DOI: 10.5061/dryad.bcc2fqzm4
title: De novo transcriptome assembly and discovery of drought-responsive genes in eastern white spruce (Picea glauca)

description: 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.
description: This <em>de novo</em> transcriptome was assembled
 from RNA-Seq data obtained from three distinct experiments involving the
 collection of <em>Picea glauca</em> 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. <em>De novo</em> transcriptome assembly
 and discovery of drought-responsive genes in eastern white spruce
 (<em>Picea glauca</em>). 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 <em>Picea glauca</em>
 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. <em>Genome Res.</em> 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. <em>Nat. Clim. Change</em> 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. <em>Bioinforma. Oxf.
 Engl.</em> 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. <em>Plant
 Physiol.</em> 157, 14–28. doi: 10.1104/pp.111.179663.
description: # De novo transcriptome assembly and discovery of drought-responsive genes
 in eastern white spruce (Picea glauca)
 [https://doi.org/10.5061/dryad.bcc2fqzm4](https://doi.org/10.5061/dryad.bcc2fqzm4) ## Description of the data and file structure This file is a FASTA file containing all transcripts generated from *de novo* assembly and having a sequence of at least 500 bp. ## Sharing/Access information The *de novo* transcriptome assembly is also freely accessible on GitHub (link in Related Works section).