Dan Liu, Kun Liu, Boqiang Tong, Haili Guo, Kai Qu, Ting Xu, Ren-Gang Zhang, Wei Zhao, Xiaoman Xie, Longxin Wang, Kai-Hua Jia
{"title":"蔷薇参考基因组的端粒到端粒无间隙组装","authors":"Dan Liu, Kun Liu, Boqiang Tong, Haili Guo, Kai Qu, Ting Xu, Ren-Gang Zhang, Wei Zhao, Xiaoman Xie, Longxin Wang, Kai-Hua Jia","doi":"10.1016/j.hpj.2024.06.005","DOIUrl":null,"url":null,"abstract":"Rosa, a genus esteemed worldwide for its ornamental plants, has encountered barriers in functional genomic studies and further genetic enhancement due to incomplete sequences and floating regions in previously sequenced genomes. Our groundbreaking study introduced a meticulously assembled, continuous, and fully bridged reference genome for <ce:italic>Rosa rugosa</ce:italic>, constructed through a sophisticated combination of PacBio High-Fidelity, ONT ultra-long reads, and Hi-C data. This robust assembly spanned 444.55 Mb and encompassed 34 109 protein-coding genes. We have uniquely assembled each chromosome into single, gap-free structures, successfully identifying all 14 telomeres and seven centromeres, a feat not achieved previously. The centromeric regions were distinguished by tandem repeats, primarily composed of centromere-specific 159-bp monomers, and a significant enrichment of <ce:italic>ATHILA</ce:italic>/<ce:italic>Gypsy</ce:italic> long terminal repeat retrotransposons in proximal regions. Our research highlighted recent tandem duplications as instrumental in bolstering <ce:italic>R. rugosa</ce:italic>'s stress tolerance, environmental adaptability, and enhanced anthocyanin synthesis. Furthermore, our study ventured into uncharted territory by predicting transcription factors potentially regulating anthocyanin biosynthesis through the employment of gene co-expression networks, providing new avenues for research. This comprehensive reference genome not only serves as a cornerstone for in-depth exploration of genomic architecture and functionalities in <ce:italic>R. rugosa</ce:italic> but also acts as a catalyst for innovative breeding strategies and genetic refinement within the genus.","PeriodicalId":13178,"journal":{"name":"Horticultural Plant Journal","volume":"32 1","pages":""},"PeriodicalIF":5.7000,"publicationDate":"2024-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Telomere-to-telomere, gap-free assembly of the Rosa rugosa reference genome\",\"authors\":\"Dan Liu, Kun Liu, Boqiang Tong, Haili Guo, Kai Qu, Ting Xu, Ren-Gang Zhang, Wei Zhao, Xiaoman Xie, Longxin Wang, Kai-Hua Jia\",\"doi\":\"10.1016/j.hpj.2024.06.005\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"Rosa, a genus esteemed worldwide for its ornamental plants, has encountered barriers in functional genomic studies and further genetic enhancement due to incomplete sequences and floating regions in previously sequenced genomes. Our groundbreaking study introduced a meticulously assembled, continuous, and fully bridged reference genome for <ce:italic>Rosa rugosa</ce:italic>, constructed through a sophisticated combination of PacBio High-Fidelity, ONT ultra-long reads, and Hi-C data. This robust assembly spanned 444.55 Mb and encompassed 34 109 protein-coding genes. We have uniquely assembled each chromosome into single, gap-free structures, successfully identifying all 14 telomeres and seven centromeres, a feat not achieved previously. The centromeric regions were distinguished by tandem repeats, primarily composed of centromere-specific 159-bp monomers, and a significant enrichment of <ce:italic>ATHILA</ce:italic>/<ce:italic>Gypsy</ce:italic> long terminal repeat retrotransposons in proximal regions. Our research highlighted recent tandem duplications as instrumental in bolstering <ce:italic>R. rugosa</ce:italic>'s stress tolerance, environmental adaptability, and enhanced anthocyanin synthesis. Furthermore, our study ventured into uncharted territory by predicting transcription factors potentially regulating anthocyanin biosynthesis through the employment of gene co-expression networks, providing new avenues for research. This comprehensive reference genome not only serves as a cornerstone for in-depth exploration of genomic architecture and functionalities in <ce:italic>R. rugosa</ce:italic> but also acts as a catalyst for innovative breeding strategies and genetic refinement within the genus.\",\"PeriodicalId\":13178,\"journal\":{\"name\":\"Horticultural Plant Journal\",\"volume\":\"32 1\",\"pages\":\"\"},\"PeriodicalIF\":5.7000,\"publicationDate\":\"2024-09-20\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Horticultural Plant Journal\",\"FirstCategoryId\":\"97\",\"ListUrlMain\":\"https://doi.org/10.1016/j.hpj.2024.06.005\",\"RegionNum\":1,\"RegionCategory\":\"农林科学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q1\",\"JCRName\":\"HORTICULTURE\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Horticultural Plant Journal","FirstCategoryId":"97","ListUrlMain":"https://doi.org/10.1016/j.hpj.2024.06.005","RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"HORTICULTURE","Score":null,"Total":0}
引用次数: 0
摘要
蔷薇属因其观赏植物而备受世人推崇,但由于之前测序的基因组中存在不完整序列和浮游区,该属在功能基因组研究和进一步基因强化方面遇到了障碍。我们的开创性研究为 Rosa rugosa 引入了一个经过精心组装、连续且完全桥接的参考基因组,该基因组是通过 PacBio 高保真、ONT 超长读数和 Hi-C 数据的复杂组合构建而成的。这个强大的基因组横跨 444.55 Mb,包含 34 109 个蛋白编码基因。我们将每条染色体独特地组装成单一、无间隙的结构,成功识别了所有 14 个端粒和 7 个中心粒,这是以前从未实现过的。中心粒区域以串联重复为特征,主要由中心粒特异性的 159-bp 单体组成,并且在近端区域显著富含 ATHILA/Gypsy 长末端重复反转座子。我们的研究突出表明,最近的串联重复有助于增强 R. rugosa 的抗逆性、环境适应性和花青素合成能力。此外,我们的研究还通过利用基因共表达网络预测了可能调控花青素生物合成的转录因子,为研究提供了新的途径。这个全面的参考基因组不仅是深入探索 R. rugosa 基因组结构和功能的基石,也是该属创新育种策略和基因改良的催化剂。
Telomere-to-telomere, gap-free assembly of the Rosa rugosa reference genome
Rosa, a genus esteemed worldwide for its ornamental plants, has encountered barriers in functional genomic studies and further genetic enhancement due to incomplete sequences and floating regions in previously sequenced genomes. Our groundbreaking study introduced a meticulously assembled, continuous, and fully bridged reference genome for Rosa rugosa, constructed through a sophisticated combination of PacBio High-Fidelity, ONT ultra-long reads, and Hi-C data. This robust assembly spanned 444.55 Mb and encompassed 34 109 protein-coding genes. We have uniquely assembled each chromosome into single, gap-free structures, successfully identifying all 14 telomeres and seven centromeres, a feat not achieved previously. The centromeric regions were distinguished by tandem repeats, primarily composed of centromere-specific 159-bp monomers, and a significant enrichment of ATHILA/Gypsy long terminal repeat retrotransposons in proximal regions. Our research highlighted recent tandem duplications as instrumental in bolstering R. rugosa's stress tolerance, environmental adaptability, and enhanced anthocyanin synthesis. Furthermore, our study ventured into uncharted territory by predicting transcription factors potentially regulating anthocyanin biosynthesis through the employment of gene co-expression networks, providing new avenues for research. This comprehensive reference genome not only serves as a cornerstone for in-depth exploration of genomic architecture and functionalities in R. rugosa but also acts as a catalyst for innovative breeding strategies and genetic refinement within the genus.
期刊介绍:
Horticultural Plant Journal (HPJ) is an OPEN ACCESS international journal. HPJ publishes research related to all horticultural plants, including fruits, vegetables, ornamental plants, tea plants, and medicinal plants, etc. The journal covers all aspects of horticultural crop sciences, including germplasm resources, genetics and breeding, tillage and cultivation, physiology and biochemistry, ecology, genomics, biotechnology, plant protection, postharvest processing, etc. Article types include Original research papers, Reviews, and Short communications.