SRS308266 SAMN00849794 278161 Pseudotsuga menziesii var. menziesii The second multi-genotype dataset (MG2_R) was derived from three tissue collection regimes. First, on each of five dates between September and April, we harvested 12 first-year seedlings and separated them into needles, stems, and buds. These seedlings were grown outdoors in Corvallis, OR, but their seed orchard parents originated from a low elevation population near Coos Bay (CB), OR. Second, we harvested three seedling tissues on 11 dates throughout the year from a total of 82 seedlots . We harvested buds (i.e., elongating apices or resting buds), shoots (stems plus needles), and roots on one or more dates from seedlings provided by the Cottage Grove Nursery of Plum Creek Timber Company. These seedlings were grown outdoors in Corvallis, and some were droughted to induce the expression of genes associated with adaptation to cold and drought. Third, we collected elongating shoots from ramets of two clonal genotypes growing at the Lebanon Forest Regeneration Center. Because these shoots were collected during June from trees that had been stimulated to produce reproductive buds, they are expected to contain differentiating male and female strobili. SRS308271 SAMN00849799 3357 Pseudotsuga menziesii The coastal Douglas-fir Coos Bay (CB_I) data set was derived from a subset of the Coos Bay RNA samples in Sample MG2, plus replicate samples that were harvested on some of the same dates. We used six bud samples and two needle samples for a total of eight Illumina sequencing runs. The Yakima (YK_I) dataset was prepared using the same collection protocol and sequencing protocol as for the CB_I dataset, but the seedlings were derived from parents growing in a high-elevation (>1500 m) inland population near Yakima WA that is thought to represent interior Douglas-fir. SRS308272 SAMN00849800 3357 Pseudotsuga menziesii The interior Douglas-fir samples were collected from mature trees growing in a provenance test near Vernon, B.C., Canada and the Cherrylane seed orchard in northern Idaho. Young shoots were collected from the provenance test in early May from two trees from each of 26 bulk seedlots collected from Arizona and New Mexico in the south, to British Columbia and Washington state in the north. Approximately equal amounts of total RNA were pooled from recently flushed buds, stems, young needles, and mature needles. The seed orchard samples were collected in early June from 18 trees originating from northern Idaho. Approximately equal amounts of total RNA were pooled from stems and needles harvested from recently flushed shoots. The two pooled RNA samples were then combined for Illumina sequencing.