Bifidobacterium Genome Assembly and Methylome Analysis Using Pacbio SMRT Sequencing

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.