A proximity ligation method to track mobile element hosts

一种追踪移动元件宿主的邻近连接方法

• 批准号: 10078597
• 负责人: Ivan Liachko
• 金额: $ 89.58万
• 依托单位: PHASE GENOMICS, INC.
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-01-01 至 2021-12-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10078597
• 关键词: Address; Agriculture; Antimicrobial Resistance; Bacteriophages; Benign; Biochemical Pathway; Biological; Biology; Cells; Chromatin; Chromosomes; Client; Communities; Complex; Complex Mixtures; Computer software; DNA; Data; Data Analyses; Data Reporting; Drug resistance; Elements; Evolution; Future; Generations; Genes; Genome; Genomics; Goals; Hi-C; Horizontal Gene Transfer; Hybrids; Individual; Laboratories; Laboratory culture; Lead; Libraries; Ligation; Metagenomics; Methods; Oranges; Organism; Phase; Plasmids; Primer Extension; Proteins; Proto-Oncogene Protein c-kit; Protocols documentation; RNA; Reporting; Research; Sampling; Services; Shotguns; Small Business Innovation Research Grant; Speed; System; Techniques; Technology; Testing; TimeLine; Virulence; Virulent; Virus; Work; base; biochemical evolution; computational platform; cost; cost effective; crosslink; design; experience; extrachromosomal DNA; innovation; interest; member; microbial community; microbiome; microorganism; next generation sequencing; novel; scaffold; software development; technology development; tool; transmission process; transposon/insertion element; user-friendly; wastewater samples; web portal

ABSTRACT In this application, we propose to develop Hi-C technology and data analysis software for a user-friendly method to associate antimicrobial resistant (AMR) and virulence gene-containing mobile elements with their associated bacterial strains. Mobile elements are extra-chromosomal DNA or RNA molecules that encode functional elements. These molecules can be transmitted between members of the same species and across disparate species, leading to the rapid evolution of biochemical pathways through the sharing of mobile element-encoded proteins. This has a profound influence on the evolution of microbial communities, with particular impact on the drug resistance and virulence profiles of the members of the communities. To date, there is no cost-effective method for identifying mobile element hosts in a mixed microbial community: A significant fraction of microorganisms are unculturable under laboratory settings and current shotgun genomic methods fail to capture host information. Therefore, a new tool is needed to provide the information critical to understanding mobile element biology. Methods such as chromosome confirmation capture (3C) and Hi-C can be used rapidly and with high accuracy to identify DNA molecules that co-exist within individual cells directly from a mixed culture or biological sample. The goal of this proposal to develop a new class of tools that can be used to identify the hosts and transmission of mobile elements in a complex microbial community. The product proposed in this SBIR Phase II application addresses the need for rapid, culture-free identification of mobile element-host relationships in complex microbial communities. The method is built upon Phase Genomics’ expertise with the use of Hi-C and 3C techniques, which allows to deconvolve complex mixtures of cells within microbial communities, without the need for laboratory culture. In this application, we propose to produce a method that reduces cost, increases speed, and simplifies the analysis of a proximity ligation-based test to associate plasmids with their host. Our approach is based on two discrete work packages: Aim 1 is focused on combining target enrichment and proximity-ligation methods to reduce sequencing costs associated with metagenomic deconvolution. In Aim 2, we will develop and design a customer-facing web portal for upload and analysis of data in which our clients can navigate easily. Upon completion of the proposed project, we will have laid the basis for a first-generation target enrichment Hi- C kit and service that will make our innovative platform commercially available.

抽象的 在此应用中，我们建议开发 Hi-C 技术和数据分析软件，以实现用户友好的方法 将含有抗菌素耐药性 (AMR) 和毒力基因的移动元件与其相关的 细菌菌株。 移动元件是编码功能元件的染色体外 DNA 或 RNA 分子。 分子可以在同一物种的成员之间和不同物种之间传播，从而导致 通过共享移动元件编码蛋白质来实现生化途径的快速进化。 对微生物群落的进化有广泛的影响，特别是对耐药性和 社区成员的毒力概况。 迄今为止，还没有一种经济有效的方法来识别混合微生物群落中的移动元素宿主： 在实验室环境和当前的鸟枪基因组下，很大一部分微生物是无法培养的 方法无法捕获主机信息，因此需要一种新工具来提供关键信息。 了解移动元件生物学等方法可以实现染色体确认捕获 (3C) 和 Hi-C 等方法。 可快速、高精度地识别单个细胞内共存的 DNA 分子 直接来自混合培养物或生物样本 该提案的目标是开发一类新的工具。 可用于识别复杂微生物群落中移动元素的宿主和传输。 SBIR II 期申请中提出的产品满足了快速、无培养物鉴定的需求 该方法建立在 Phase 的基础上。 Genomics 在使用 Hi-C 和 3C 技术方面的专业知识，可以对复杂的混合物进行解卷积 微生物群落内的细胞，无需实验室培养。 在此应用中，我们建议提出一种降低成本、提高速度并简化流程的方法。 对基于邻近连接的测试进行分析，以将质粒与其宿主相关联 我们的方法基于两个。 离散工作包： 目标 1 侧重于结合靶标富集和邻近连接方法以降低测序成本 在目标 2 中，我们将开发和设计一个面向客户的门户网站。 用于上传和分析数据，我们的客户可以轻松导航。 拟议项目完成后，我们将为第一代目标浓缩Hi-奠定基础 C 套件和服务将使我们的创新平台实现商业化。

项目成果

Chromosome-scale genome assembly of the sea louse Caligus rogercresseyi by SMRT sequencing and Hi-C analysis.

通过 SMRT 测序和 Hi-C 分析对海虱 Caligus rogercresseyi 进行染色体规模的基因组组装。

• 发表时间: 2021-02-11
• 影响因子: 9.8
• 作者: Gallardo;Valenzuela;Nuñez;Valenzuela;Gonçalves, Ana Teresa;Escobar;Liachko, Ivan;Nelson, Bradley;Roberts, Steven;Warren, Wesley
• 通讯作者: Warren, Wesley

The genome of the zebra mussel, Dreissena polymorpha: a resource for comparative genomics, invasion genetics, and biocontrol.

斑马贻贝（Dreissena polymorpha）的基因组：比较基因组学、入侵遗传学和生物防治的资源。

• 发表时间: 2022-02-04
• 作者: McCartney, Michael A;Auch, Benjamin;Kono, Thomas;Mallez, Sophie;Zhang, Ying;Obille, Angelico;Becker, Aaron;Abrahante, Juan E;Garbe, John;Badalamenti, Jonathan P;Herman, Adam;Mangelson, Hayley;Liachko, Ivan;Sullivan, Shawn;Sone, Eli D;Koren
• 通讯作者: Koren

Proximity ligation strategy for the genomic reconstruction of microbial communities associated with the ectoparasite Caligus rogercresseyi.

与外寄生虫 Caligus rogercresseyi 相关的微生物群落基因组重建的邻近连接策略。

• 发表时间: 2022-01-17
• 影响因子: 4.6
• 作者: Valenzuela;Gonçalves, Ana Teresa;Valenzuela;Nuñez;Liachko, Ivan;Nelson, Bradley;Gallardo
• 通讯作者: Gallardo