A method for achieving complete microbial genomes and improving bins from metagenomics data.

Area of Science:

• Microbial genomics
• Bioinformatics
• Metagenomics

Background:

• Metagenomics enables studying uncultured microbes but assembling complete genomes is challenging due to complexity and diversity.
• Few circular bacterial and archaeal genomes (<100) are published from metagenomics data, limiting genomic reference collections.
• Circular genomes are crucial for confirming completeness, assessing contamination, and understanding gene context.

Purpose of the Study:

• To develop a semi-automated method (Jorg) for circularizing small bacterial, archaeal, and viral genomes from metagenomic data.
• To improve the accuracy of genome assembly by identifying and correcting misassemblies.
• To facilitate novel discoveries in microbial genomics, particularly for organisms with limited existing genomic data.

Main Methods:

• Iterative assembly, binning, and read mapping were employed in the Jorg method.
• The method was initially applied to Candidate Phyla Radiation (CPR) species due to their small genomes and single ribosomal RNA operon.
• Analysis of 19 public datasets was performed to test the efficacy of the Jorg method.

Main Results:

• Successfully circularized 34 Candidate Phyla Radiation (CPR) genomes, one Margulisbacteria genome, one Chloroflexi genome, and two megaphage genomes.
• The Jorg method identified potential misassemblies missed by k-mer based assemblies.
• New insights were gained, including evidence that ribosomal genes are likely not operonic in most CPR, and the discovery of diverged RNase P RNA in some CPR.

Conclusions:

• The Jorg method is effective for semi-automated circularization of small microbial genomes from metagenomics data.
• Circularized genomes provide critical data for reference collections and understanding microbial biology.
• This work expands the collection of circularized genomes and reveals novel biological insights into CPR and other microbial groups.