ArticleGenome biology and evolution2018
Patterns of Nucleotide Deletion and Insertion Inferred from Bacterial Pseudogenes.
Article in Genome biology and evolution, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- The transcriptional and translational outcomes for pseudogenes in bacterial endosymbionts.Molecular biology and evolution · 2026Article
- The pangenome: a statistical model, not a fixed biological property.Bioinformatics advances · 2026Review
- Structural and energetic analysis of stabilizing indel mutations.bioRxiv : the preprint server for biology · 2024Article
- Article
- Pseudogenes act as a neutral reference for detecting selection in prokaryotic pangenomes.Nature ecology & evolution · 2024Article
- De Novo Structural Variations of Escherichia coli Detected by Nanopore Long-Read Sequencing.Genome biology and evolution · 2023Article
- Pseudofinder: Detection of Pseudogenes in Prokaryotic Genomes.Molecular biology and evolution · 2022Article
- Genic Selection Within Prokaryotic Pangenomes.Genome biology and evolution · 2021Review
- GENCODE Pseudogenes.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Evolution along the parasitism-mutualism continuum determines the genetic repertoire of prophages.PLoS computational biology · 2020Article
- Bacteriophage-Insensitive Mutants of Antimicrobial-ResistantInternational journal of molecular sciences · 2020Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Pseudogenes are a paradigm of neutral evolution and their study has the potential to reveal intrinsic mutational biases. However, this potential is mitigated by the fact that pseudogenes are quickly purged from bacterial genomes. Here, we assembled a large set of pseudogenes from genomes experiencing reductive evolution as well as functional references for which we could establish reliable phylogenetic relationships. Using this unique dataset, we identified 857 independent insertion and deletion mutations and discover a pervasive bias towards deletions, but not insertions, with sizes multiples of 3 nt. We further show that selective constraints for the preservation of gene frame are unlikely to account for the observed mutational bias and propose that a mechanistic bias in alternative end-joining repair, a recombination-independent double strand break DNA repair mechanism, is responsible for the accumulation of 3n deletions.
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