Chromosome-scale genomic assembly of Lewis flax (Linum lewisii Pursh.)

Authors: INNES, PETER - University Of Colorado; SMART, BRIAN - North Dakota State University; BARHAM, JOSEPH - North Dakota State University; Hulke, Brent; KANE, NOLAN - University Of Colorado

Submitted to: bioRxiv
Publication Type: Pre-print Publication
Publication Acceptance Date: 10/10/2023
Publication Date: 10/10/2023
Citation: Innes, P., Smart, B., Barham, J., Hulke, B.S., Kane, N. 2023. Chromosome-scale genomic assembly of Lewis flax (Linum lewisii Pursh.). bioRxiv. https://doi.org/10.1101/2023.10.10.561607.
DOI: https://doi.org/10.1101/2023.10.10.561607

Interpretive Summary: The perennial flax relative, Lewis flax, is a widely adapted plant that can thrive under various climates. It is a candidate for domestication and has the potential to be a source of omega-3 rich vegetable oils and other products. Not much is known about the genetics of the plant, and the genome has not been studied. This is the first report of a high quality reference genome of Lewis flax. The only publicly available Lewis flax cultivar, 'Maple Grove', was sequenced using long-read DNA sequence technology and the genome was further characterized by sequencing expressed genes. This knowledge will allow us to make full use of modern genetic and genomic methods to study inheritance of many relevant plant traits in the future.

Technical Abstract: Linum lewisii, a perennial pale 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 relatively low insect or 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 offers promising potential 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, distributed 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 amount 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.