Muelbaier, H. | bioRxiv Science

bioRxiv2025

Targeted ortholog search in unannotated genome assemblies with fDOG-Assembly

Whole genome shotgun sequencing and assembly is routine. However, identifying protein-coding genes in newly assembled genomes remains complex, time-consuming, and labour-intensive. Therefore, most eukaryotic genome assemblies in public databases lack gene annotations reducing their value for evolutionary and functional genomics. Here, we present fDOG-Assembly, a novel tool for targeted, feature architecture-aware ortholog searches directly in unannotated genome assemblies. Benchmarking shows that fDOG-Assembly performs similarly to BUSCO and Compleasm in ortholog identification while offering the advantage of not being restricted to universal single-copy genes. Applied to identify orthologs of 5,000 human genes in rat and Nematostella vectensis, fDOG-Assembly approaches the performance of traditional ortholog search tools that rely on pre-annotated proteomes. Importantly, it can recover orthologs missed by conventional methods because of incomplete gene annotations, helping to fill gaps in phylogenetic profiles. As a case study, we screened 176 soil invertebrate genome assemblies for genes involved in antibacterial compound production. We found that orthologs of {beta}-lactam biosynthesis genes are widespread in springtails, with individual species possessing nearly complete cephamycin biosynthetic gene sets, suggesting they may represent previously unrecognized natural producers of {beta}-lactam antibiotics. Overall, fDOG-Assembly is a powerful resource for orthology-based analyses of the rapidly growing collection of unannotated genome assemblies.

bioinformatics↗

bioRxiv2024

Tracing the taxonomic distribution of plant cell wall degrading enzymes across the tree of life using feature architecture aware orthology assignments

The decomposition of plant material is a key driver of the global carbon cycle, traditionally attributed to fungi and bacteria. However, some invertebrates also possess orthologs to bacterial or fungal cellulolytic enzymes, likely acquired via horizontal gene transfer. This reticulated mode of evolution necessitates ortholog searches in large taxon sets to comprehensively map the repertoire of plant cell wall degrading enzymes (PCDs) across the tree of life, a task surpassing capacities of current software. Here, we use fDOG, a novel profile-based ortholog search tool to trace 235 potential PCDs across more than 18,000 taxa. fDOG allows to start the ortholog search from a single protein sequence as a seed, it performs on par with state-of-the-art software that require the comparison of entire proteomes, and it is unique in routinely scoring protein feature architecture differences between the seed protein and its orthologs. Visualizing the presence-absence patterns of PCD orthologs using a UMAP highlights taxa where recent changes in the enzyme repertoire indicate a change in lifestyle. Three invertebrates have a particularly rich set of PCD orthologs encoded in their genome. Only few of the orthologs show differing protein feature architectures relative to the seed that suggest functional modifications. Thus, the corresponding species represent lineages within the invertebrates that may contribute to the global carbon cycle. This study shows how fDOG can be used to create a multi-scale view on the taxonomic distribution of a metabolic capacity that ranges from tree of life-wide surveys to individual feature architecture changes within a species.

bioinformatics↗