Fruit Tree Research Institute, Chongqing Academy of Agricultural Sciences, Chongqing 401329, China.
Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China.
Gigascience. 2024 Jan 2;13. doi: 10.1093/gigascience/giae084.
Sweet orange (Citrus sinensis 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.
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" (Citrus sinensis [L.] Osb. cv. LHH) and its wild-type counterpart "Newhall" (C. sinensis [L.] Osb. cv. Newhall). Comprehensive evaluations based on multiple criteria revealed that both genomes exhibit high continuity, completeness, and accuracy. The genome sizes were 340.28 Mb and 346.33 Mb, with contig N50 of 39.31 Mb and 36.77 Mb, respectively. In total, 31,456 and 30,021 gene models were annotated in the respective genomes. Leveraging these assembled genomes, comparative genomics analyses were performed, elucidating the evolutionary history of the sweet orange genome. Moreover, the study identified 2,886 structural variants between the 2 genomes, with several SVs located in the upstream, downstream, or intronic regions of homologous genes known to be associated with cold resistance.
The study de novo assembled 2 T2T reference genomes of sweet orange varieties exhibiting different levels of cold tolerance. These genomes serve as valuable foundational resources for genomic research and molecular breeding aimed at enhancing cold tolerance in sweet oranges. Additionally, they expand the existing repository of reference genomes and sequencing data resources for C. sinensis. Moreover, these genomes provide a critical data foundation for comparative genomics analyses across different plant species.
甜橙（Citrus sinensis Osbeck）是一种具有高营养价值的水果作物，在世界各地广泛食用。然而，其对低温胁迫的敏感性限制了其在易受霜害地区的种植和生产，严重影响了甜橙产业的可持续发展。因此，开发抗寒甜橙品种是非常必要的。由于甜橙的多胚现象，传统的杂交育种方法不可行，需要通过分子育种来增强其种质。高质量的参考基因组对于研究作物对生物和非生物胁迫的抗性非常有价值。然而，缺乏抗寒甜橙品种的基因组资源阻碍了开发此类品种和研究其抗寒分子机制的进展。
本研究整合了 PacBio HiFi、ONT、Hi-C 和 Illumina 测序数据，组装了抗寒甜橙突变体“龙回红”（Citrus sinensis [L.] Osb. cv. LHH）及其野生型对照“纽荷尔”（C. sinensis [L.] Osb. cv. Newhall）的端粒到端粒（T2T）参考基因组。基于多个标准的综合评估表明，两个基因组都具有高度的连续性、完整性和准确性。基因组大小分别为 340.28 Mb 和 346.33 Mb，分别有 39.31 Mb 和 36.77 Mb 的 contig N50。总共在两个基因组中注释了 31456 和 30021 个基因模型。利用这些组装的基因组进行了比较基因组学分析，阐明了甜橙基因组的进化历史。此外，研究还鉴定了 2 个基因组之间的 2886 个结构变异，其中一些 SV 位于与冷胁迫相关的同源基因的上游、下游或内含子区域。
本研究从头组装了 2 个具有不同耐寒性的甜橙品种的 T2T 参考基因组。这些基因组为甜橙的基因组研究和分子育种提供了有价值的基础资源，以提高甜橙的耐寒性。此外，它们扩展了现有的 C. sinensis 参考基因组和测序数据资源库。此外，这些基因组为不同植物物种的比较基因组学分析提供了关键的数据基础。
