ArticleCurrent biology : CB2022
Mixing genome annotation methods in a comparative analysis inflates the apparent number of lineage-specific genes.
Article in Current biology : CB, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 60 papers.
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Who cites it
60 citing papers in PubMed.
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- Convergent genomic trajectories shape adaptation to life on land across animal lineages.Nature communications · 2026Article
- The genome of Doleromyrma darwiniana and annotations for five additional Dolichoderinae species.Scientific data · 2026Article
- PlantGATA: a comprehensive database for plant GATA transcription factors.Functional & integrative genomics · 2026Article
- The evolution of the immune system of bees is defined by conservation, expansions, and losses.BMC biology · 2026Article
- Evolutionary and methodological considerations when interpreting gene presence-absence variation in pangenomes.NAR genomics and bioinformatics · 2026Review
- GeneExt: a gene model extension tool for enhanced single-cell RNA-seq analysis.Bioinformatics (Oxford, England) · 2026Article
- Annotation of 200 Insect Genomes with BRAKER for Consistent Comparisons across Species.Scientific data · 2026Article
- Comparative gene annotation and orthology assignments across 301 species of Drosophilidae.bioRxiv : the preprint server for biology · 2026Article
- Comparative gene annotation and orthology assignments across 301 species of Drosophilidae.PLoS biology · 2026Article
- Genomes of the entomopathogenic nematode Steinernema hermaphroditum and its associated bacteria.Genetics · 2025Article
- Genomic, Proteomic, and Biochemical Study ofJournal of agricultural and food chemistry · 2025Article
- Evolutionary Analysis of Gene-Expression Localization in the Model Crustacean, Daphnia pulex.Molecular ecology · 2025Article
- De Novo Gene Emergence: Summary, Classification, and Challenges of Current Methods.Genome biology and evolution · 2025Review
- Propensity for proto-gene emergence in bacteria.Genome biology · 2025Article
- DeNoFo: a file format and toolkit for standardized, comparable de novo gene annotation.Bioinformatics (Oxford, England) · 2025Article
- Gene Family Expansions Provide Molecular Flexibility Required for Context-Dependent Species Interactions.Ecology letters · 2025Article
- Review
- EASYstrata: an all-in-one workflow for genome annotation and genomic divergence analysis.NAR genomics and bioinformatics · 2025Article
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3 authors.
Funding
Abstract
Comparisons of genomes of different species are used to identify lineage-specific genes, those genes that appear unique to one species or clade. Lineage-specific genes are often thought to represent genetic novelty that underlies unique adaptations. Identification of these genes depends not only on genome sequences, but also on inferred gene annotations. Comparative analyses typically use available genomes that have been annotated using different methods, increasing the risk that orthologous DNA sequences may be erroneously annotated as a gene in one species but not another, appearing lineage specific as a result. To evaluate the impact of such "annotation heterogeneity," we identified four clades of species with sequenced genomes with more than one publicly available gene annotation, allowing us to compare the number of lineage-specific genes inferred when differing annotation methods are used to those resulting when annotation method is uniform across the clade. In these case studies, annotation heterogeneity increases the apparent number of lineage-specific genes by up to 15-fold, suggesting that annotation heterogeneity is a substantial source of potential artifact.
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