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 Melnikova9
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.

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Elena Zemlyanskaya
Elena Zemlyanskaya
1 year ago

Very valuable work!
I have a couple of questions.
1) How does the flax genome annotation obtained in your work correlate with other existing flax genome annotations?
2) Did you try to cluster the transcriptomes? Which tissues have close expression profiles, and which transcriptomes are specific?

Elena Pushkova
Elena Pushkova
1 year ago

Dear Dr. Zemlyanskaya,
Thank you for your questions and sorry for the late response!
1) In the NCBI genome database, assemblies only for three L. usitatissimum genomes are presented: linseed cultivar CDC Bethune (chromosome level, reference, GenBank: GCA_000224295.2), oil-used cultivar Longya 10 (scaffold level, GenBank: GCA_010665275.1), and fiber-used flax cultivar Heiya 14 (scaffold level, GenBank: GCA_010665265.1). For all three genomes, annotations are not submitted that complicates the use of these sequencing data in flax studies. Transcriptome sequencing and annotation of different tissues for particular flax genotypes were performed, however, there is no generalization of flax genome and transcriptome sequencing data and annotations, so, one of the aims of our study was to fill this gap.
2) We did not cluster the obtained flax transcriptomes yet, but we are actively working with our data now. For the assessment of distinctions in expression profiles between different genotypes and tissues, we plan to generate multidimensional scaling plots and a distance matrix.

Best regards,
Elena