Mixing genome annotation methods in a comparative analysis inflates the apparent number of lineage-specific genes Article Swipe

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Caroline M. Weisman , Andrew W. Murray , Sean R. Eddy ·

YOU? · · 2022 · Open Access · · DOI: https://doi.org/10.1101/2022.01.13.476251

Summary 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.

Related Topics

Biology

Clade

Human Genome Project

Computational Biology

Evolutionary Biology

Genomics

Phylogenetics

Concepts

Annotation Genome Biology Lineage (genetic) Gene Clade Gene Annotation Genetics DNA sequencing Genome project Computational biology Evolutionary biology Comparative genomics Genomics Phylogenetics

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Type: preprint
Language: en
Landing Page: https://doi.org/10.1101/2022.01.13.476251
PDF: https://www.biorxiv.org/content/biorxiv/early/2022/01/15/2022.01.13.476251.full.pdf
OA Status: green
Cited By: 9
References: 36
Related Works: 10
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DOI: https://doi.org/10.1101/2022.01.13.476251

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Title: Mixing genome annotation methods in a comparative analysis inflates the apparent number of lineage-specific genes

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Type: preprint

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Language: en

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Publication year: 2022

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Publication date: 2022-01-15

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Authors: Caroline M. Weisman, Andrew W. Murray, Sean R. Eddy

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Landing page: https://doi.org/10.1101/2022.01.13.476251

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Concepts: Annotation, Genome, Biology, Lineage (genetic), Gene, Clade, Gene Annotation, Genetics, DNA sequencing, Genome project, Computational biology, Evolutionary biology, Comparative genomics, Genomics, Phylogenetics

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Cited by: 9

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Citations by year (recent): 2023: 4, 2022: 5

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