Comparative analysis of flax (Linum usitatissimum L.) genomes and transcriptomes

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Elena Pushkova¹, George Krasnov², Roman Novakovskiy³, Liubov Povkhova⁴, Artemy Beniaminov⁵, Nadezhda Bolsheva⁶, Tatiana Rozhmina⁷, Alexey Dmitriev⁸, Nataliya Melnikova^9
1Engelhardt Institute of Molecular Biology, RAS, Moscow, Russia, pushkova18@gmail.com
²Engelhardt Institute of Molecular Biology, RAS, Moscow, Russia, gskrasnov@mail.ru
³Engelhardt Institute of Molecular Biology, RAS, Moscow, Russia, 0legovich46@mail.ru
⁴Engelhardt Institute of Molecular Biology, RAS, Moscow, Russia; Moscow Institute of Physics and Technology, Dolgoprudny, Russia, povhova.lv@phystech.edu
⁵Engelhardt Institute of Molecular Biology, RAS, Moscow, Russia, abeniaminov@mail.ru
⁶Engelhardt Institute of Molecular Biology, RAS, Moscow, Russia, nlbolsheva@mail.ru
⁷Engelhardt Institute of Molecular Biology, RAS, Moscow, Russia; Federal Research Center for Bast Fiber Crops, Torzhok, Russia, tatyana_rozhmina@mail.ru
⁸Engelhardt Institute of Molecular Biology, RAS, Moscow, Russia, alex_245@mail.ru
⁹Engelhardt Institute of Molecular Biology, RAS, Moscow, Russia, mnv-4529264@yandex.ru

Flax (Linum usitatissimum L.) is an agriculturally important plant that has a wide range of applications in industry, and the direction of cultivar application is determined by its genetic characteristics. The present work aimed to obtain high-quality sequences of flax genomes and transcriptomes for genetically diverse cultivars and lines, which have breeding value and different direction of use. Six cultivars/lines (LM98, #3896, Diplomat, Atlant, Universal, Alizee) were selected for the present work. We have developed an optimal method for the extraction of pure high-molecular-weight DNA from flax plants and performed genome and transcriptome sequencing. From 6 to 10 Gb was obtained for each of the studied flax cultivars/lines on the Oxford Nanopore platform and 20-25 million reads on the Illumina platform. Transcriptome sequencing of different flax tissues was also performed. Genome assembly using Flye resulted in the N50 value from 200 kb to 1 Mb depending on the genotype. Genome annotation was then performed. The obtained genome assemblies are the basis for molecular genetic studies in flax and allow assessment of the differences in L. usitatissimum cultivars/lines at the genome-wide level.