Forsythia suspensa, commonly known as weeping forsythia, holds significance in traditional medicine and horticulture. Despite its ecological and cultural importance, the existing reference genome presents challenges with duplications and gaps, hindering in-depth genomic analyses. Here, we present a Telomere-to-Telomere (T2T) assembly of the F. suspensa genome, integrating Oxford Nanopore Technologies (ONT) ultra-long, Hi-C datasets, and high-fidelity (HiFi) sequencing data. The T2T reference genome (Fsus-CHAU) consists of 14 chromosomes, totaling 688.79 Mb, and encompasses 33,932 predicted protein-coding genes. Additionally, we characterize functional centromeres in the F. suspensa genome by developing a specific CENH3 antibody. We demonstrate that centromeric regions in F. suspensa exhibit a diverse array of satellites, showcasing distinctive types with unconventional lengths across various chromosomes. This discovery offers implications for the adaptability of CENH3 and the potential influence on centromere dynamics. Furthermore, after assessing the insertion time of full-length LTRs within centromeric regions, we found that they are older compared to those across the entire genome, contrasting with observations in other species where centromeric retrotransposons are typically young. We hypothesize that asexual reproduction may impact retrotransposon dynamics, influencing centromere evolution. In conclusion, our T2T assembly of the F. suspensa genome, accompanied by detailed genomic annotations and centromere analysis, significantly enhances F. suspensa potential as a subject of study in fields ranging from ecology and horticulture to traditional medicine.

中文翻译：

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连翘的无间隙基因组阐明了着丝粒的复杂景观


连翘，俗称垂连翘，在传统医学和园艺中具有重要意义。尽管其具有生态和文化重要性，但现有的参考基因组带来了重复和缺口的挑战，阻碍了深入的基因组分析。在这里，我们展示了悬铃木基因组的端粒到端粒（T2T）组装，整合了牛津纳米孔技术（ONT）超长、Hi-C数据集和高保真（HiFi）测序数据。 T2T 参考基因组 (Fsus-CHAU) 由 14 条染色体组成，总计 688.79 Mb，包含 33,932 个预测的蛋白质编码基因。此外，我们通过开发特定的 CENH3 抗体来表征 F. suspensa 基因组中的功能着丝粒。我们证明，F. suspensa 的着丝粒区域表现出各种各样的随体，展示了不同染色体上具有非常规长度的独特类型。这一发现为 CENH3 的适应性及其对着丝粒动力学的潜在影响提供了启示。此外，在评估着丝粒区域内全长LTR的插入时间后，我们发现它们比整个基因组中的LTR更老，这与在其他物种中观察到的着丝粒逆转录转座子通常年轻的情况形成鲜明对比。我们假设无性繁殖可能会影响逆转录转座子动力学，从而影响着丝粒的进化。总之，我们对悬铃木基因组的 T2T 组装，加上详细的基因组注释和着丝粒分析，显着增强了悬铃木作为生态学、园艺到传统医学等领域研究对象的潜力。