Lu Jianyu, Wu Hanlu, Wang Fu, Li Jinxi, Wang Yifei, Zhao Qian, Wang Yingping, Wang Xiaonan, Lei Xiujuan, Sun Ruidong, Zhang Jun, Xiong Aisheng, Deyholos Michael K, Zhang Jian
Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China.
International Biotechnology Laboratory for Fiber Plants, Changchun 130118, China.
Hortic Res. 2025 May 7;12(8):uhaf127. doi: 10.1093/hr/uhaf127. eCollection 2025 Aug.
One of China's most important resources is flax ( L.), an ancient crop with significant nutritional and therapeutic benefits. Despite its importance, existing flax reference genomes remain incomplete, with many unassembled sequences. Here, we report a gapless 482.51 Mb telomere-to-telomere (T2T) flax genome assembly, predicting 46 634 genes, of which 42 805 were functionally annotated. Repetitive sequences constitute 60.05% of the genome, and we identified 30 telomeres and 15 centromeres across the chromosomes. Whole-genome duplication (WGD) events were detected at approximately 11.5, 53.5, and 114 million years ago (MYA) based on synonymous substitution rates (Ks). The T2T assembly enabled the reconstruction of the fatty acid metabolic pathway, identifying 49 related genes, including six newly annotated ones. Furthermore, genomic colocalization was observed between fatty acid metabolism pathway-related genes and transposable elements, suggesting that functional differentiation of these genes in flax evolution may have occurred through transposon-mediated duplication events. Phylogenetic analysis of and gene families revealed that genes segregate into and subfamilies. Gene structure and motif analyses demonstrated conserved exon-intron architectures and motif organization within each phylogenetic clade of and genes. Promoter region characterization identified numerous -acting elements responsive to phytohormones (MeJA and abscisic acid) and abiotic stresses (low temperature and anaerobic induction) in both and genes. Our knowledge of the evolution of the flax genome is improved by this excellent genome assembly, which also offers a strong basis for enhancing agricultural attributes and speeding up molecular breeding.
亚麻（L.）是中国最重要的资源之一，它是一种古老的作物，具有显著的营养和治疗功效。尽管其很重要，但现有的亚麻参考基因组仍不完整，存在许多未组装的序列。在此，我们报告了一个无间隙的、长度为482.51 Mb的端粒到端粒（T2T）亚麻基因组组装结果，预测有46634个基因，其中42805个基因得到了功能注释。重复序列占基因组的60.05%，我们在染色体上鉴定出30个端粒和15个着丝粒。基于同义替换率（Ks），在大约1.15亿年、5.35亿年和1.14亿年前（百万年前，MYA）检测到全基因组复制（WGD）事件。T2T组装使得脂肪酸代谢途径得以重建，鉴定出49个相关基因，包括6个新注释的基因。此外，在脂肪酸代谢途径相关基因和转座元件之间观察到基因组共定位，这表明这些基因在亚麻进化中的功能分化可能是通过转座子介导的复制事件发生的。对 和 基因家族的系统发育分析表明， 基因分为 和 亚家族。基因结构和基序分析表明，在 和 基因的每个系统发育分支内，外显子 - 内含子结构和基序组织是保守的。启动子区域特征分析在 和 基因中均鉴定出许多响应植物激素（茉莉酸甲酯和脱落酸）和非生物胁迫（低温和厌氧诱导）的顺式作用元件。这个出色的基因组组装改进了我们对亚麻基因组进化的认识，也为增强农业特性和加速分子育种提供了坚实基础。
