Predicting the operon structure of the Mycococcus xanthus genome using the novel software DiscOperon

ABSTRACT Motivation: Myxococcus xanthus is a predatory soil bacterium with a large genome of 9.14 MB due to a genome duplication event. While complete genome sequences of M. xanthus are available, gene annotation remains challenging due to its size and the resulting large number of duplicated genes. Operons, so syntenic block of genes that are co-regulated in bacterial genomes, are an important resource to help predict gene function accurately. Results: In order to help improve the annotation of complex genomes such as the one from M. xanthus, we developed a novel operon prediction tool, DiscOperon, which combines gene expression data with homology searches to identify syntenic blocks: Co-expression data of neighbouring genes across the genome are first used to define gene clusters, which are then used to search for conserved syntenic blocks in fully sequenced bacterial genomes using sequence homology searches. This strategy enables DiscOperon to account for gene insertions, rearrangements and deletions, which is its most distinguishing feature. We have tested DiscOperon against ground truths gene pair information on 3 different species from ODB and RegulonDB and compared it to state-of-the-art and still available operon prediction software and we demonstrate its general usability for operon prediction of any bacterial complete genome. We have applied DiscOperon to predict the operons of M. xanthus, which we are making available for the research community. Availability and implementation: DiscOperon is lightweight, user-friendly python tool with minimal dependencies. It is freely available at https://gitlab.com/habermann_lab/discoperon for general usage. Contact: Theo Brunet (theo.brunet@univ-amu.fr); Bianca Habermann (bianca.habermann@univ-amu.fr). Supplementary information: The operon-structured and annotated M. xanthus genome is available from this manuscript, as well as from Zenodo (https://doi.org/10.5281/zenodo.21976167). We furthermore plan to submit the M. xanthus operon information to the operon database OBD.