Semi-automatic in silico gap closure enabled de novo assembly of two Dehalobacter genomes from metagenomic data

Typically, the assembly and closure of a complete bacterial genome requires substantial additional effort spent in a wet lab for gap resolution and genome polishing. Assembly is further confounded by subspecies polymorphism when starting from metagenome sequence data. In this paper, we describe an in silico gap-resolution strategy that can substantially improve assembly. This strategy resolves assembly gaps in scaffolds using pre-assembled contigs, followed by verification with read mapping. It is capable of resolving assembly gaps caused by repetitive elements and subspecies polymorphisms. Using this strategy, we realized the de novo assembly of the first two Dehalobacter genomes from the metagenomes of two anaerobic mixed microbial cultures capable of reductive dechlorination of chlorinated ethanes and chloroform. Only four additional PCR reactions were required even though the initial assembly with Newbler v. 2.5 produced 101 contigs within 9 scaffolds belonging to two Dehalobacter strains. By applying this strategy to the re-assembly of a recently published genome of Bacteroides, we demonstrate its potential utility for other sequencing projects, both metagenomic and genomic.