Towards an Anchored Reference Genome for Field Pennycress (Thlaspi arvense L.)

Field pennycress (Thlaspi arvense L.) is being developed as a new winter annual biodiesel feedstock and cover crop to fit within the corn/soybean rotation. As a winter cover crop, pennycress can provide important ecosystem services such as limiting soil erosion and nutrient runoff, as well as providing an additional source of income for farmers. Current lines can yield up to 1,500 pounds per acre of oilseed without displacing land currently used for food production. Pennycress currently exhibits numerous advantageous agronomic traits, however, improvements in key traits like decreased seed dormancy, rapid spring maturity, and reduced seed glucosinolate levels are needed to maximize the potential of this exciting new winter crop. To date, we have generated a de novo transcriptome assembly and draft genome for one high yielding line (MN106), which is being used to guide a mutation breeding approach currently underway. The first version of the draft genome was incomplete (<75% of the predicted genome size) and fragmented (6,780 scaffolds), thus a more complete and contiguous genome sequence for pennycress is needed. To this end, we have utilized the new Illumina TruSeq Synthetic Long Read technology to generate >5x coverage of the pennycress genome, yielding reads >1,500 bp. Combining these synthetic reads with an additional 150x coverage from the Illumina HiSeq 2500 platform (150bp paired end), a more complete genome assembly has been produced. Additionally, we have utilized a two-enzyme RADseq approach to create the first high-density genetic linkage map for pennycress. Ongoing work to anchor the long-read genome assembly to the linkage map will result in a highly contiguous and complete reference genome for pennycress. This resource will serve as an unprecedented resource for the rapid domestication of pennycress.