Insights from Low-Throughput Genomic DNA Sequencing.

A pilot genomic DNA sequencing study was done to serve as a platform for genetic marker development in turfgrass species with little genome sequence information.  Genomes of Danthonia spicata (poverty oatgrass), Agrostis canina (velvet bentgrass), A. capillaris (colonial bentgrass), and Poa pratensis (Kentucky bluegrass) were targeted along with three A. stolonifera (creeping bentgrass) accessions.  SSR and transposable element-based molecular markers derived from this data set have been previously reported. However this study also represents a significant sequencing effort and offers a unique opportunity to apply comparative genomic approaches to better understand these turfgrass species.  In total, 1.08 million Roche 454 FLX sequences were obtained with an average read length of 511 bp (552 MB total yield). Sequencing reads were mapped to Brachypodium distachyon or Setaria italica. Biased distribution of mapped reads to the reference genomes was observed; turf specific mapped sequencing reads were over or under represented in certain regions of the reference genomes. The basic local alignment search tool (BLAST) was used to characterize the anomalous mapped reads.  A majority of the sequences were similar to previously reported transposable elements. Genotype and species-specific transposable elements were discovered for each turf species, providing insights into genome organization and potentially speciation events and sources of genome plasticity. This study describes a comparative genomics approach to identify transposable elements in turfgrass species with limited upfront genome sequence information. Since the method does not rely on previous transposable element sequence information, it has potential to efficiently discover new transposable element classes.