AUTHOR=Vignolle Gabriel A. , Mach Robert L. , Mach-Aigner Astrid R. , Zimmermann Christian 

TITLE=FunOrder 2.0 – a method for the fully automated curation of co-evolved genes in fungal biosynthetic gene clusters

JOURNAL=Frontiers in Fungal Biology

VOLUME=Volume 3 - 2022

YEAR=2022

URL=https://www.frontiersin.org/journals/fungal-biology/articles/10.3389/ffunb.2022.1020623

DOI=10.3389/ffunb.2022.1020623

ISSN=2673-6128

ABSTRACT=Coevolution is an important biological process that shapes interacting proteins – may it be physically interacting proteins or consecutive enzymes in a metabolic pathway, such as the biosynthetic pathways for secondary metabolites. Previously, we developed FunOrder, a semi-automated method for the detection of co-evolved genes, and demonstrated that FunOrder can be used to identify essential genes in biosynthetic gene clusters from different ascomycetes. A major drawback of this original method was the need for a manual assessment, which may create a user bias and prevents a high-throughput application. Here we present a fully automated version of this method termed FunOrder 2.0. In the improved version, we use several mathematical indices to determine the optimal number of clusters in the FunOrder output, and a subsequent k-means clustering based on the first three principal components of a principal component analysis of the FunOrder output to automatically detect co-evolved genes. Further, we replaced the BLAST tool with the DIAMOND tool as a prerequisite for using larger proteome databases. The introduced changes slightly decreased the sensitivity of this method, which is outweighed by enhanced overall speed and specificity.