Sato Mitsuhiko P, Arafa Ramadan A, Rakha Mohamed T, Emeran Amero A, Isobe Sachiko, Shirasawa Kenta
Kazusa DNA Research Institute, Chiba 292-0818, Japan.
Plant Pathology Research Institute, Agricultural Research Center, Giza 12619, Egypt.
DNA Res. 2024 Dec 27;32(1). doi: 10.1093/dnares/dsae036.
Egyptian clover (Trifolium alexandrinum L.), also known as berseem clover, is an important forage crop to semi-arid conditions that was domesticated in ancient Egypt in 5,5000 BCE and introduced and well adapted to numerous countries including India, Pakistan, Turkey, and Mediterranean region. Despite its agricultural importance, genomic research on Egyptian clover has been limited to developing efficient modern breeding programs. In the present study, we constructed near-complete telomere-to-telomere-level genome assemblies for 2 Egyptian clover cultivars, Helaly and Fahl. Initial assemblies were established by using highly fidelity long-read technology. To extend sequence contiguity, we developed a gap-targeted sequencing (GAP-Seq) method, in which contig ends are targeted for sequencing to obtain long reads bridging 2 contigs. The total length of the resultant chromosome-level assemblies was 547.7 Mb for Helaly and 536.3 Mb for Fahl. These differences in sequence length can be attributed to the expansion of DNA transposons. Population genomic analysis using single-nucleotide polymorphisms revealed genomic regions highly differentiated between 2 cultivars and increased genetic uniformity within each cultivar. Gene ontologies associated with metabolic and biosynthetic processes and developmental processes were enriched in these genomic regions, indicating that these genes may determine the unique characteristics of each cultivar. Comprehensive genomic resources can provide valuable insights into genetic improvements in Egyptian clover and legume genomics.
埃及三叶草（Trifolium alexandrinum L.），也被称为berseem三叶草，是一种适应半干旱条件的重要饲料作物，于公元前5500年在古埃及被驯化，并被引入包括印度、巴基斯坦、土耳其和地中海地区在内的许多国家且适应性良好。尽管其在农业上具有重要意义，但埃及三叶草的基因组研究一直局限于开发高效的现代育种计划。在本研究中，我们为两个埃及三叶草品种Helaly和Fahl构建了近乎完整的端粒到端粒水平的基因组组装。最初的组装是通过使用高保真长读长技术建立的。为了扩展序列连续性，我们开发了一种缺口靶向测序（GAP-Seq）方法，其中对重叠群末端进行靶向测序以获得跨越两个重叠群的长读长。最终得到的染色体水平组装的总长度，Helaly为547.7 Mb，Fahl为536.3 Mb。这些序列长度的差异可归因于DNA转座子的扩增。使用单核苷酸多态性的群体基因组分析揭示了两个品种之间高度分化的基因组区域以及每个品种内遗传一致性的增加。与代谢、生物合成过程和发育过程相关的基因本体在这些基因组区域中富集，表明这些基因可能决定了每个品种的独特特征。全面的基因组资源可为埃及三叶草的遗传改良和豆科植物基因组学提供有价值的见解。
