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 (BUSCO) scores as a quality measure while the exclusion of possible contaminating sequences from genomic resources and the possible mis-identification 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 mis-identification 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 NCBI nt database, will 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, then retracted due to contaminations.