Draft Genome for Artemisia tridentata subsp. tridentata

Submission information
Submission Number: 104
Created: Mon, 09/27/2021 - 07:36
Dataset General Information
Draft Genome for Artemisia tridentata subsp. tridentata
Biological sciences

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

Dataset Key Terms
GEM3 Project Affiliation(s)
Internal Affiliation(s)
Boise State University
Mechanisms
External Affiliation(s)
Project Keywords
adaptation, Artemisia tridentata (sagebrush), climate change, drought, environmental change, genome to phenome, genomics
  • aquaporins
  • drought stress
  • genome mining
Dataset Authors & Contact Information

Data Authors/Creators

Authors/Creators
  • Other Author(s): James Beck
    ORCiD: 0000-0002-9086-2653
  • Other Author(s): Jerry Jenkins
    ORCiD: 0000-0002-7943-3997
  • Other Author(s): Lori Handley
    ORCiD: 0000-0002-9968-6051
  • Other Author(s): Min Kim
  • Other Author(s): Jane Grimwood
    ORCiD: 0000-0002-8356-8325
  • Other Author(s): Jeremy Schmutz
    ORCiD: 0000-0001-8062-9172
  • Other Author(s): Marcelo Serpe

Contact Information

Dataset Contact Information
Sven Buerki
svenbuerki@boisestate.edu
Geographic and Temporal Information
Geographic Research Space
This project involves a research component conducted at field site(s) or collecting data from a target population within a specific geographic area, This project involves a laboratory research component conducted within research facilities
  • Illumina NovaSeq platform, HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
Geographic Information
{Empty}
{Empty}
{Empty}
GEM3 Research Sites
Temporal Information
{Empty}
{Empty}
Dataset Files & Links
Metadata Files
{Empty}
{Empty}
{Empty}
Data Files
Dataset Resources
Administrative Submission Details
  • English
DOI Details
{Empty}
Data Licensing & Availability
Data is already in the public domain
2021-12-31
Funding Information
NSF Idaho EPSCoR Program: Award OIA‐1757324
{Empty}