菠萝参考基因组:端粒到端粒组装、人工标注和比较分析。

IF 9.3 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY
Junting Feng, Wei Zhang, Chengjie Chen, Yinlong Liang, Tangxiu Li, Ya Wu, Hui Liu, Jing Wu, Wenqiu Lin, Jiawei Li, Yehua He, Junhu He, Aiping Luan
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引用次数: 0

摘要

菠萝是全球第三大重要热带水果,有五个品种。迄今为止,已发布了不同菠萝品种的基因组,但没有一个是完整的,所有基因组都有很大差距,仅代表五个菠萝品种中的两个。这极大地阻碍了菠萝育种工作的进展。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栽培的食用菠萝品种。我们为菠萝构建了第一个无间隙参考基因组(Ref)。通过整合多种证据来源并人工修订每个基因结构注释,我们确定了 26656 个蛋白质编码基因。BUSCO 评估显示其完整性为 99.2%,表明该基因组中基因结构注释的质量很高。利用这些资源,我们在三个品种中发现了 7,209 个结构变异。约 30.8% 的菠萝基因位于结构变异的 ±5 kb 范围内,其中包括 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 的高表达与花青素在叶片中的积累相一致,两者都可能受到 1.9 kb 插入片段的影响。此外,我们还开发了 Ananas 基因组数据库,该数据库提供数据浏览、检索、分析和下载功能。该数据库的建立解决了菠萝基因组资源数据库缺乏的问题。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,为菠萝基因组学奠定了坚实的基础,也为菠萝育种提供了宝贵的参考。
本文章由计算机程序翻译,如有差异,请以英文原文为准。

The pineapple reference genome: Telomere-to-telomere assembly, manually curated annotation, and comparative analysis

The pineapple reference genome: Telomere-to-telomere assembly, manually curated annotation, and comparative analysis

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.

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来源期刊
Journal of Integrative Plant Biology
Journal of Integrative Plant Biology 生物-生化与分子生物学
CiteScore
18.00
自引率
5.30%
发文量
220
审稿时长
3 months
期刊介绍: Journal of Integrative Plant Biology is a leading academic journal reporting on the latest discoveries in plant biology.Enjoy the latest news and developments in the field, understand new and improved methods and research tools, and explore basic biological questions through reproducible experimental design, using genetic, biochemical, cell and molecular biological methods, and statistical analyses.
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