Cui Jian, Zhu Congle, Shen Lisha, Yi Congyang, Wu Rong, Sun Xiaoyang, Han Fangpu, Li Yong, Liu Yang
School of Architecture & Built Environment, The University of Adelaide, Adelaide, 5005, Australia.
Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
Hortic Res. 2024 Jul 10;11(9):uhae185. doi: 10.1093/hr/uhae185. eCollection 2024 Sep.
, 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 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 genome by developing a specific CENH3 antibody. We demonstrate that centromeric regions in 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 genome, accompanied by detailed genomic annotations and centromere analysis, significantly enhances potential as a subject of study in fields ranging from ecology and horticulture to traditional medicine.
连翘，俗称金钟花，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存在重复和缺口问题，阻碍了深入的基因组分析。在此，我们展示了连翘基因组的端粒到端粒（T2T）组装，整合了牛津纳米孔技术（ONT）超长读长、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33932个预测的蛋白质编码基因。此外，我们通过开发一种特异性的CENH3抗体来表征连翘基因组中的功能着丝粒。我们证明连翘的着丝粒区域呈现出多种卫星序列，在不同染色体上展示出具有非常规长度的独特类型。这一发现对CENH3的适应性以及对着丝粒动态的潜在影响具有启示意义。此外，在评估全长LTRs在着丝粒区域的插入时间后，我们发现它们比整个基因组中的LTRs更古老，这与其他物种中着丝粒逆转座子通常较年轻的观察结果形成对比。我们推测无性繁殖可能影响逆转座子动态，进而影响着丝粒进化。总之，我们对连翘基因组的T2T组装，以及详细的基因组注释和着丝粒分析，显著提升了连翘在从生态、园艺到传统医学等领域作为研究对象的潜力。
