ShanghaiTech University Knowledge Management System
| High-coverage, massively parallel sequencing of single-cell genomes with CAP-seq | |
| 2024-09-11 | |
| 状态 | 已发表 |
| 摘要 | Microorganisms dominate Earth's ecosystems in both abundance and diversity. Studying these organisms relies on their genome information, but obtaining high-quality genomes has long been challenging due to technical limitations in genomic sequencing. Traditional genome sequencing methods are limited by the need to culture isolated strains, excluding unculturable taxa and restricting the study of complex communities. Metagenomics bypasses this but lacks single-cell resolution and often misses rare, critical species. Droplet-based single-cell genomics offers high-throughput genome library preparation but faces challenges like requiring complex microfluidic setups and low genome coverage. To address these challenges, we introduce CAP-seq, a high-throughput single-cell genomic sequencing method with markedly improved genome coverage and ease of use. CAP-seq employs semi-permeable compartments that allow reagent exchange while retaining large DNA fragments, enabling efficient genome processing. This innovation results in higher-quality single amplified genomes (SAGs) and significantly improves resolution. In validation tests with simple and complex microbial communities, CAP-seq yielded high-quality SAGs with over 50% genome coverage, capturing rare taxa more accurately and providing detailed insights into strain-level variation. CAP-seq thus offers a scalable, high-resolution solution for microbial genomic analysis, overcoming the limitations of droplet-based single-cell genomics and enhancing the study of complex microbial ecosystems. |
| 关键词 | single-cell whole genome sequencing microbe microfluidics metagenomics |
| 语种 | 英语 |
| DOI | 10.1101/2024.09.10.612220 |
| 相关网址 | 查看原文 |
| 出处 | bioRxiv |
| 收录类别 | PPRN.PPRN |
| WOS记录号 | PPRN:91815352 |
| WOS类目 | Genetics & Heredity |
| 文献类型 | 预印本 |
| 条目标识符 | https://kms.shanghaitech.edu.cn/handle/2MSLDSTB/427475 |
| 专题 | 物质科学与技术学院 物质科学与技术学院_硕士生 物质科学与技术学院_博士生 物质科学与技术学院_PI研究组_刘一凡组 |
| 通讯作者 | Wei, Wu; Liu, Yifan |
| 作者单位 | 1.ShanghaiTech Univ, Sch Phys Sci & Technol, Shanghai 201210, Peoples R China 2.Lingang Lab, Shanghai 200031, Peoples R China 3.Chinese Acad Sci, Shanghai Inst Microsyst & Informat Technol, State Key Lab Transducer Technol, Shanghai 200050, Peoples R China 4.ShanghaiTech Univ, State Key Lab Adv Med Mat & Devices, Shanghai 201210, Peoples R China 5.Shanghai Clin Res & Trial Ctr, Shanghai 201210, Peoples R China 6.Chinese Acad Sci, Univ Chinese Acad Sci, Shanghai Inst Nutr & Hlth, CAS Key Lab Computat Biol, Shanghai 200031, Peoples R China |
| 推荐引用方式 GB/T 7714 | Li, Mengzhen,Zhai, Xuanpei,Li, Jie,et al. High-coverage, massively parallel sequencing of single-cell genomes with CAP-seq. 2024. |
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