Climate change presents distinct ecological and physiological challenges to plants as extreme climate events become more common. Understanding how species have adapted to drought, especially ecologically important non-model organisms, will be crucial to elucidate potential biological pathways for drought adaptation and inform conservation strategies. To aid in genome-to-phenome research, a draft genome was assembled for a diploid individual of Artemisia tridentata subsp. tridentata, a threatened keystone shrub in western North America. While this taxon has few genetic resources available and genetic/genomics work has proven difficult due to genetic heterozygosity in the past, a draft genome was successfully assembled. Aquaporin (AQP) genes and their promoter sequences were mined from the draft genome to predict mechanisms regulating gene expression and generate hypotheses on key genes underpinning drought response. Fifty-one AQP genes were fully assembled within the draft genome. Promoter and phylogenetic analyses revealed putative duplicates of A. tridentata subsp. tridentata AQPs which have experienced differentiation in promoter elements, potentially supporting novel biological pathways. Comparison with non-drought-tolerant congener supports enrichments of AQP genes in this taxon during adaptation to drought-stress. Differentiation of promoter elements revealed that paralogues of some genes have evolved to function in different pathways, highlighting these genes as potential candidates for future research and providing critical hypotheses for future genome-to-phenome work.

The data from this project have been submitted to NCBI and are available from the following accession numbers:

BioProject: PRJNA722258
BioSample: SAMN18747788
Draft genome assembly: JAHAUY000000000
SRA raw read submissions: SRR14309371, SRR14309372, and SRR14309373
Code utilized for analysis within the associated manuscript can be found in Release v0.0.1 of the DraftGenomeMineR GitRepo.

Supplementary documents, including scaffolds and alignment fasta, are openly accessible as "Supporting Information" within the Ecology and Evolution open access peer reviewed manuscript article. https://doi.org/10.1002/ece3.8245

Funding
US National Science Foundation and Idaho EPSCoR: OIA-1757324