplast sequences will be for describing variation in the host genetics.
As part of my exploration of this topic, I thought I would post here and see if anyone has any ideas, or if any of you are familiar with people doing anything like this.
Thanks for any help or ideas!