ArticleGenome biology and evolution2013
Sequence context of indel mutations and their effect on protein evolution in a bacterial endosymbiont.
Article in Genome biology and evolution, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
28 citing papers in PubMed, 51 citations in OpenAlex.
- Article
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- Comparative Genomics Insights Into the Evolutionary Disparities Between Nitroplast-Evolved Ecotype UCYN-A2 and Its Closest Relative UCYN-A1.Ecology and evolution · 2025Article
- Comprehensive Analysis of the Fourteen Complete Genome Sequences ofJournal of microbiology and biotechnology · 2024Article
- Environmental and genetic influence on the rate and spectrum of spontaneous mutations inMicrobiology (Reading, England) · 2024Article
- Coevolution of Metabolic Pathways in Blattodea and TheirMicrobiology spectrum · 2022Article
- Convergent evolution of a labile nutritional symbiosis in ants.The ISME journal · 2022Article
- Complete pan-plastome sequences enable high resolution phylogenetic classification of sugar beet and closely related crop wild relatives.BMC genomics · 2022Article
- Variable Spontaneous Mutation and Loss of Heterozygosity among Heterozygous Genomes in Yeast.Molecular biology and evolution · 2020Article
- Insertion and deletion evolution reflects antibiotics selection pressure in a Mycobacterium tuberculosis outbreak.PLoS pathogens · 2020Article
- Bacteriophage-Insensitive Mutants of Antimicrobial-ResistantInternational journal of molecular sciences · 2020Article
- Complete mitochondrial genome sequence ofMitochondrial DNA. Part B, Resources · 2019Article
- Patterns of Nucleotide Deletion and Insertion Inferred from Bacterial Pseudogenes.Genome biology and evolution · 2018Article
- Genomic Comparison Among Global Isolates ofFrontiers in cellular and infection microbiology · 2018Article
- Evolution of intrinsic disorder in eukaryotic proteins.Cellular and molecular life sciences : CMLS · 2017Review
- Solving the master equation for Indels.BMC bioinformatics · 2017Article
- Next-Generation Sequencing of Two Mitochondrial Genomes from Family Pompilidae (Hymenoptera: Vespoidea) Reveal Novel Patterns of Gene Arrangement.International journal of molecular sciences · 2016Article
- The pioneering role of PRDM9 indel mutations in tarsier evolution.Scientific reports · 2016Article
- Adaptation by Deletogenic Replication Slippage in a Nascent Symbiont.Molecular biology and evolution · 2016Article
- Article
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Authors and funding
2 authors at 1 institution in 2 countries.
Funding
Abstract
Indel mutations play key roles in genome and protein evolution, yet we lack a comprehensive understanding of how indels impact evolutionary processes. Genome-wide analyses enabled by next-generation sequencing can clarify the context and effect of indels, thereby integrating a more detailed consideration of indels with our knowledge of nucleotide substitutions. To this end, we sequenced Blochmannia chromaiodes, an obligate bacterial endosymbiont of carpenter ants, and compared it with the close relative, B. pennsylvanicus. The genetic distance between these species is small enough for accurate whole genome alignment but large enough to provide a meaningful spectrum of indel mutations. We found that indels are subjected to purifying selection in coding regions and even intergenic regions, which show a reduced rate of indel base pairs per kilobase compared with nonfunctional pseudogenes. Indels occur almost exclusively in repeat regions composed of homopolymers and multimeric simple sequence repeats, demonstrating the importance of sequence context for indel mutations. Despite purifying selection, some indels occur in protein-coding genes. Most are multiples of three, indicating selective pressure to maintain the reading frame. The deleterious effect of frameshift-inducing indels is minimized by either compensation from a nearby indel to restore reading frame or the indel's location near the 3'-end of the gene. We observed amino acid divergence exceeding nucleotide divergence in regions affected by frameshift-inducing indels, suggesting that these indels may either drive adaptive protein evolution or initiate gene degradation. Our results shed light on how indel mutations impact processes of molecular evolution underlying endosymbiont genome evolution.
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