Two 5 mm stainless steel beads

Fetal and maternal tissues were processed with RNAlater (Invitrogen, Carlsbad, CA) according to the manufacturer protocols. Viral RNA was isolated from the tissues using the Maxwell 16 LEV simplyRNA Tissue Kit (Promega, Madison, WI) on a Maxwell 16 MDx instrument (Promega, Madison, WI). A range of 20–40 mg of each tissue was homogenized using homogenization buffer from the Maxwell 16 LEV simplyRNA Tissue Kit, the TissueLyser (Qiagen, Hilden, Germany) and two 5 mm stainless steel beads (Qiagen, Hilden, Germany) in a 2 ml snapcap tube, shaking twice for 3 minutes at 20 Hz each side. The isolation was continued according to the Maxwell 16 LEV simplyRNA Tissue Kit protocol, and samples were eluted into 50 μl RNase free water.

Two 5 mm stainless steel beads (Qiagen, Hilden, Germany) were added to each 2 ml round-bottom tube containing approximately 150 mg wet mycelia and run at 30 hz for 2 minutes using a Retsch MM400 Tissuelyser (Newton, PA). Extractions were then done using a DNeasy Plant Mini Kit (Qiagen) according to the manufacturer’s instructions. Prior to sample submission DNA quality was evaluated by gel electrophoresis, and DNA was quantified using a Qubit (Thermo Fisher Scientific, Waltham, MA). Following quality control checks, 30 μl of each DNA sample at 50–100 ng/μl were pipetted into 96 well plates (95 samples per plate plus one blank well), placed on ice, and immediately submitted to the Cornell University Institute for Genomic Diversity (IGD). Library preparation and GBS were done at the Cornell IGD as previously described [33 (link)]. Briefly, adapters were ligated to DNA samples following digestion by the restriction enzyme ApeKI [33 (link)]. Samples were then pooled, enriched by PCR, and purified prior to 100 bp single-end sequencing on an Illumina Hi-Seq 2500 (Illumina, San Diego, CA). All GBS data are available from the National Center for Biotechnology Information Sequence Read Archive (Accession number XXX available upon acceptance).