Oomycete ITS, isolated from a freshly cut stem
To characterize the initial endophyte community, sawdust was generated from three replicate individuals per species each for both small and large size classes and stored at -20oC until processing for DNA extraction and chemical analysis as described in Lee et al. 2019 Ecology (doi:10.1002/ecy.2790; unless otherwise indicated, cited references can be found in that paper). Briefly, DNA was extracted from 60 mg of wood shavings using a modified CTAB DNA extraction protocol (Doyle and Doyle 1987, Soltis et al. 1991) and samples were submitted to the Ramaciotti Centre for Genomics (UNSW Sydney, NSW, Australia) for fungal amplicon sequencing or the Western Sydney University Next Generation Sequencing Facility (Richmond, NSW, Australia) for oomycete amplicon sequencing. Amplicons to identify fungal taxa were generated using fITS7 (5-GTGARTCATCGAATCTTTG-3; (Ihrmark et al. 2012)) and ITS4 (5'-TCCTCCGCTTATTGATATGC-3'; (White et al. 1990)). Amplicons to identify oomycete taxa were generated using ITS1oo (5-GGAAGGATCATTACCACA-3; (Riit et al., 2016; doi:10.3897/mycokeys.14.9244) and ITS4. Amplicons were purified using the Agencourt AMpure XP system (Beckman Coulter, Lane Cove, NSW, Australia) and genomic libraries were prepared using the Nextera XT Index Kit (Illumina, San Diego, CA, USA). Paired-end (2 x 251 bases) sequencing was performed on the Illumina MiSeq platform.