Transcriptomic dataset
For each seedling, up to three fascicles from the current year’s growth were sampled and flash frozen in liquid nitrogen for RNA extraction. Tissue sampling was performed across two days with consistent weather conditions between the hours of 12:00 and 17:00. A maximum of 100 mg of needle tissue per seedling was ground into a fine powder using liquid nitrogen with a mortar and pestle with 40 mg of polyvinylpyrrolidone (PVP-40) added. Total RNA was extracted using Spectrum Plant Total RNA Kits (Sigma-Aldrich). Following polyA tail selection to enrich for mRNA, libraries were prepared following standard protocols for the NEBNext Ultra II RNA Library Prep (Illumina) and sequenced on the Novaseq6000 platform at Novogene Corporation (Sacramento, CA).
Raw data were assessed for quality using fastqc and trimmed to remove adapters and low-quality reads using TrimGalore v.0.6.4 (Krueger, 2015). Due to lack of a well-annotated genome from a closely related species, we built a de novo transcriptome assembly using Trinity v.2.8.5 (Grabherr et al ., 2011; Haas et al ., 2013) with ak -mer length of 24 and a minimum contig size of 300bp. Further details about the assembly pipeline, filtering steps, quality assessment and annotations using EnTAP (Hart et al ., 2020) are detailed in the Supporting Information (Methods S1).