Improving Genome Assembly of Flax Line 3896 with High-Precision Illumina Reads

Flax (Linum usitatissimum L.) is a valuable agricultural crop grown for seed and fiber. Complete and accurate genome assemblies are the basis for molecular genetic studies and efficient breeding of flax. In the present work, we aimed to improve the accuracy of the Nanopore-assembled genome of line 3896, which is currently a reference genome for L. usitatissimum in the NCBI database. We sequenced the DNA of this line on the Illumina platform and obtained about 50x flax genome coverage. High-precision Illumina reads were used to polish the genome assembly of line 3896 by the POLCA tool. This significantly increased the accuracy of the assembly, which was reflected in the QUAST reference-based statistics, primarily in a drastic reduction in the number of single nucleotide polymorphisms (SNPs) and insertions/deletions (InDels). We also demonstrated the effect of polishing with Illumina reads on individual gene sequences. This procedure allowed us to correct erroneous SNPs and InDels in 14 of 25 examined genes of the SAD and FAD families, including those causing erroneous frameshifts and amino acid substitutions. Thus, we significantly improved the genome assembly of flax line 3896 and increased its value for basic and applied research on L. usitatissimum.