National Key Laboratory for Tropical Crop Breeding, Laboratory of Crop Gene Resources and Germplasm Enhancement in South China, Ministry of Agriculture and Rural Affairs, Key Laboratory of Tropical Crops Germplasm Resources Genetic Improvement and Innovation of Hainan Province, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China.
National Key Laboratory for Tropical Crop Breeding, Sanya Research Institute, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 572024, China.
J Integr Plant Biol. 2024 Oct;66(10):2208-2225. doi: 10.1111/jipb.13748. Epub 2024 Aug 7.
Pineapple is the third most crucial tropical fruit worldwide and available in five varieties. Genomes of different pineapple varieties have been released to date; however, none of them are complete, with all exhibiting substantial gaps and representing only two of the five pineapple varieties. This significantly hinders the advancement of pineapple breeding efforts. In this study, we sequenced the genomes of three varieties: a wild pineapple variety, a fiber pineapple variety, and a globally cultivated edible pineapple variety. We constructed the first gap-free reference genome (Ref) for pineapple. By consolidating multiple sources of evidence and manually revising each gene structure annotation, we identified 26,656 protein-coding genes. The BUSCO evaluation indicated a completeness of 99.2%, demonstrating the high quality of the gene structure annotations in this genome. Utilizing these resources, we identified 7,209 structural variations across the three varieties. Approximately 30.8% of pineapple genes were located within ±5 kb of structural variations, including 30 genes associated with anthocyanin synthesis. Further analysis and functional experiments demonstrated that the high expression of AcMYB528 aligns with the accumulation of anthocyanins in the leaves, both of which may be affected by a 1.9-kb insertion fragment. In addition, we developed the Ananas Genome Database, which offers data browsing, retrieval, analysis, and download functions. The construction of this database addresses the lack of pineapple genome resource databases. In summary, we acquired a seamless pineapple reference genome with high-quality gene structure annotations, providing a solid foundation for pineapple genomics and a valuable reference for pineapple breeding.
菠萝是全球第三大重要热带水果，有五个品种。迄今为止，不同菠萝品种的基因组已经发布；然而，它们都不完整，所有基因组都存在大量缺口，只代表五个菠萝品种中的两个。这极大地阻碍了菠萝的育种工作。在这项研究中，我们对三个品种的基因组进行了测序：一个野生菠萝品种、一个纤维菠萝品种和一个全球种植的可食用菠萝品种。我们构建了第一个无间隙参考基因组（Ref）。通过整合多个来源的证据并手动修改每个基因结构注释，我们鉴定了 26656 个蛋白质编码基因。BUSCO 评估表明完整性为 99.2%，表明该基因组中基因结构注释的高质量。利用这些资源，我们在三个品种中鉴定了 7209 个结构变异。大约 30.8%的菠萝基因位于结构变异的±5kb 范围内，包括 30 个与花青素合成相关的基因。进一步的分析和功能实验表明，AcMYB528 的高表达与叶片中花青素的积累一致，这两者可能都受到一个 1.9kb 插入片段的影响。此外，我们开发了 Ananas 基因组数据库，该数据库提供了数据浏览、检索、分析和下载功能。该数据库的构建解决了缺乏菠萝基因组资源数据库的问题。总之，我们获得了一个具有高质量基因结构注释的无缝菠萝参考基因组，为菠萝基因组学提供了坚实的基础，为菠萝育种提供了有价值的参考。
