Liu Yu, Chen Yijun, Ren Zizheng, Li Kui, Wang Xu, Wu Kai, Liu Jinfeng, Sade Nir, He Hang, Li Shouke, Jiang Haiyang, Han Xue
National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China.
Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, 261325, China.
Sci Data. 2025 May 14;12(1):791. doi: 10.1038/s41597-025-05057-x.
Yellowhorn (Xanthoceras sorbifolium) is widely used in northern China for landscaping, desertification control, and oil production. However, the lack of high-quality genomes has hindered breeding and evolutionary studies. Here, we present the first haplotype-resolved, telomere-to-telomere (T2T) yellowhorn genomes of PBN-43 (white single-flowered) and PBN-126 (white double-flowered) using PacBio HiFi and Hi-C data. These assemblies range from 464.34 Mb to 468.97 Mb and include all centromeres and telomeres. Genome annotation revealed that an average of 67.99% (317.09 Mb) of yellowhorn genomic regions consist of repetitive elements across all haplotypes. The number of protein-coding genes ranges from 35,039 to 35,174 among assemblies, representing an average 50.16% increase over the first published yellowhorn genome. Additionally, 93.90% of the annotated genes have functional annotations. We found yellowhorn experienced an LTR-RT burst during the last 0.45-0.48 Mya. These data provide a resource for investigating genomic variations, phylogenetic relationships, duplication modes, and the distribution of nucleotide-binding leucine-rich repeat (NLR) genes, and support further research into yellowhorn breeding.
文冠果（Xanthoceras sorbifolium）在中国北方广泛用于景观美化、荒漠化治理和石油生产。然而，高质量基因组的缺乏阻碍了育种和进化研究。在这里，我们利用PacBio HiFi和Hi-C数据，首次展示了单瓣白花品种PBN - 43和重瓣白花品种PBN - 126的单倍型解析的端粒到端粒（T2T）文冠果基因组。这些组装基因组大小在464.34 Mb至468.97 Mb之间，包含所有着丝粒和端粒。基因组注释显示，文冠果所有单倍型基因组区域平均有67.99%（317.09 Mb）由重复元件组成。各组装基因组中蛋白质编码基因数量在35,039至35,174之间，比首次发表的文冠果基因组平均增加了50.16%。此外，93.90%的注释基因有功能注释。我们发现文冠果在过去45万至48万年前经历了一次长末端重复反转录转座子（LTR - RT）爆发。这些数据为研究基因组变异、系统发育关系、复制模式以及核苷酸结合富亮氨酸重复序列（NLR）基因的分布提供了资源，并支持对文冠果育种的进一步研究。
