Progress in Flax Genome Assembly from Nanopore Sequencing Data

Pushkova, Elena N.; Arkhipov, Alexander A.; Bolsheva, Nadezhda L.; Rozhmina, Tatiana A.; Zhuchenko, Alexander A.; Borkhert, Elena V.; Barsukov, Nikolai M.; Oleshnya, Gavriil A.; Milovanova, Alina V.; Moskalenko, Olesya D.; Kostromskoy, Fedor D.; Ivankina, Elizaveta A.; Dvorianinova, Ekaterina M.; Krupskaya, Daiana A.; Melnikova, Nataliya V.; Dmitriev, Alexey A.

doi:10.3390/plants15010151

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Progress in Flax Genome Assembly from Nanopore Sequencing Data

by

Elena N. Pushkova

^1,†,

Alexander A. Arkhipov

^1,2,†

,

Nadezhda L. Bolsheva

^1,†,

Tatiana A. Rozhmina

³,

Alexander A. Zhuchenko

^3,4,

Elena V. Borkhert

¹

,

Nikolai M. Barsukov

¹

,

Gavriil A. Oleshnya

^1,5,

Alina V. Milovanova

^1,5,

Olesya D. Moskalenko

^1,2,

Fedor D. Kostromskoy

¹

,

Elizaveta A. Ivankina

^1,2

,

Ekaterina M. Dvorianinova

¹

,

Daiana A. Krupskaya

¹

,

Nataliya V. Melnikova

¹

and

Alexey A. Dmitriev

^1,*

¹

Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia

²

Moscow Center for Advanced Studies, 123592 Moscow, Russia

³

Federal Research Center for Bast Fiber Crops, 172002 Torzhok, Russia

⁴

All-Russian Horticultural Institute for Breeding, Agrotechnology and Nursery, 115598 Moscow, Russia

⁵

Russian State Agrarian University—Moscow Timiryazev Agricultural Academy, 127434 Moscow, Russia

^*

Author to whom correspondence should be addressed.

^†

These authors contributed equally to this work.

Plants 2026, 15(1), 151; https://doi.org/10.3390/plants15010151

Submission received: 4 November 2025 / Revised: 19 December 2025 / Accepted: 24 December 2025 / Published: 4 January 2026

(This article belongs to the Special Issue Applications of Bioinformatics in Plant Science)

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Abstract

In recent years, the quality of genome assemblies has notably improved, primarily due to advances in third-generation sequencing technologies and bioinformatics tools. In the present study, we obtained genome assemblies for two flax (Linum usitatissimum L.) varieties, K-3018 and Svyatogor, using Oxford Nanopore Technologies (ONT) simplex R10.4.1 data and the Hifiasm algorithm optimized for ONT reads. The K-3018 genome assembly was 491.1 Mb and consisted of thirteen full-length chromosomes and two one-gap chromosomes. The Svyatogor genome assembly was 497.8 Mb and consisted of twelve full-length chromosomes and three one-gap chromosomes. All chromosomes had telomeric repeats at their ends for both varieties. Hi-C contact maps and Illumina genomic data supported the accuracy of the obtained assemblies. The K-3018 and Svyatogor genome assemblies surpassed the quality of the best currently available flax genome assembly of variety T397, which serves as a reference for L. usitatissimum in the NCBI Genome database. Comparative analysis revealed that the flax genomes are generally quite similar at the chromosome level, with only a few large-scale differences. Thus, two near-T2T (telomere-to-telomere) flax genomes were assembled from the ONT simplex R10.4.1 reads using Hifiasm ONT without involving Pacific Biosciences (PacBio) HiFi or ultra-long ONT reads as well as optical maps. High-quality flax genomes are essential for improving the efficiency of genetic research, evaluating genetic diversity at the whole-genome level, and developing breeding and genome editing approaches of this valuable multipurpose crop.

Keywords: flax; Linum usitatissimum; Nanopore; long-read sequencing; genome assembly; telomere-to-telomere; Hifiasm

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MDPI and ACS Style

Pushkova, E.N.; Arkhipov, A.A.; Bolsheva, N.L.; Rozhmina, T.A.; Zhuchenko, A.A.; Borkhert, E.V.; Barsukov, N.M.; Oleshnya, G.A.; Milovanova, A.V.; Moskalenko, O.D.; et al. Progress in Flax Genome Assembly from Nanopore Sequencing Data. Plants 2026, 15, 151. https://doi.org/10.3390/plants15010151

AMA Style

Pushkova EN, Arkhipov AA, Bolsheva NL, Rozhmina TA, Zhuchenko AA, Borkhert EV, Barsukov NM, Oleshnya GA, Milovanova AV, Moskalenko OD, et al. Progress in Flax Genome Assembly from Nanopore Sequencing Data. Plants. 2026; 15(1):151. https://doi.org/10.3390/plants15010151

Chicago/Turabian Style

Pushkova, Elena N., Alexander A. Arkhipov, Nadezhda L. Bolsheva, Tatiana A. Rozhmina, Alexander A. Zhuchenko, Elena V. Borkhert, Nikolai M. Barsukov, Gavriil A. Oleshnya, Alina V. Milovanova, Olesya D. Moskalenko, and et al. 2026. "Progress in Flax Genome Assembly from Nanopore Sequencing Data" Plants 15, no. 1: 151. https://doi.org/10.3390/plants15010151

APA Style

Pushkova, E. N., Arkhipov, A. A., Bolsheva, N. L., Rozhmina, T. A., Zhuchenko, A. A., Borkhert, E. V., Barsukov, N. M., Oleshnya, G. A., Milovanova, A. V., Moskalenko, O. D., Kostromskoy, F. D., Ivankina, E. A., Dvorianinova, E. M., Krupskaya, D. A., Melnikova, N. V., & Dmitriev, A. A. (2026). Progress in Flax Genome Assembly from Nanopore Sequencing Data. Plants, 15(1), 151. https://doi.org/10.3390/plants15010151

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