Abstract
BackgroundBig sagebrush (Artemisia tridentata) is one of the most widely distributed and ecologically important shrub species in western North America. This species serves as a critical habitat and food resource for many animals and invertebrates. Habitat loss due to a combination of disturbances followed by establishment of invasive plant species is a serious threat to big sagebrush ecosystem sustainability. Lack of genomic data has limited our understanding of the evolutionary history and ecological adaptation in this species. Here, we report on the sequencing of expressed sequence tags (ESTs) and detection of single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) markers in subspecies of big sagebrush.ResultscDNA of A. tridentata sspp. tridentata and vaseyana were normalized and sequenced using the 454 GS FLX Titanium pyrosequencing technology. Assembly of the reads resulted in 20,357 contig consensus sequences in ssp. tridentata and 20,250 contigs in ssp. vaseyana. A BLASTx search against the non-redundant (NR) protein database using 29,541 consensus sequences obtained from a combined assembly resulted in 21,436 sequences with significant blast alignments (≤ 1e-15). A total of 20,952 SNPs and 119 polymorphic SSRs were detected between the two subspecies. SNPs were validated through various methods including sequence capture. Validation of SNPs in different individuals uncovered a high level of nucleotide variation in EST sequences. EST sequences of a third, tetraploid subspecies (ssp. wyomingensis) obtained by Illumina sequencing were mapped to the consensus sequences of the combined 454 EST assembly. Approximately one-third of the SNPs between sspp. tridentata and vaseyana identified in the combined assembly were also polymorphic within the two geographically distant ssp. wyomingensis samples.ConclusionWe have produced a large EST dataset for Artemisia tridentata, which contains a large sample of the big sagebrush leaf transcriptome. SNP mapping among the three subspecies suggest the origin of ssp. wyomingensis via mixed ancestry. A large number of SNP and SSR markers provide the foundation for future research to address questions in big sagebrush evolution, ecological genetics, and conservation using genomic approaches.
Highlights
Big sagebrush (Artemisia tridentata) is one of the most widely distributed and ecologically important shrub species in western North America
Assuming a limited amount of sequence divergence between the two subspecies’ coding sequence, both sets of expressed sequence tags (ESTs) were combined into a single, de novo assembly (Table 1)
The analysis showed that 8,598 (29%) of the total consensus sequences contained at least one single nucleotide polymorphism (SNP) and SNPs per contig ranged from 4,037 contigs with a single SNP to a single contig with 39 SNPs (Figure 4)
Summary
Big sagebrush (Artemisia tridentata) is one of the most widely distributed and ecologically important shrub species in western North America. Changes in land use and disturbance regimes (e.g., conversion to agriculture, overgrazing and wildfire frequencies) are major factors in the degradation of these ecosystems Such disturbances can lead to invasions by cheat grass (Bromus tectorum) and other weeds that fundamentally change the wildfire frequency and severely reduce the frequency of sagebrush in ecosystems where it historically dominated [6,7]. Restoration of these ecosystems requires replanting of big sagebrush, but the replanting should be carried out with a basis of scientific knowledge. Restoration of sustainable populations necessitates understanding of the local and landscape level genetic structure of natural big sagebrush populations
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