Alternative Biomass Production Study for Resilient Economic Agricultural Practices in Morris, Minnesota The Tillage Study was established in 1997 to assess the effect of a variety of tillage intensities on soil C. The initial eight treatments included no-tillage, moldboard + disk tillage, chisel tillage, and fall and spring residue management, with or without strip-tillage and strip-tillage + subsoiling (Archer and Reicosky, 2009). In 2004, treatments were reduced to no-tillage, moldboard tillage, and fall and spring residue management without strip-tillage, but all had an early or late planting date. The last comprehensive set of soil samples were collected in 2006. In 2008, the strip-tilled subset of the Tillage Study plots were repurposed for the Alternative Biomass Production Systems study, which was designed to explore alternative strategies to support bioenergy including planting of cellulosic feedstock. The Alternative Biomass Production plots included perennials in an extended 6-year rotation, winter cereal rye cover crops in a corn-soybean rotation, and an alternative Sorghum-Sudan grass hybrid forage system, all of which have and will continue to be monitored for agronomic and soil properties.

Carbon Crops Study for Greenhouse gas Reduction through Agricultural Carbon Enhancement network and Resilient Economic Agricultural Practices in Morris, Minnesota The overall goal of the Carbon Crop study, established in 2000, was to assess strategies for increasing soil C sequestration including converting to no till systems and including perennial grasses (e.g., switchgrass and big bluestem) Overall, the goal of the study has remained constant, although individual treatments were changed after an incremental soil sampling, in response to new hypotheses and questions. Soil sampling is conducted as treatment changes are implemented. In 2012, two of the perennial grass systems (spring harvest of Switchgrass and Big Bluestem) were changed to corn/soybean rotations, beginning with a soybean entry point, to determine if the SOC accrued under the perennial system was lost by converting to a short annual rotation managed without tillage. The second change made was to compare the productivity between recent and traditional switchgrass cultivars. The final change was conversion of autumn harvest of Big Bluestem treatment replaced with an annual biomass crop – Sorghum-Sudan grass. Soil samples were taken to 1 m in 2000, 2006, 2011, and 2016. Nitrous oxide and carbon dioxide fluxes from the soil were measured from June 2009 through March 2012.

Within this dataset: 1. Genome assembly of Linum lewisii (NDSU_LiLewi_1.0.fasta) * First 9 scaffolds represent all 9 chromosomes (e.g. Scaffold_1 is Chromosome 1, Scaffold_9 is Chromosome 9) * Remaining scaffolds are unplaced contigs * 4 scaffolds shorter than 200bp were removed (Scaffold_[1710-1713]) * Scaffold_919 was also removed due to identified contamination (a-proteobacteria) 2. Genome annotation file in GFF3 format 3. RNA-Seq data for tissue grown in dark conditions 4. RNA-Seq data for tissue grown in light conditions 5. RNA-Seq data of meristem tissue grown in cold conditions 6. RNA-Seq data of pre-flower (developing bud) tissue 7. RNA-Seq data of flowering tissue 8. RNA-Seq data of post-flower (developing seed capsules) tissue 9. Raw Omni-C reads Linum lewisii, a perennial blue flax native to North America, holds potential as a sustainable perennial crop for oilseed production due to its ecological adaptability, upright harvestable structure, nutritious seeds, and low insect and disease issues. Its native distribution spans a large geographic range, from the Pacific Coast to the Mississippi River, and from Alaska to Baja California. Tolerant to cold and drought conditions, this species is also important for native ecosystem rehabilitation. Its enhancement of soil health, support for pollinators, and carbon sequestration underscore its agricultural relevance. This study presents a high-quality, chromosome-scale assembly of the L. lewisii (2n = 2x = 18) genome, derived from PacBio HiFi and Dovetail Omni-C sequencing of the “Maple Grove” variety. The initial assembly contained 642,903,787 base pairs across 2,924 scaffolds. Following HiRise scaffolding, the final assembly contained 643,041,835 base pairs, across 1,713 scaffolds, yielding an N50 contig length of 66,209,717 base pairs. Annotation of the assembly revealed 38,808 genes, including 37,599 protein-coding genes and 7,108 putative transposable elements. Analysis of synteny with other flax species revealed a striking number of chromosomal rearrangements. We also found an intriguing absence of the single-copy TSS1 gene in the L. lewisii genome, potentially linked to its transition from heterostyly to homostyly. Taken together, these findings represent a significant advancement in our understanding of the Linum genus and provide a resource for future domestication efforts and basic research on Lewis flax.