Do we need a more structured system for gene names and pathways now that omics studies revealed a higher complexity of fungal carbon metabolism?

Abstract

Omics studies have revealed a much higher complexity and diversity of fungal primary carbon metabolism than was previously assumed, especially with respect to the number of genes/enzymes involved in individual pathway steps. These new insights sometimes conflict with historical gene naming systems which may lead to confusion, especially in comparative studies with multiple fungi. To reduce such issues in the future, especially taking into account the increasing use of AI-methods in data mining and comparative genomics, a more systematic and uniform naming system could be beneficial. This would require some gene renaming and prevention of using different names for the same biological function or the same name for genes with different biological functions and likely will depend on a fungal community-wide effort to achieve this. In this opinion paper we suggest such a structure, based on the genes involved in primary carbon metabolism of one of the best studied fungi in this field, the ascomycete Aspergillus niger. The proposed restructuring in this opinion paper therefore represents a model-derived framework rather than a universally applicable solution.