Cross-kingdom comparative genomics and phylogenetics of aromatic catabolic enzymes in bacteria and fungi

This dataset contains raw protein sequences and analyzed data from our study in comparative genomics and phylogenetics of aromatic catabolic enzymes in bacteria and fungi. In this study, we retrieved protein sequences from hundreds of bacteria and fungal genomes from public databases. To detect aromatic catabolic enzymes in each genome, we identified IPR domains from reference enzymes validated in biochemical studies. Genome-wide IPR scanning was performed for each genome, and then we examined the abundance of each aromatic catabolic enzymes through the presence of proteins with proxy IPR domains. Protein sequences with the proxy domains for aromatic catabolic enzymes were selected for association analyses (nutrition/lineage) and phylogenetic analyses.This dataset is associated with our published article in Nature Ecology and Evolution (Kijpornyongpan et al., 2025 Title "Cross-kingdom comparative genomics reveal the metabolic potential of fungi for lignin turnover in deadwood"). Details of files in this dataset are described as follows:Bacterial_protein_sequences.zip and Fungal_protein_Sequences.zip contain raw protein sequences from 255 bacterial genomes and 317 fungal genomes. These genomes were previously published and data are available in public database. More information of genomes used in this study can be found in Supplementary Information of the research article.Bacterial_IPRscan_5.44-79_annotation.zip and Fungal_IPRscan_5.44-79_annotation.zip contain results from genome-wide IPR domain searching through Interproscan 5.44-79.Bacterial_eggNOG_annotation and Fungal_eggNOG_annotation contain genome-wide gene annotation results through eggNOG 4.5 and eggNOG-mapper 1.0. Gene orthology data are informative for phylogenomic reconstruction and for retrieving specific sequences for each type of aromatic catabolic enzymes.Reference_enzymes.zip contains protein sequences of aromatic catabolic enzymes previously reported from biochemical studies.CrossKingdomGenomics_Phylogenomics.zip contains raw protein sequences, and gene presence/absence data used for species tree phylogenomic reconstruction.CrossKingdomComparativeGenomics_scripts.zip contains customized scripts in R and Perl used for fetching results from Interproscan and eggNOG-mapper, as well as used for data analyses (enzyme distribution and association analyses).SpecificEnzymes_Phylogeny.zip contains selected protein sequences from all studied genomes for each type of enzyme. These sequences were used for phylogenetic analyses, and SignalP analyses.Kijpornyongpan_2025_Supplementary.zip contains Supplementary Information that are associated with the publication.<br>