Genome sequencing of fiber flax cultivar Atlant Using Oxford Nanopore and Illumina Platforms

In this study, the genome of fiber flax cultivar Atlant was sequenced for the first time, using both Oxford Nanopore and Illumina platforms. For successful Nanopore sequencing, a protocol for extraction of pure high-molecular-weight DNA from the leaves of a single flax plant was developed. Sequencing of this DNA on the ONT platform resulted in 23 × flax genome coverage (8.4 Gb, N50 = 12 kb).

On the Illumina platform, 30 × genome coverage was obtained (22.6 million of 250 + 250 paired-end reads). Genome assemblies were performed using Canu, Flye, Shasta, and wtdbg2. Subsequent polishing by Racon, Medaka, and POLCA was used to improve the contig accuracy. The most complete and accurate assembly was achieved by Canu with the polishing scheme Racon + Medaka + POLCA: total length = 361.7 Mb, N50 = 350 kb, and 97.40% completeness according to BUSCO.

The genome was annotated using the funannotate pipeline and our transcriptome sequencing data for 5 different tissues of cultivar Atlant. The obtained results are useful for the evaluation of L. usitatissimum polymorphism at the genome level, the identification of sequences specific to fiber flax, as a reference in studies of fiber flax cultivars, and the development of flax genomic selection and genome editing.

These findings can also be used for the analysis of flax DNA methylation at the whole-genome level, as information on this DNA modification can be derived from Nanopore reads.