从宏基因组中提取 CRISPR 靶向序列。

Extraction of CRISPR-targeted sequences from the metagenome.

机构信息

Human Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan.

Human Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan; Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Mishima, Shizuoka 411-8540, Japan.

出版信息

STAR Protoc. 2022 Sep 16;3(3):101525. doi: 10.1016/j.xpro.2022.101525. Epub 2022 Jul 2.

DOI:10.1016/j.xpro.2022.101525

PMID:35780428

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC9256941/

Abstract

Homology-based search is commonly used to uncover mobile genetic elements (MGEs) from metagenomes, but it heavily relies on reference genomes in the database. Here we introduce a protocol to extract CRISPR-targeted sequences from the assembled human gut metagenomic sequences without using a reference database. We describe the assembling of metagenome contigs, the extraction of CRISPR direct repeats and spacers, the discovery of protospacers, and the extraction of protospacer-enriched regions using the graph-based approach. This protocol could extract numerous characterized/uncharacterized MGEs. For complete details on the use and execution of this protocol, please refer to Sugimoto et al. (2021).

摘要

基于同源性的搜索常用于从宏基因组中发现移动遗传元件（MGEs），但它严重依赖于数据库中的参考基因组。在这里，我们介绍了一种从组装的人类肠道宏基因组序列中提取 CRISPR 靶向序列的方案，而无需使用参考数据库。我们描述了宏基因组 contigs 的组装、CRISPR 直接重复序列和间隔序列的提取、原间隔序列的发现以及基于图的方法提取原间隔序列富集区。该方案可以提取大量已鉴定/未鉴定的 MGEs。有关此方案的使用和执行的完整详细信息，请参阅 Sugimoto 等人（2021 年）。