Biases in genome reconstruction from metagenomic data

William C Nelson; Benjamin J Tully; Jennifer M Mobberley

doi:10.7717/peerj.10119

Biases in genome reconstruction from metagenomic data

PeerJ. 2020 Oct 30:8:e10119. doi: 10.7717/peerj.10119. eCollection 2020.

Authors

William C Nelson¹, Benjamin J Tully^{2

3}, Jennifer M Mobberley⁴

Affiliations

¹ Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.
² Department of Biological Sciences, Marine Environmental Biology Section, University of Southern California, Los Angeles, CA, USA.
³ Center for Dark Energy Biosphere Investigations, University of Southern California, Los Angeles, CA, USA.
⁴ Chemical and Biological Signature Science Group, Pacific Northwest National Laboratory, Richland, WA, USA.

Abstract

Background: Advances in sequencing, assembly, and assortment of contigs into species-specific bins has enabled the reconstruction of genomes from metagenomic data (MAGs). Though a powerful technique, it is difficult to determine whether assembly and binning techniques are accurate when applied to environmental metagenomes due to a lack of complete reference genome sequences against which to check the resulting MAGs.

Methods: We compared MAGs derived from an enrichment culture containing ~20 organisms to complete genome sequences of 10 organisms isolated from the enrichment culture. Factors commonly considered in binning software-nucleotide composition and sequence repetitiveness-were calculated for both the correctly binned and not-binned regions. This direct comparison revealed biases in sequence characteristics and gene content in the not-binned regions. Additionally, the composition of three public data sets representing MAGs reconstructed from the Tara Oceans metagenomic data was compared to a set of representative genomes available through NCBI RefSeq to verify that the biases identified were observable in more complex data sets and using three contemporary binning software packages.

Results: Repeat sequences were frequently not binned in the genome reconstruction processes, as were sequence regions with variant nucleotide composition. Genes encoded on the not-binned regions were strongly biased towards ribosomal RNAs, transfer RNAs, mobile element functions and genes of unknown function. Our results support genome reconstruction as a robust process and suggest that reconstructions determined to be >90% complete are likely to effectively represent organismal function; however, population-level genotypic heterogeneity in natural populations, such as uneven distribution of plasmids, can lead to incorrect inferences.

Keywords: Binning; Metagenome assembled genome; Metagenomics.

Associated data

figshare/10.6084/m9.figshare.4902923

Grants and funding

William C. Nelson and Jennifer M. Mobberley were supported by the U.S. Department of Energy (DOE), Office of Biological and Environmental Research (BER), as part of BER’s Genomic Science Program (GSP). This contribution originates from the GSP Foundational Scientific Focus Area (FSFA) at the Pacific Northwest National Laboratory (PNNL). The Pacific Northwest National Laboratory is operated for DOE by Battelle Memorial Institute under contract DE-AC05-76RL01830. Sequence data presented was generated at the DOE Joint Genome Institute under contract no. DE-AC02-05CH11231 and Community Science Project 701. Benjamin J. Tully was funded through the Center for Dark Energy Biosphere Investigations (OCE-0939654). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.