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<p><i>Gardenia jasminoides</i>, an evergreen shrub in the Rubiaceae family, is widely cultivated across southern China, particularly in regions south of the Yangtze River. With a long history of use in traditional Chinese medicine, its fruits and flowers are valued for their rich diversity of bioactive compounds. In this study, Oxford Nanopore (ONT) sequencing produced 37–34 Gb of long-read data (60–66× coverage) per accession. Complementary PacBio HiFi sequencing generated 28–32 Gb (50–58× coverage), while Hi-C sequencing provided 61–67 Gb (108–119× coverage) to support chromosome-scale assembly. To ensure accuracy, contigs were polished through multiple iterations using Medaka (ONT-based) and Racon (HiFi-based). The final assemblies resolved all 11 chromosomes at telomere-to-telomere continuity, with no gaps. Functional annotation assigned roles to more than 94% of predicted genes (34,397–34,440) through homology and domain-based searches. This high-quality genome resource enables the study of structural variation underlying agronomic traits and supports advances in molecular breeding, bioactive compound biosynthesis, and comparative genomics in <i>Gardenia</i>.</p>

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Three Near telomere-to-telomere Genomes for Gardenia jasminoides

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年4月23日

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  • Zhijun Zeng,
  • Wenjie Lu,
  • Chaohuang Liu,
  • Xiang Zhang,
  • Ziheng Yao,
  • Ying Wang,
  • Shurong Xia,
  • Xiaojun Yan,
  • Xinjun Liao,
  • Lan Cao,
  • Yanhua Ji,
  • Hongning Liu

摘要

Gardenia jasminoides, an evergreen shrub in the Rubiaceae family, is widely cultivated across southern China, particularly in regions south of the Yangtze River. With a long history of use in traditional Chinese medicine, its fruits and flowers are valued for their rich diversity of bioactive compounds. In this study, Oxford Nanopore (ONT) sequencing produced 37–34 Gb of long-read data (60–66× coverage) per accession. Complementary PacBio HiFi sequencing generated 28–32 Gb (50–58× coverage), while Hi-C sequencing provided 61–67 Gb (108–119× coverage) to support chromosome-scale assembly. To ensure accuracy, contigs were polished through multiple iterations using Medaka (ONT-based) and Racon (HiFi-based). The final assemblies resolved all 11 chromosomes at telomere-to-telomere continuity, with no gaps. Functional annotation assigned roles to more than 94% of predicted genes (34,397–34,440) through homology and domain-based searches. This high-quality genome resource enables the study of structural variation underlying agronomic traits and supports advances in molecular breeding, bioactive compound biosynthesis, and comparative genomics in Gardenia.