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Pseudogenes act as a neutral reference for detecting selection in prokaryotic pangenomes.

التفاصيل البيبلوغرافية
العنوان: Pseudogenes act as a neutral reference for detecting selection in prokaryotic pangenomes.
المؤلفون: Douglas GM; Department of Microbiology and Immunology, McGill University, Montréal, Québec, Canada. gavin.douglas@mcgill.ca.; McGill Genome Centre, McGill University, Montréal, Québec, Canada. gavin.douglas@mcgill.ca., Shapiro BJ; Department of Microbiology and Immunology, McGill University, Montréal, Québec, Canada. jesse.shapiro@mcgill.ca.; McGill Genome Centre, McGill University, Montréal, Québec, Canada. jesse.shapiro@mcgill.ca.; McGill Centre for Microbiome Research, McGill University, Montréal, Québec, Canada. jesse.shapiro@mcgill.ca.
المصدر: Nature ecology & evolution [Nat Ecol Evol] 2024 Feb; Vol. 8 (2), pp. 304-314. Date of Electronic Publication: 2024 Jan 04.
نوع المنشور: Journal Article
اللغة: English
بيانات الدورية: Publisher: Springer Nature Country of Publication: England NLM ID: 101698577 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 2397-334X (Electronic) Linking ISSN: 2397334X NLM ISO Abbreviation: Nat Ecol Evol Subsets: MEDLINE
أسماء مطبوعة: Original Publication: [London] : Springer Nature
مواضيع طبية MeSH: Pseudogenes* , Biological Evolution*, Genome ; Bacteria/genetics
مستخلص: A long-standing question is to what degree genetic drift and selection drive the divergence in rare accessory gene content between closely related bacteria. Rare genes, including singletons, make up a large proportion of pangenomes (all genes in a set of genomes), but it remains unclear how many such genes are adaptive, deleterious or neutral to their host genome. Estimates of species' effective population sizes (N e ) are positively associated with pangenome size and fluidity, which has independently been interpreted as evidence for both neutral and adaptive pangenome models. We hypothesized that pseudogenes, used as a neutral reference, could be used to distinguish these models. We find that most functional categories are depleted for rare pseudogenes when a genome encodes only a single intact copy of a gene family. In contrast, transposons are enriched in pseudogenes, suggesting they are mostly neutral or deleterious to the host genome. Thus, even if individual rare accessory genes vary in their effects on host fitness, we can confidently reject a model of entirely neutral or deleterious rare genes. We also define the ratio of singleton intact genes to singleton pseudogenes (s i /s p ) within a pangenome, compare this measure across 668 prokaryotic species and detect a signal consistent with the adaptive value of many rare accessory genes. Taken together, our work demonstrates that comparing with pseudogenes can improve inferences of the evolutionary forces driving pangenome variation.
(© 2024. The Author(s), under exclusive licence to Springer Nature Limited.)
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تواريخ الأحداث: Date Created: 20240104 Date Completed: 20240214 Latest Revision: 20240722
رمز التحديث: 20240723
DOI: 10.1038/s41559-023-02268-6
PMID: 38177690
قاعدة البيانات: MEDLINE
الوصف
تدمد:2397-334X
DOI:10.1038/s41559-023-02268-6