Zhu Yanxia, Tan Guiyu, Dong Qingsong, Huang Baoyou, Peng Yude, Jiang Jianping
National Center for TCM Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Naning, 530023, China.
Sci Data. 2024 Dec 2;11(1):1311. doi: 10.1038/s41597-024-04174-3.
Dried roots of Zanthoxylum nitidum (2n=2x=70, family Rutaceae) was referred as "Liang-Mian-Zhen" in Chinese, acting as a valuable species due to its notable pharmacological activities. Herein, we combined PacBio HiFi data together with Hi-C mapping technology to construct a chromosome-scale reference genome assembly for Z. nitidum. The assembly reached a length of 2.24 Gb, successfully anchoring 99.31% of sequences onto 35 pseudo-chromosomes. Among these, 26 chromosomes achieved telomere-to-telomere assembly, and 11 chromosomes were gap-free. The contigs N50 and scaffolds N50 reached 57.61 Mb and 78.00 Mb, respectively. Transposable elements comprised 81.44% of the Z. nitidum genome, and over 78% of them were long-terminal repeat retrotransposon elements. Furthermore, 32,737 protein-coding genes were identified and 99.38% of all were functionally annotated. The completeness of the genome assembly and final gene sets reached 97.83% and 96.47% based on Benchmarking Universal Single-Copy Orthologs (BUSCO), respectively. Taken together, our results provided a high-quality chromosome-level assembly of Z. nitidum genome and will be a valuable resource that will facilitate breeding varieties with higher alkaloids content.
两面针（2n=2x=70，芸香科）的干燥根在中文中被称为“两面针”，因其显著的药理活性而成为一种珍贵的物种。在此，我们将PacBio HiFi数据与Hi-C图谱技术相结合，构建了两面针的染色体水平参考基因组组装。该组装长度达到2.24Gb，成功将99.31%的序列锚定到35条假染色体上。其中，26条染色体实现了端粒到端粒的组装，11条染色体无间隙。重叠群N50和支架N50分别达到57.61Mb和78.00Mb。转座元件占两面针基因组的81.44%，其中超过78%是长末端重复逆转座子元件。此外，鉴定出32737个蛋白质编码基因，其中99.38%在功能上得到注释。基于基准通用单拷贝直系同源基因（BUSCO），基因组组装和最终基因集的完整性分别达到97.83%和96.47%。综上所述，我们的结果提供了高质量的两面针基因组染色体水平组装，将成为促进培育高生物碱含量品种的宝贵资源。
