Transcriptome characterization and polymorphism detection between subspecies of big sagebrush (Artemisia tridentata)

Prabin Bajgain, Bryce A. Richardson, Jared C. Price, Richard C. Cronn, Joshua A. Udall

Research output: Contribution to journalArticlepeer-review

Abstract

Background: Big 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.Results: cDNA 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.Conclusion: We 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.

Original languageEnglish (US)
Article number370
JournalBMC Genomics
Volume12
DOIs
StatePublished - Jul 18 2011
Externally publishedYes

Bibliographical note

Funding Information:
The funding for this work was provided by USDA Forest Service Western Forest Transcriptome Survey, National Fire Plan (research joint venture 09-JV-11221632-200) and the Great Basin Native Plant Selection and Increase Project (GBNPSIP). We sincerely thank Nancy Shaw for her help with ssp. wyomingensis seed collection; Stewart Sanderson for ploidy analyses; Edward Wilcox for his assistance with 454-pyrosequencing; Scott Yourstone and Brian Knaus for bioinformatic support; and Felix Jimenez for his assistance with polymorphism validation. We also express our thanks to E. Durant McArthur and Leigh Johnson for reviewing the manuscript and providing helpful suggestions.

Fingerprint

Dive into the research topics of 'Transcriptome characterization and polymorphism detection between subspecies of big sagebrush (Artemisia tridentata)'. Together they form a unique fingerprint.

Cite this