High-Quality Genome Sequences of Cultivated (Linum usitatissimum) and Wild (L. bienne) Flax

Citation

You FM, Rashid K, Cloutier S, Chen W, Luo M-C, Zhu (2018) High-quality genome sequences of cultivated (Linum usitatissimum) and wild (L. bienne) flax. Proc 26th Plant and Animal Genome Conference, San Diego, CA, January 13-17, P0911 (poster)

Abstract

The cultivated flax (L. usitatissimum) and its wild progenitor (L. bienne) are important germplasm for flax breeding. Both species are diploids and have a haploid chromosome number of 15 with a genome size of ~370 Mb. The cultivated flax cv. CDC Bethune has been sequenced using Illumina platform (Wang et al. 2012) and sorted onto chromosomes (You et al. 2016). Additional sequencing using the PacBio Sequel system was performed to ~60× to fill gaps and lengthen scaffolds. We also sequenced the wild flax accession LIN1917 using the long reads of the PacBio RS II system to ~50×. De novo assembly was performed using the canu software followed by polishing using Quiver or Arrow (for raw PacBio reads) and Pilon (for Illumina reads). The CDC Bethune assembly contained 2315 contigs in 359 Mb with an N50 of 2.13 Mb while LIN1917 assembled into 1152 contigs totalling 313Mb with an N50 of 0.90 Mb. To validate, orient and order the PacBio contigs to chromosomes, we constructed BioNano optical maps for CDC Bethune, Macbeth (pedigree similar to CDC Bethune) and LIN1917. With BioNano optical maps, consensus genetic map (Cloutier et al. 2012), BAC fingerprint-based physical map (Ragupathy et al. 2011) and the previous version of cultivated flax pseudomolecules, we generated high-quality, chromosome-based pseudomolecules with fewer and smaller gaps for both cultivated and wild flax. These pseudomolecules will be useful to study genome evolution, for genome-wide SNP discovery, QTL identification, and comparative genome analysis and to capitalize upon wild flax germplasm in breeding.

Publication date

2018-01-17