Artemisia (family: Asteraceae) is a widely distributed plant genus that is predominantly found in temperate regions of the northern hemisphere. Some species within this genus are valued for medicinal properties, cooking, herbs and forage for wildlife and livestock [1-2]. Others like big sagebrush (Artemisia tridentata) are recognized for their importance to ecosystem function. Big sagebrush is one of the most abundant, widespread and ecologically important woody shrubs in the intermountain regions of western North America. This species contains three widespread subspecies (A. t. ssp. tridentata, A. t. ssp. vaseyana, and A. t. ssp. wyomingensis) that occupy distinct ecotypes and two less common subspecies (A. t. ssp. spiciformis and A. t. ssp. xericensis) [3-4]. Prior to Anglo-settlement, big sagebrush was estimated to occupy up to 100 million ha of western United States, while contemporary estimates have shown that the area might have been reduced to 43 million ha . Changes in land use and disturbance regimes (e.g., conversion to agriculture, overgrazing and wildfire frequencies, respectively) are major factors in the degradation of these ecosystems, but their severity depends on the sagebrush ecotype. Such disturbances can lead to invasions of cheat grass (Bromus tectorum) or other invasive weeds like medusahead (Taeniatherum caput-medusa) that fundamentally change the wildfire frequency inhibiting big sagebrush recruitment [6-7]. Restoration of these ecosystems requires replanting big sagebrush, which necessitates understanding the local and landscape level genetic structure.
Polyploidy and intra- and interspecific hybridization are likely important factors in big sagebrush adaptation and landscape dominance. Big sagebrush subspecies occupy specific ecological niches: ssp. tridentata grows in alluvial flats at elevation lower than 1800 m, ssp. vaseyana is found in higher altitude uplands at elevation above 1660 m up to timberline, and ssp. wyomingensis typically occupies drier sites with shallow soils . Subspecies wyomingensis is tetraploid, where as ssp. tridentata and vaseyana are typically diploid. In some ecotones, hybridization between ssp. vaseyana and ssp. tridentata is common. Hybridization has been well studied using reciprocal transplants showing that natural selection tends to limit hybrids of A.t. ssp. tridentata and A.t. ssp. vaseyana to an ecotone between subspecies [8-9]. McArthur and Sanderson  suggest that hybrid zones could be repositories of genetic variation, gene exchange and influence the evolution of big sagebrush.
Though widely acknowledged as an important shrub of the intermountain ecosystem in western North America, very limited DNA sequence data has been collected on big sagebrush. A search for A. tridentata nucleotide sequences in the NCBI database yielded 32 nucleotide sequences. As a genus, Artemisia has approximately 3.8 million sequences (or ~823 Mbp) of which 3.7 million reads are archived in the Sequence Read Archive (SRA), from A. annua Expressed Sequence Tag (EST) project , and an ongoing A. annua genome project (http://www.ncbi.nlm.nih.gov). A. annua is a medicinal herb native to temperate Asia and not found in the western hemisphere. Sequences of A. tridentata are needed to conduct research studies involving phylogenetics, population genetics or functional genetics. Hence, performing transcriptome sequencing and subsequent annotation and marker detection on big sagebrush would provide a foundation for future studies.
Despite the ubiquity of sagebrush, the history and even accurate identification of sagebrush has been a source of contention among researchers. Much of these limitations stem from morphological and ecological similarities between species and subspecies. Accurate identification of sagebrush is not only a scientific issue, but an economic one. To prevent invasive species from redefining the Western United States requires that sagebrush maintain its dominate role on the landscape. In order to maintain this role, accurate identification of the correct species/subspecies of sagebrush for reseeding the landscape after a fire is critical. Today's technologies combining SNP detection and next-generation sequencing allow for identification of species and population specific markers. These SNPs also help researchers to understand population structure. Furthermore, they allow tracing of inheritance patterns that elucidate the complex evolutionary history of sagebrush.
The Sagebrush Amplicon Sequencing was published in the American Journal of Botany
Sagebrush Amplicon Sequencing pdf
The Sagebrush EST was published in the journal BMC Genomics.
Big sagebrush (Artemisia tridentata) dominates the landscapes of the western United States. Its distribution alone warrants its scientific and ecological importance. However, despite its ubiquity, taxonomic identification of big sagebrush subspecies has been a source of contention among botanists. Much of these limitations stem from variation in morphological characters caused by polyploidy and hybridization. Accurate identification of big sagebrush is not only a scientific issue, but an economic one. To prevent invasive species from altering sage-steppe ecosystems requires that big sagebrush maintain its dominant role on the landscape. In order to maintain this role, accurate identification of the subspecies is critical to ensure successful restoration after disturbances. Today's technologies of combining SNP detection and next-generation sequencing allow for identification of subspecies and population specific markers. These SNPs also help researchers to define population structure. Furthermore, they allow tracing of inheritance patterns that elucidate the complex evolutionary history of big sagebrush.
Primers have been designed for targeted resequencing of 192 samplings of sagebrush representing multiple populations across the western United States. These primers enrich the polymorphic regions of the chloroplast. Targeting of the cytoplasmic genome allows for the analysis of greater conserved markers and eliminates the need for haplotype phasing. Using the Fluidigm Access Array System, each sample was amplified with 48 primers and is awaiting sequencing. Aligning the sequence data with a reference genome will help develop markers at both the subspecies and population levels.