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

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 qualitymeasure, 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 ofWGSreads, 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.

Automated summary

When comparing the requirements of diverse journals to publish microbial 'Genome Reports,' we found that some focus on universal single-copy orthologs scores as a quality measure, while paying less attention to excluding possible contaminating sequences and possible misidentification of target microbes. To address these issues, we suggest extracting widely accepted DNA barcodes for identification and including them in phylogenetic analyses to confirm microorganism identity before publishing Genome Reports. Additionally, contig similarity values, such as GC content, remapping coverage of WGS reads, and BLASTN searches against the NCBI nucleotide database, can also detect contamination issues. These recommendations are demonstrated through analysis and retraction of a draft genome published in Molecular Plant-Microbe Interactions due to contamination.