Li Juncheng, Luo Wenlong, Jiang Biao, Kumar Satish, Lin Mengfei, Sun Qingming
Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences; Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural Affairs; Guangdong Provincial Key Laboratory of Science and Technology Research on Fruit Tree, Guangzhou, 510640, China.
Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China.
Sci Data. 2025 Apr 1;12(1):549. doi: 10.1038/s41597-025-04678-6.
Pitaya, (Selenicereus spp.), a fruit originating from North and Central America and extensively cultivated in China and Vietnam, holds significant economic value. Utilizing PacBio HiFi sequencing and Oxford Nanopore Technologies ultra-long sequencing, aided by Hi-C data, we have assembled a chromosome-level haplotype-resolved genome. The sizes of the two haplotype genomes were determined to be 1.477 Gb (hap1, contig N50 = 133.35 Mb) and 1.442 Gb (hap2, contig N50 = 132.57 Mb), with 96.7% (hap1) and 98.4% (hap2) respectively allocated to 11 pseudochromosomes. Hap1 comprises 58.94% repeat sequences and predicts a total of 29,139 protein-coding gene models and 18,378 non-coding RNAs. Hap2 comprises 58.37% repeat sequences and predicts a total of 28,538 protein-coding gene models and 19,458 non-coding RNAs. Notably, 93.5% and 93.6% of protein-coding genes were annotated for the two haplotypes. The high-quality genome assembly presented in this study provides a valuable resource for future ecological, evolutionary, biological, and breeding research in pitaya.
火龙果（Selenicereus spp.）原产于北美洲和中美洲，在中国和越南广泛种植，具有重要的经济价值。我们利用PacBio HiFi测序和牛津纳米孔技术超长测序，并借助Hi-C数据，组装出了一个染色体水平的单倍型解析基因组。两个单倍型基因组的大小分别为1.477 Gb（hap1，重叠群N50 = 133.35 Mb）和1.442 Gb（hap2，重叠群N50 = 132.57 Mb），其中hap1和hap2分别有96.7%和98.4%的序列被分配到11条假染色体上。Hap1包含58.94%的重复序列，共预测出29139个蛋白质编码基因模型和18378个非编码RNA。Hap2包含58.37%的重复序列，共预测出28538个蛋白质编码基因模型和19458个非编码RNA。值得注意的是，两个单倍型中分别有93.5%和93.6%的蛋白质编码基因得到了注释。本研究中展示的高质量基因组组装为火龙果未来的生态、进化、生物学和育种研究提供了宝贵资源。
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