Flax is a globally important crop valued for its fiber, industrial uses, and omega-3-rich oil, yet incomplete genomic information has long limited efforts to understand and improve its key traits. A new study delivers the first fully gapless, telomere-to-telomere genome assembly of flax, providing a complete and highly accurate genetic blueprint. By reconstructing the entire genome without missing regions, the research reveals previously hidden genes, structural variations, and evolutionary signals that shape fatty acid biosynthesis and genome organization. The work not only refines the genetic map underlying oil composition but also uncovers how genome duplication and transposable elements may have driven functional diversification. Together, these insights establish a powerful foundation for advancing flax biology, breeding, and crop innovation.
Flax ( Linum usitatissimum L. ) is one of the richest plant sources of alpha-linolenic acid, an essential omega-3 fatty acid linked to human health benefits ranging from cardiovascular protection to metabolic regulation. Understanding how flax produces and regulates these fatty acids requires high-quality genome references. However, previously available flax genomes contained numerous gaps, unresolved repetitive regions, and incomplete telomere and centromere sequences, limiting accurate gene annotation and evolutionary analysis. These shortcomings have obscured key genes, masked structural variation, and constrained molecular breeding efforts. Based on these challenges, there is a clear need to generate a complete, gapless flax genome to enable deeper investigation of fatty acid metabolism, genome evolution, and trait improvement.
Researchers from Jilin Agricultural University, Nanjing Agricultural University, and the University of British Columbia reported (DOI: 10.1093/hr/uhaf127) on 7 May 2025 in Horticulture Research the first telomere-to-telomere genome assembly of flax. Using a combination of PacBio HiFi sequencing, Oxford Nanopore ultralong reads, and Hi-C scaffolding, the team produced a complete 482.51-Mb genome covering all 15 chromosomes without gaps. The study focuses on genome evolution and fatty acid metabolism, offering unprecedented resolution of genes, repetitive elements, and regulatory features that were previously inaccessible.
The gapless flax genome revealed substantial improvements over earlier assemblies, including a contig N50 exceeding 33 Mb, identification of all 30 telomeres and 15 centromeres, and annotation of more than 46,000 genes. Comparative analyses showed that repetitive sequences account for about 60% of the genome, dominated by long terminal repeat retrotransposons, which appear to play an active role in genome expansion and gene diversification. Evolutionary analysis uncovered three whole-genome duplication events occurring approximately 11.5, 53.5, and 114 million years ago, helping to explain the expansion of gene families linked to metabolism and stress responses.
Using the complete genome, the researchers reconstructed the flax fatty acid metabolic pathway in detail, identifying 49 structural genes, including six that were previously unannotated. Key desaturase gene families—stearoyl-ACP desaturase (SAD) and fatty acid desaturase (FAD)—were systematically analyzed, revealing conserved gene structures, motif patterns, and regulatory elements responsive to hormones and environmental stresses. Expression profiling across seed development stages showed coordinated yet distinct activity among gene copies, suggesting functional redundancy combined with stage-specific regulation. Notably, many fatty acid–related genes were found near transposable elements, supporting the idea that transposon-mediated duplication contributed to metabolic innovation during flax evolution.
“This genome represents a milestone for flax research,” said one of the study’s corresponding authors. “By achieving a truly complete, telomere-to-telomere assembly, we can now observe genomic regions that were invisible before, including centromeres, telomeres, and complex repeats. These features are not just structural—they influence gene regulation, evolution, and important agronomic traits. The ability to precisely locate and analyze fatty acid–related genes will significantly accelerate both fundamental research and molecular breeding aimed at improving oil quality and stress resilience.”
The complete flax genome provides a critical resource for crop improvement, enabling more accurate marker-assisted selection and genome-informed breeding strategies. Insights into fatty acid biosynthesis pathways can guide the development of flax varieties with tailored oil profiles, supporting nutrition, health, and industrial applications. Beyond flax, the study demonstrates the value of telomere-to-telomere assemblies for complex plant genomes, highlighting how repetitive elements and genome duplications shape trait evolution. As sequencing technologies continue to advance, such complete genomes are expected to transform research on crop domestication, metabolic engineering, and climate-resilient agriculture worldwide.
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References
DOI
Original Source URL
https://doi.org/10.1093/hr/uhaf127
Funding information
Jilin Agricultural University high-level researcher grant: JLAUHLRG20102006; Jilin Provincial Department of Human Resources and Social Security Grant No.: 201020012. This study is also supported by the 111 Project, Northeast Advantageous Characteristic Resources and Health Food Discipline Innovation Introduction Base, Grant No: D23007.
About Horticulture Research
Horticulture Research is an open access journal of Nanjing Agricultural University and ranked number one in the Horticulture category of the Journal Citation Reports ™ from Clarivate, 2023. The journal is committed to publishing original research articles, reviews, perspectives, comments, correspondence articles and letters to the editor related to all major horticultural plants and disciplines, including biotechnology, breeding, cellular and molecular biology, evolution, genetics, inter-species interactions, physiology, and the origination and domestication of crops.
Horticulture Research
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Telomere to telomere flax (Linum usitatissimum L.) genome assembly unlocks insights beyond fatty acid metabolism pathways
7-May-2025
The authors declare that they have no competing interests.