EST characterization and polymorphism detection of two Artemisia tridentata subspecies

Ranging over millions of acres of the western North America’s desert topology, sagebrush (Artemisia ssp.) is one of the most important ecological shrubs in the arid habitat. It is home to several rare fauna, food for domesticated and wild herbivores and plays a vital role in maintaining the desert rangeland eco-cycle in balance. We report here the 454 pyrosequencing of the EST libraries of two important subspecies of A. tridentata, for putative functional characterization of the ESTs as well as polymorphism detection for potential genotype based phylogeny study. Approximately 1.5 million sequence-reads with an average read length of 360 bp were generated from two 454-pyrosequencing runs. De novo assembly of the sequences produced an average read length of 670 bp with 20X coverage. A total of 20961 Single Nucleotide Polymorphisms (SNPs) with a 20X coverage were identified between the two subspecies. Also, 959 SSRs with 78% tri-nucleotide motifs and 507 Simple Sequence Repeats (SSRs) with 88% tri-nucleotide motifs were located in tridentata and vsaseyana, respectively. How many SNPs and SSRs were validated? Putative characterization of the ESTs for biological processes revealed that most genes are involved in metabolic and cellular processes, with about 55% each in tridentata and vaseyana.