ArticleMicrobial genomics2020
An assessment of genome annotation coverage across the bacterial tree of life.
Article in Microbial genomics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 64 papers.
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Who cites it
64 citing papers in PubMed, 122 citations in OpenAlex.
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- Uniform pre-processing of bacterial single-cell RNA-seq.bioRxiv : the preprint server for biology · 2026Article
- Genome-resolved metagenomics reveals rare taxa and functional traits in two contrasting agricultural fields.ISME communications · 2026Article
- Limitations of current machine learning models in predicting enzymatic functions for uncharacterized proteins.G3 (Bethesda, Md.) · 2025Article
- Exploring homology detection via k-means clustering of proteins embedded with a large language model.Bioinformatics (Oxford, England) · 2025Article
- Linking genomic evolutionary transitions to ecological phenotypic adaptations inbioRxiv : the preprint server for biology · 2025Article
- Discovery of effectors for casein kinase signaling in the African trypanosome.Scientific reports · 2025Article
- Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets.Communications biology · 2025Article
- Comparative genomics of native plasmids from plant pathogenic Gammaproteobacteria.DNA research : an international journal for rapid publication of reports on genes and genomes · 2025Article
- The type IV secretion system ofMicrobial genomics · 2025Article
- Trait-Based Life History Strategies Shape Bacterial Niche Breadth.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- EvoWeaver: large-scale prediction of gene functional associations from coevolutionary signals.Nature communications · 2025Article
- Microbiome metabolic capacity is buffered against phylotype losses by functional redundancy.Applied and environmental microbiology · 2025Article
- OftenFrontiers in microbiology · 2025Article
- Protein functional domain analysis enhances genotype-phenotype associations in comparative genomic studies ofFrontiers in microbiology · 2025Article
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- Discovery and synthesis of leaderless bacteriocins from the Actinomycetota.Journal of bacteriology · 2024Article
4 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Although gene-finding in bacterial genomes is relatively straightforward, the automated assignment of gene function is still challenging, resulting in a vast quantity of hypothetical sequences of unknown function. But how prevalent are hypothetical sequences across bacteria, what proportion of genes in different bacterial genomes remain unannotated, and what factors affect annotation completeness? To address these questions, we surveyed over 27 000 bacterial genomes from the Genome Taxonomy Database, and measured genome annotation completeness as a function of annotation method, taxonomy, genome size, 'research bias' and publication date. Our analysis revealed that 52 and 79 % of the average bacterial proteome could be functionally annotated based on protein and domain-based homology searches, respectively. Annotation coverage using protein homology search varied significantly from as low as 14 % in some species to as high as 98 % in others. We found that taxonomy is a major factor influencing annotation completeness, with distinct trends observed across the microbial tree (e.g. the lowest level of completeness was found in the
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