Transcriptome dynamics in the dormancy-­‐spring growth transition of Douglas-­‐fir needles

Douglas-fir (Pseudotsuga menziesii) is an ecologically and economically important tree in the Pacific Northwest of North America that shows clear adaptive differences in the timing and rate of spring bud break and shoot growth.  Initial attempts to construct the Douglas-fir transcriptome from diverse tissues produced 25,002 isogroups (genes) totaling 53.6 Mbp and including 38,589 isoforms (alternatively spliced forms of a gene).  We have updated this reference by pooling 36 strand-specific RNA-Seq libraries from spring needle samples that span the transition from dormancy to early growth. Using an input of ~500 million strand-specific Illumina reads, de novo assembly produced 90,086 isogroups that together include 112.8 Mbp and 143,392 isoforms. Needle samples from three seed sources (two families each) were collected at seven time points spanning the dormant state, the time of spring bud break, and during active shoot elongation. Differential expression analysis identified 1,954 transcripts as occurring in significantly different abundances.  Of these transcripts, 19.0% were more abundant during dormancy than during periods of growth, 10.6% were more abundant during the transition from dormancy to growth and 70.4% were more abundant during growth than in dormancy.  A small fraction of these differentially expressed transcripts are attributable to organisms living on or in the needles of Douglas-fir (the needle meta-transcriptome); antisense transcripts are also evident, and contribute to differential expression between individuals, sources and times. This work contributes to the Douglas-fir Transcriptome Observatory, a project to document needle transcript regulation in a common garden through an entire growing season.