Ding Ye, Zhao Yi, Xie Yangqin, Wang Fan, Bi Wu, Wu Mengyao, Zhao Guilin, Gong Yun, Li Wenli, Zhang Peng
Department of Chinese Materia Medica, Hunan Institute for Drug Control, Changsha, Hunan, 410001, P. R. China.
Zhuzhou Qianjin Pharmaceutical Co., Ltd. Zhuzhou, Zhuzhou, Hunan, 412000, P. R. China.
BMC Genomics. 2025 May 26;26(1):535. doi: 10.1186/s12864-025-11705-8.
Flemingia macrophylla, a prominent shrub species within the Fabaceae family, is widely distributed across China and Southeast Asia. In addition to its ecological importance, it possesses notable medicinal value, with its roots traditionally used for treating rheumatism, enhancing blood circulation, and alleviating joint pain. We employed Nanopore sequencing platforms to generate a high-quality reference genome for F. macrophylla, with an assembled genome size of 1.01 Gb and a contig N50 of 59.43 Mb. A total of 33,077 protein-coding genes were predicted, and BUSCO analysis indicated a genome completeness of 99%. Phylogenomic analyses showed that F. macrophylla is most closely related to Cajanus cajan among the sampled taxa, with an estimated divergence time of 13.2-20.0 MYA. Evidence of whole-genome duplication (WGD) events was detected in F. macrophylla, C. cajan, and P. vulgaris, with these species sharing two WGD events. The unique gene families in F. macrophylla are associated with strong resistance to both abiotic and biotic stress, supporting its remarkable ecological adaptability. Furthermore, gene family expansion analysis revealed a significant enrichment of genes related to secondary metabolites biosynthesis, providing a molecular basis for its high medicinal value. In summary, this study provides a foundational genomic resource for F. macrophylla, offering valuable insights into its genetic architecture, evolutionary history, and potential applications in medecine and agriculture. The comprehensive analyses lay the groundwork for future research into the species's medicinal properties and evolutionary biology.
大叶千斤拔是豆科中一种重要的灌木物种，在中国和东南亚广泛分布。除了具有生态重要性外，它还具有显著的药用价值，其根传统上用于治疗风湿病、促进血液循环和缓解关节疼痛。我们利用纳米孔测序平台为大叶千斤拔生成了高质量的参考基因组，组装后的基因组大小为1.01 Gb，重叠群N50为59.43 Mb。共预测了33077个蛋白质编码基因，BUSCO分析表明基因组完整性为99%。系统基因组分析表明，在采样的分类群中，大叶千斤拔与木豆关系最为密切，估计分化时间为1320-2000万年前。在大叶千斤拔、木豆和菜豆中检测到全基因组复制（WGD）事件的证据，这些物种共享两个WGD事件。大叶千斤拔中独特的基因家族与对非生物和生物胁迫的强抗性相关，支持其显著的生态适应性。此外，基因家族扩展分析显示与次生代谢物生物合成相关的基因显著富集，为其高药用价值提供了分子基础。总之，本研究为大叶千斤拔提供了基础基因组资源，为其遗传结构、进化历史以及在医学和农业中的潜在应用提供了有价值的见解。这些综合分析为该物种的药用特性和进化生物学的未来研究奠定了基础。
