使用 Pacbio SMRT 测序进行双歧杆菌基因组组装和甲基组分析。

Bifidobacterium Genome Assembly and Methylome Analysis Using Pacbio SMRT Sequencing.

机构信息

APC Microbiome Ireland, University College Cork, Cork, Ireland.

School of Microbiology & APC Microbiome Ireland, University College Cork, Cork, Ireland.

出版信息

Methods Mol Biol. 2021;2278:225-232. doi: 10.1007/978-1-0716-1274-3_18.

DOI:10.1007/978-1-0716-1274-3_18

PMID:33649960

Abstract

In this chapter, we present a generic method to achieve de novo genome assembly and methylome analysis of Bifidobacterium genomes using the Pacbio SMRT sequencing and SMRT Link pipeline. The methods described here cover the de novo Pacbio or hybrid Illumina-Pacbio assembly ideally intended to obtain a complete genome sequence, followed by the detection of base modifications and methylome analysis.The identified DNA motifs obtained by methylome analysis can be used to predict active restriction-modification (RM) systems in Bifidobacterium strains. The presence of active RM systems and knowledge on their target motifs may guide selection of suitable cloning or mutagenesis vectors for bifidobacteria.

摘要

在本章中，我们提出了一种使用 Pacbio SMRT 测序和 SMRT Link 管道进行双歧杆菌基因组从头组装和甲基组分析的通用方法。这里描述的方法涵盖了从头开始的 Pacbio 或 Illumina-Pacbio 混合组装，旨在获得完整的基因组序列，然后检测碱基修饰和甲基组分析。通过甲基组分析获得的鉴定 DNA 基序可用于预测双歧杆菌菌株中活性限制修饰（RM）系统。活性 RM 系统的存在及其靶基序的知识可指导选择适合双歧杆菌的克隆或诱变载体。