A high-throughput platform for assembling genome data: the Saphyr

用于组装基因组数据的高通量平台：Saphyr

• 批准号: NE/T008709/1
• 负责人: Stephen Rossiter
• 金额: $ 34.58万
• 依托单位: Queen Mary University of London
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2019
• 资助国家: 英国
• 起止时间: 2019 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=NE%2FT008709%2F1
• 关键词: throughput; platform; assembling; genome; data

Since the completion of the human genome project in 2003, after 13 years of work and billions of dollars, the ability to produce genomic data has accelerated at phenomenal rates. Advances in sequencing technologies mean that just 20 years on we can now sequence a genome in hours, not years, at the cost of a few hundred dollars. As such, genome sequence data can be produced by small and large labs alike, and numerous regional, national and global consortia have been newly launched with the goal of sequencing millions of species worldwide in the coming years.Unfortunately, while the explosion of thousands of genome datasets has created new opportunities - such as screening genomes for variants that correlate with ecologically-important traits such as disease resistance - it has also created equally steep challenges. A particular problem concerns the nature of genomic datasets; even after deep-sequencing, most "genomes" actually comprise large numbers of non-contiguous fragments that cannot be stitched together into chromosomes. This incomplete assembly obstructs inferences of linkage, synteny, and genotype-phenotype association, and is especially severe for non-model plants, fungi and animals that are characterised by large complex genomes. The Saphyr platform (Bionano Genomics) overcomes this obstacle by directly imaging megabase length fluorescently barcoded optical molecules. DNA is treated with an enzyme that deposits fluorescent marks based at specific sites, and then millions of large DNA molecules are passed through proprietary nanochannels and their images are converted to graphical barcodes. Using software, barcoded molecules are compared against each other, and, based on matching patterns of fluro-marks, assembled into 'optical contigs'; these are structural scaffolds, independent of sequence, that represent very large regions. Since these contigs easily span breaks in sequence assembly, they allow the generation of chromosome length 'hybrid scaffolds' made up of optical and sequence contigs, where the short-read sequence assemblies have been in silico enzyme treated so that they exhibit the same barcode patterns as the optical molecules.Optical mapping is considered an essential step in producing high quality genomes, and features in the pipelines used by many large sequencing consortia, including the newly-launched Darwin Tree of Life Project, which aims to capture the genomic information of the ~66,000 UK species. The Saphyr is the only high-throughput optical mapping platform, yet there is currently no dedicated facility for NERC-funded research working at the interface of genomics and environmental science.We will establish a NERC-oriented next generation optical mapping facility at QMUL, underpinned by our technical support for isolating ultra-high molecular weight DNA from a range of biological samples and species. This high throughout facility will meet current demand for generating high quality genomes, and will thus enhance the UK's technical capacity in the fast developing field of environmental genomics. Specifically, the facility will enable researchers to (1) include genome assemblies in current and future projects, (2) play more active roles in large genome networks, and (3) exploit the platform's versatility to tackle novel research questions regarding the genome-wide distributions of specific DNA motifs and features. At an institutional level, the Saphyr will allow us to expand our research portfolio and address fundamental questions in ecological and evolutionary genomics in diverse non-model organisms, which range from trees and bacteria to mammals and annelids. Moreover, the Saphyr will enhance training of specialised staff, enhance our capacity to establish collaborations with other UK research institutions, and thus emerge as a common technical resource for the environmental-oriented research community.

自2003年人类基因组项目完成以来，经过13年的工作和数十亿美元，生产基因组数据的能力以惊人的速度加速了。测序技术的进步意味着，仅20年的时间，我们现在就可以在几个小时而不是数年的时间内以几百美元的价格对基因组进行序列。因此，基因组序列数据可以由大小实验室都可以产生，并且新启动的许多区域，国家和全球财团的目标是在未来几年内对全球数百万个物种进行测序，这是不幸的。陡峭的挑战。一个特定的问题涉及基因组数据集的性质；即使经过深入的序列，大多数“基因组”实际上也包含了大量无法将其缝合成染色体的非连续片段。这种不完整的组装阻碍了连锁，同步和基因型 - 表型关联的推断，并且对于以大型复杂基因组为特征的非模型植物，真菌和动物特别严重。 Saphyr平台（Bionano Genomics）通过直接成像巨型荧光荧光分子光学分子来克服这一障碍。用一种酶处理DNA，该酶在特定位点沉积荧光标记，然后将数百万个大的DNA分子通过专有纳米渠道通过，并将其图像转换为图形条形码。使用软件，将条形码分子相互比较，并基于Fluro-Marks的匹配模式组装成“光学重叠群”；这些是独立于序列的结构支架，代表了非常大的区域。由于这些重叠群很容易按顺序组装跨越，因此它们允许由光学和序列重叠群组成的染色体长度“混合脚手架”，其中短读序列组件已在经过处理的硅酶中，以便它们与光学分子相同的型号和较高的型号。对财团的测序，包括新推出的达尔文生命项目，旨在捕获约66,000种英国物种的基因组信息。 Saphyr是唯一的高通量光学映射平台，但是目前尚无专门的设施用于NERC资助的研究，在基因组学和环境科学的界面上工作。我们将在Qmul建立一个面向NERC的下一代光学映射设施，该设施在我们的技术支持下，由我们的技术支持隔离了超高的分子量DNA，并将其从生物学范围内隔离出来。整个设施的这一高度将满足当前对高质量基因组的需求，因此将增强英国在快速发展的环境基因组学领域的技术能力。具体而言，该设施将使研究人员能够（1）在当前和将来的项目中包括基因组组件，（2）在大型基因组网络中扮演更积极的角色，（3）利用该平台的多功能性来解决有关特定DNA图案和特定基因组分布的新颖研究问题。在机构层面上，Saphyr将使我们能够扩大研究组合，并解决各种非模型生物的生态和进化基因组学中的基本问题，这些生物学从树木和细菌到哺乳动物和annelids。此外，Saphyr将增强对专业员工的培训，增强我们与其他英国研究机构建立合作的能力，从而成为面向环境的研究社区的共同技术资源。

项目成果

The comparative genomic landscape of adaptive radiation in crater lake cichlid fishes.

• DOI: 10.1111/mec.15774
• 发表时间: 2021-03
• 期刊: Molecular ecology
• 影响因子: 4.9
• 作者: Xiong P;Hulsey CD;Fruciano C;Wong WY;Nater A;Kautt AF;Simakov O;Pippel M;Kuraku S;Meyer A;Franchini P
• 通讯作者: Franchini P

Genome editing reveals that pSCL4 is required for chromosome linearity in Streptomyces clavuligerus.

• DOI: 10.1099/mgen.0.000669
• 发表时间: 2021-11
• 期刊: Microbial genomics
• 影响因子: 3.9
• 作者: Gomez-Escribano JP;Algora Gallardo L;Bozhüyük KAJ;Kendrew SG;Huckle BD;Crowhurst NA;Bibb MJ;Collis AJ;Micklefield J;Herron PR;Wilkinson B
• 通讯作者: Wilkinson B

Annelid functional genomics reveal the origins of bilaterian life cycles.

• DOI: 10.1038/s41586-022-05636-7
• 发表时间: 2023-03
• 期刊: NATURE
• 影响因子: 64.8
• 作者: Martin-Zamora, Francisco M.;Liang, Yan;Guynes, Kero;Carrillo-Baltodano, Allan M.;Davies, Billie E.;Donnellan, Rory D.;Tan, Yongkai;Moggioli, Giacomo;Seudre, Oceane;Tran, Martin;Mortimer, Kate;Luscombe, Nicholas M.;Hejnol, Andreas;Marletaz, Ferdinand;Martin-Duran, Jose M.
• 通讯作者: Martin-Duran, Jose M.