The Good, The Bad, and The Misleading: How to Improve the Quality of ‘Genome Announcements’?

Abstract

When comparing the requirements of diverse journals to publish microbial ‘Genome Reports,’ we noticed that some mostly focus on benchmarking universal single-copy orthologs scores as a quality measure, while the exclusion of possible contaminating sequences from genomic resources and the possible misidentification of the target microbes receive less attention. To deal with these quality issues, we suggest that DNA barcodes that are widely accepted for the identification of the target microbe species should be extracted from newly reported genome resources and included in phylogenetic analyses to confirm the identity of the sequenced microorganisms before Genome Reports are published. This approach, applied, for example, by the journal IMA Fungus, largely prevents the misidentification of the microbes that are targeted for whole-genome sequencing (WGS). In addition, contig similarity values, including GC content, remapping coverage of WGS reads, and BLASTN searches against the National Center for Biotechnology Information nucleotide database, would also reveal contamination issues. The values of these two recommendations to improve the publication criteria for microbial Genome Reports in diverse journals are demonstrated here through analyses of a draft genome published in Molecular Plant-Microbe Interactions and then retracted due to contaminations. [Graphic: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Keywords

• benchmarking universal single-copy orthologs (BUSCO)
• genome assembly
• obligate biotrophic plant pathogens
• powdery mildews
• quality control
• whole-genome sequencing (WGS)