Amplicon-seq of P. trichocarpa microbiome
Amplicon metagenomic sequencing libraries were prepared as described in the Illumina 16s metagenomic sequencing library preparation guide (Part 15044223 Rev B) with a mixture of custom 515F and 806R primers for archaea/bacteria and primers designed to the ITS2 gene region for fungi (Dove et al. 2020; Rogers et al. 2018).  Pooled libraries for each sample type were validated on an Agilent Bioanalyzer (Agilent, Santa Clara, CA) using a DNA7500 chip, and the final library pool concentration was determined on an Invitrogen Qubit (Waltham, MA) with the broad range double stranded DNA assay. Paired end sequencing (2x 251x 8x 8) was competed on an Illumina MiSeq instrument (Illumina, San Diego, CA) using v2 chemistry.  Due to low base diversity of the amplicons, PhiX control DNA was included in the sequencing run.