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<p><i>Flemingia macrophylla</i>, a perennial shrub of the family Fabaceae, possesses pharmacological properties such as anti-inflammatory and antibacterial activities. However, its whole genome has remained largely unexplored. In this study, we generated a chromosome-level genome assembly of <i>F</i>. <i>macrophylla</i> by integrating high-fidelity (HiFi) long-read sequencing generated by Pacific Biosciences (PacBio) and high-throughput chromosome conformation capture (Hi-C) scaffolding. The assembled genome spans 1.13 Gb, with 93.29% of sequences anchored to 11 pseudochromosomes (scaffold N50 = 105.36 Mb), closely matching the estimated genome size based on <i>k</i>-<i>mer</i> analysis (1.07 Gb). Repetitive sequences account for 59.58% of the genome, with long terminal repeat (LTR) retrotransposons representing 39.25% of these elements. A total of 28,548 protein-coding genes were predicted in the assembled genome, of which 27,936 (97.86%) were functionally annotated. This high-quality genome provides a valuable foundation for elucidating medicinal compound biosynthesis, stress resistance mechanisms, and the genetic improvement of <i>F</i>. <i>macrophylla</i>, while also enriching the genomic resources available for the Fabaceae family.</p>

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Chromosome-scale genome assembly of Flemingia macrophylla

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2025年12月16日

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  • Ting Yuan,
  • Xiangyu Wang,
  • Ying Liang,
  • Ying Hu,
  • Yunfang Zhang,
  • Baoyou Huang,
  • Lingyun Chen,
  • Kunhua Wei

摘要

Flemingia macrophylla, a perennial shrub of the family Fabaceae, possesses pharmacological properties such as anti-inflammatory and antibacterial activities. However, its whole genome has remained largely unexplored. In this study, we generated a chromosome-level genome assembly of F. macrophylla by integrating high-fidelity (HiFi) long-read sequencing generated by Pacific Biosciences (PacBio) and high-throughput chromosome conformation capture (Hi-C) scaffolding. The assembled genome spans 1.13 Gb, with 93.29% of sequences anchored to 11 pseudochromosomes (scaffold N50 = 105.36 Mb), closely matching the estimated genome size based on k-mer analysis (1.07 Gb). Repetitive sequences account for 59.58% of the genome, with long terminal repeat (LTR) retrotransposons representing 39.25% of these elements. A total of 28,548 protein-coding genes were predicted in the assembled genome, of which 27,936 (97.86%) were functionally annotated. This high-quality genome provides a valuable foundation for elucidating medicinal compound biosynthesis, stress resistance mechanisms, and the genetic improvement of F. macrophylla, while also enriching the genomic resources available for the Fabaceae family.