The genomic data of Longhuihong (Citrus sinensis [L.] Osb. cv. LHH)

Sweet orange (<i>Citrus sinensis</i><em> </em>Osbeck) is a fruit crop of high nutritional value that is widely consumed around the world. However, its susceptibility to low-temperature stress limits its cultivation and production in regions prone to frost damage, severely impacting the sustainable development of the sweet orange industry. Therefore, developing cold-resistant sweet orange varieties is of great necessity. Traditional hybrid breeding methods are not feasible due to the polyembryonic phenomenon in sweet oranges, necessitating the enhancement of its germplasm through molecular breeding. High-quality reference genomes are valuable for studying crop resistance to biotic and abiotic stresses. However, the lack of genomic resources for cold-resistant sweet orange varieties has hindered the progress in developing such varieties and researching their molecular mechanisms of cold resistance. <br>This study integrated PacBio HiFi, ONT, Hi-C, and Illumina sequencing data to assemble telomere-to-telomere (T2T) reference genomes for the cold-resistant sweet orange mutant Longhuihong (<i>Citrus sinensis</i> [L.] Osb. cv. LHH). Comprehensive evaluations based on multiple criteria revealed that the genome exhibits high continuity, completeness, and accuracy. The genome size was calculated as 340.28 Mb with contig N50 of 39.31 Mb. In total, 31,456 gene models were annotated in the genomes. Leveraging this assembled genome in comparative genomics analysis with another cultivar genome we have examined the evolutionary history of the sweet orange genome.甜橙（*Citrus sinensis* Osbeck）是一种高营养价值的果品作物，在全球范围内广受消费。然而，其对低温胁迫的敏感性限制了其在易发生霜冻害地区的种植与生产，严重制约了甜橙产业的可持续发展。因此，培育抗寒甜橙品种具有重要的现实必要性。由于甜橙存在多胚现象，传统杂交育种方法难以实施，亟需通过分子育种手段改良其种质资源。高质量参考基因组对于研究作物抗生物及非生物胁迫具有重要价值，但目前抗寒甜橙品种的基因组资源匮乏，阻碍了抗寒品种培育及其抗寒分子机制研究的进展。 本研究整合PacBio HiFi、ONT、Hi-C及Illumina测序数据，对抗寒甜橙突变体‘隆回红’（*Citrus sinensis* [L.] Osb. cv. LHH）进行了端粒到端粒（T2T）参考基因组组装。基于多维度标准的综合评估显示，该基因组具有极高的连续性、完整性与准确性。该基因组组装大小为340.28 Mb，重叠群（contig）N50达39.31 Mb。本基因组中共注释得到31456个基因模型。本研究利用该组装基因组与已解析的另一甜橙栽培品种基因组开展比较基因组学分析，揭示了甜橙基因组的进化历程。