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产副丝藻纤细眼虫的染色体水平基因组组装

A chromosome-level genome assembly for the paramylon-producing microalga Euglena gracilis

Nature 等信源发布 2024-07-16 20:44

可切换为仅中文

AbstractEuglena gracilis (E. gracilis), pivotal in the study of photosynthesis, endosymbiosis, and chloroplast development, is also an industrial microalga for paramylon production. Despite its importance, E. gracilis genome exploration faces challenges due to its intricate nature. In this study, we achieved a chromosome-level de novo assembly (2.37 Gb) using Illumina, PacBio, Bionano, and Hi-C data.

摘要Euglena gracilis（E.gracilis）是光合作用，内共生和叶绿体发育研究的关键，也是一种用于生产paramylon的工业微藻。尽管其重要性，但由于其复杂的性质，纤细芽孢杆菌基因组探索面临挑战。在这项研究中，我们使用Illumina，PacBio，Bionano和Hi-C数据实现了染色体水平的从头组装（2.37Gb）。

The assembly exhibited a contig N50 of 619 Kb and scaffold N50 of 1.12 Mb, indicating superior continuity. Approximately 99.83% of the genome was anchored to 46 chromosomes, revealing structural insights. Repetitive elements constituted 58.84% of the sequences. Functional annotations were assigned to 39,362 proteins, enhancing interpretative power.

该组件显示重叠群N50为619 Kb，支架N50为1.12 Mb，表明具有优异的连续性。大约99.83%的基因组锚定在46条染色体上，揭示了结构见解。重复元件占序列的58.84%。功能注释被分配给39362个蛋白质，增强了解释能力。

BUSCO analysis confirmed assembly completeness at 80.39%. This first high-quality E. gracilis genome offers insights for genetics and genomics studies, overcoming previous limitations. The impact extends to academic and industrial research, providing a foundational resource..

BUSCO分析证实组装完整性为80.39%。这第一个高质量的纤细埃希氏菌基因组为遗传学和基因组学研究提供了见解，克服了以前的局限性。影响扩展到学术和工业研究，提供了基础资源。。

Background & SummaryEuglena, a genus of single-celled flagellate eukaryotes, is ubiquitously distributed in both freshwater and saltwater environments. Possessing photosynthetic chloroplasts, Euglena exhibits autotrophic characteristics akin to plants, while also displaying heterotrophic attributes similar to animals1,2,3.

背景与总结Euglena是一种单细胞鞭毛真核生物，广泛分布于淡水和盐水环境中。眼虫具有光合叶绿体，表现出类似于植物的自养特性，同时也表现出类似于动物的异养特性1,2,3。

E. gracilis, a prominent species within the genus, serves as a widely utilized model organism in both academic and industrial research due to its rich array of valuable compounds, including pigments, unsaturated fatty acids, vitamins, amino acids, and the distinctive β-1,3-glucan, paramylon—an advantageous functional food ingredient4,5,6.

E、 gracilis是该属中的一个重要物种，由于其丰富的有价值的化合物，包括色素，不饱和脂肪酸，维生素，氨基酸和独特的β-1,3-葡聚糖，paramylon是一种有利的功能性食品成分4,5,6，因此在学术和工业研究中被广泛使用。

Notably, recent studies, such as Wu et al.’s pilot-scale fermentation achieving maximal biomass and paramylon content7, underscore the industrial potential of E. gracilis.Despite substantial advancements in genetic modification8,9,10,11,12,13, hindered by the absence of a high-quality genome, E. gracilis remains a subject of limited genetic engineering tools and applications.

值得注意的是，最近的研究，例如Wu等人的中试规模发酵，实现了最大的生物量和paramylon含量7，强调了纤细芽孢杆菌的工业潜力。尽管由于缺乏高质量的基因组，遗传修饰取得了实质性进展8,9,10,11,12,13，但纤细芽孢杆菌仍然是有限的基因工程工具和应用的主题。

In 2019, Ebenezer et al. presented an initial genome assembly of E. gracilis (1.43 Gb), which, though informative, proved significantly fragmented14. Consequently, researchers have resorted to omics approaches, including de novo transcriptome assembly14,15 and proteomic analysis1,14, to explore physiological and genomic aspects.

2019年，Ebenezer等人提出了E.gracilis（1.43Gb）的初始基因组组装，尽管提供了信息，但证明了显着的碎片化14。因此，研究人员采用组学方法，包括从头转录组组装14,15和蛋白质组学分析1,14，以探索生理和基因组方面。

Nevertheless, a definitive high-quality genome assembly remains a critical prerequisite for advancing genetic engineering and synthetic biology applications in E. gracilis6.This study addresses the existing gap by introducing a chromosome-level genome assembly of E. gracilis through the integration of Illumina, PacBio, Bionano, and Hi-C technologies (Table 1).

然而，确定的高质量基因组组装仍然是推进基因工程和合成生物学在纤细芽孢杆菌中应用的关键先决条件6。本研究通过整合Illumina，PacBio，Bionano和Hi-C技术引入纤细芽孢杆菌的染色体水平基因组组装来解决现有差距（表1）。

The resulting assembly, spanning 2.37 Gb, with contig N50 of .

产生的组件跨越2.37Gb，重叠群N50为。

Code availability

代码可用性

All commands and pipelines employed for data processing adhered strictly to the guidelines specified in the manuals of the pertinent bioinformatics software, with the parameters explicitly detailed in the Methods section. In instances where no specific parameters were explicitly stated for a particular software, default parameters were applied.

用于数据处理的所有命令和管道严格遵守相关生物信息学软件手册中规定的指南，参数在方法部分中有明确的详细说明。在没有明确说明特定软件的特定参数的情况下，将应用默认参数。

It is noteworthy that no bespoke scripts or custom code were formulated or utilized throughout the course of this study..

值得注意的是，在整个研究过程中，没有制定或使用定制脚本或自定义代码。。

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Download referencesAcknowledgementsThis work was partially supported by China’s National Key R&D Programs (2021YFA0910800, 2018YFA0902500, 2020YFA0908703), the National Natural Science Foundation of China (41876188), the Science Technology and Innovation Committee of Shenzhen Municipality (KCXFZ202002011006448), Shenzhen Science and Technology Program (KCXST20221021111206015 and KCXFZ20201221173404012), and Natural Science Foundation of Guangdong Province (2024B1515020034).Author informationAuthor notesThese authors contributed equally: Zixi Chen, Yang Dong, Shengchang Duan.Authors and AffiliationsShenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, ChinaZixi Chen, Jiayi He, Huan Qin, Chao Bian, Zhenfan Chen, Chenchen Liu, Chao Zheng, Ming Du, Rao Yao, Chao Li, Yun Wang, Shuangfei Li, Ning Xie, Ying Xu, Qiong Shi, Zhangli Hu, Anping Lei & Jiangxin WangState Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, ChinaYang Dong & Shengchang DuanYunnan Research Institute for Local Plateau Agriculture and Industry, Kunming, 650201, ChinaYang Dong & Shengchang DuanShenzhen Rare Disease Engineering Research Center of Metabolomics in Precision Medicine, Shenzhen Aone Medical Laboratory Co, Ltd, Shenzhen, 518000, ChinaPanpan JiangCollege of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, 518060, ChinaLiqing ZhaoAuthorsZixi ChenView author publicationsYou can also search for this author in.

下载参考文献致谢这项工作得到了中国国家重点研发计划（2021YFA0910802018YFA09025002020YFA0908703），国家自然科学基金（41876188），深圳市科学技术与创新委员会（KCXFZ202002011006448），深圳市科学技术计划（KCXST20221021111206015和KCXFZ20201221173404012）和广东省自然科学基金（2024B1515020034）的部分支持。作者信息作者注意到这些作者做出了同样的贡献：Zixi Chen，Yang Dong，Shengchang Duan。作者和单位深圳市海洋生物资源与生态环境科学重点实验室，深圳市海藻生物技术工程实验室，深圳大学生命科学与海洋学院广东省植物表观遗传学重点实验室，深圳，518060，中国陈子喜，何嘉怡，秦焕，赵扁，陈振凡，刘晨晨，郑超，杜明耀，姚超，王云，李双飞，谢宁，徐英，石琼，胡张丽，雷安平，王江新云南省生物资源保护与利用国家重点实验室，云南农业大学，昆明，650201，中国杨东&盛昌段云南研究昆明当地高原农业与工业研究所，650201，中国杨东和盛昌段深圳精密医学代谢组学罕见病工程研究中心，深圳市奥恩医学实验室有限公司，深圳，518000，中国深圳大学化学与环境工程学院，深圳，518060，中国赵丽青作者Zixi ChenView作者出版物您也可以在中搜索该作者。

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PubMed Google ScholarContributionsZixi Chen, Yang Dong and Shengchang Duan analysed the data and wrote the manuscript. Jiayi He, Huan Qin, Zhenfan Chen, Chenchen Liu, Chao Zheng, Ming Du, Rao Yao and Chao Li performed the experiments. Chao Bian, Panpan Jiang and Qiong Shi analysed the data.

PubMed Google ScholarContributionsZixi Chen，Yang Dong和Shengchang Duan分析了数据并撰写了手稿。何家义、秦欢、陈振凡、刘晨晨、郑超、杜明、饶耀和李超进行了实验。Chao Bian、Panpan Jiang和Qiong Shi分析了数据。

Yun Wang, Shuangfei Li, Ning Xie, Ying Xu and Zhangli Hu revised the manuscript. Anping Lei, Liqing Zhao and Jiangxin Wang conceived and designed the whole project, and revised the manuscript. All authors read and approved the final manuscript.Corresponding authorsCorrespondence to.

王云，李双飞，谢宁，徐颖和胡张丽修改了手稿。雷安平、赵丽清和王江新构思并设计了整个项目，并修改了手稿。所有作者都阅读并批准了最终稿件。通讯作者通讯。

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Reprints and permissionsAbout this articleCite this articleChen, Z., Dong, Y., Duan, S. et al. A chromosome-level genome assembly for the paramylon-producing microalga Euglena gracilis.

转载和许可本文引用本文Chen，Z.，Dong，Y.，Duan，S。等人。产生paramylon的微藻Euglena gracilis的染色体水平基因组组装。

Sci Data 11, 780 (2024). https://doi.org/10.1038/s41597-024-03404-yDownload citationReceived: 16 January 2024Accepted: 22 May 2024Published: 16 July 2024DOI: https://doi.org/10.1038/s41597-024-03404-yShare this articleAnyone you share the following link with will be able to read this content:Get shareable linkSorry, a shareable link is not currently available for this article.Copy to clipboard.

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