Survey of the Sugar Pine (Pinus lambertiana) Transcriptome By Deep Sequencing.

While rapid progress has been made in characterizing the genomes of angiosperms, the same is not true for gymnosperms, in part due to their size and complexity. The advent of high-throughput sequencing technologies has enabled complete genomes in a few economically important conifer species. In this study, we present a comprehensive transcriptome of one of the largest conifer genomes, sugar pine. The natural range of this white pine extends from the west slope of the Cascade Range in Oregon to the Sierra San Pedro Martir in Baja California. Over 30 tissue-specific RNA libraries have been constructed, including needle, root, stem, pollen, cone, strobili, and embryonic tissues. A variety of treatments were applied to seedlings before RNA extraction, including: cold/heat shock, flood/drought stress, wounding and salicylic or methyl jasmonate exposure. Additionally, tissue samples from white pine blister rust (Cronartium ribicola Fisch.) resistant and susceptible individuals were sequenced. Short read technologies (Illumina MiSeq and HiSeq) and the Pacific Biosciences Iso-Seq reads which result from size-selected libraries ranging from 1,000 to over 6,000 bp, have been included in the de novo assembly. The combination of long and short reads combats many of the existing challenges in transcriptome assembly. These data represent the first comprehensive survey of the sugar pine transcriptome. This assembly will provide insight on disease resistance as well as a resource for scaffolding and annotating the full genome assembly that is currently underway.