Forests face an escalating threat from the increasing frequency of extreme drought events driven by climate change. To address this challenge, it is crucial to understand how widely distributed species of economic or ecological importance may respond to drought stress. Here, we used RNA-sequencing to investigate transcriptome responses at increasing levels of water stress in white spruce (Picea glauca (Moench) Voss), distributed across North America. We began by generating an expanded transcriptome assembly emphasizing short-term drought stress at different developmental stages. We also analyzed differential gene expression at four time points over 22 days in a controlled drought stress experiment involving 2-year-old plants and three genetically unrelated clones. De novo transcriptome assembly and gene expression analysis revealed a total of 33,287 transcripts (18,934 annotated unique genes), with 4,425 unique drought-responsive genes. Many transcripts that had predicted functions associated with photosynthesis, cell wall organization, and water transport were down-regulated under drought conditions, while transcripts linked to abscisic acid response and defense response were up-regulated. Our study highlights a previously uncharacterized effect of drought stress on lipid metabolism genes in conifers and significant changes in the expression of several transcription factors, suggesting a regulatory response potentially linked to drought response or acclimation. Our research represents a fundamental step in unraveling the molecular mechanisms underlying short-term drought responses in white spruce seedlings. In addition, it provides a valuable source of new genetic data that could contribute to genetic selection strategies aimed at enhancing the drought resistance and resilience of white spruce to changing climates.

This de novo transcriptome was assembled from RNA-Seq data obtained from three distinct experiments involving the collection of Picea glauca foliage. Sample types were selected to cover a wide range of conditions, with a particular focus on drought conditions, and represent diverse genes that are regulated in response to stress. A total of 16 samples came from a common garden experiment belonging to the International Diversity Experiment Network with Trees (IDENT) network, where eight trees had been subjected to water exclusion and eight others to summer irrigation since 2014. Six other samples came from a greenhouse experiment with a budworm-induced biotic stress treatment. Six samples were from a greenhouse drought stress experiment on young clonal seedlings including three water-stressed and three well-watered seedlings. For details please refer to the following paper: Ribeyre et al. De novo transcriptome assembly and discovery of drought-responsive genes in eastern white spruce (Picea glauca). Submitted to Frontiers in Plant Science.

De novo assembly

For each sample, clean reads were used to produce a transcriptome assembly using the SGA (Simpson and Durbin, 2012) and IDBA-UD assemblers (Peng et al., 2012) integrated within the a5 pipeline (Coil et al., 2015). Transcriptome assemblies were then scaffolded with one another using LINKS 1.8.6 (Warren et al., 2015). The resulting consensus assembly was then scaffolded again with a previously published Picea glauca transcriptome assembly (Rigault et al., 2011) using LINKS 1.8.6, and sequences shorter than 500 bp were removed as they were not likely to code for functional proteins.

• Simpson, J. T., and Durbin, R. (2012). Efficient de novo assembly of large genomes using compressed data structures. Genome Res. 22, 549–556. doi: 10.1101/gr.126953.111.
• Peng, C., Ma, Z., Lei, X., Zhu, Q., Chen, H., Wang, W., et al. (2011). A drought-induced pervasive increase in tree mortality across Canada’s boreal forests. Nat. Clim. Change 1, 467–471. doi: 10.1038/nclimate1293.
• Coil, D., Jospin, G., and Darling, A. E. (2015). A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data. Bioinforma. Oxf. Engl. 31, 587–589. doi: 10.1093/bioinformatics/btu661.
• Rigault, P., Boyle, B., Lepage, P., Cooke, J. E. K., Bousquet, J., and MacKay, J. J. (2011). A white spruce gene catalog for conifer genome analyses. Plant Physiol. 157, 14–28. doi: 10.1104/pp.111.179663.