Academic Journal
A natural ANI gap that can define intra-species units of bacteriophages and other viruses
| العنوان: | A natural ANI gap that can define intra-species units of bacteriophages and other viruses |
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| المؤلفون: | Aldeguer-Riquelme, Borja, Conrad, Roth E., Anton, Josefa, Rossello-Mora, Ramon, Konstantinidis, Konstantinos T. |
| المساهمون: | Universidad de Alicante. Departamento de Fisiología, Genética y Microbiología, Ecología Microbiana Molecular |
| بيانات النشر: | American Society for Microbiology |
| سنة النشر: | 2024 |
| المجموعة: | RUA - Repositorio Institucional de la Universidad de Alicante |
| مصطلحات موضوعية: | ANI gap, Bacteriophages, Genomovars, Strains |
| الوصف: | Despite the importance of intra-species variants of viruses for causing disease and/or disrupting ecosystem functioning, there is no universally applicable standard to define these. A (natural) gap in whole-genome average nucleotide identity (ANI) values around 95% is commonly used to define species, especially for bacteriophages, but whether a similar gap exists within species that can be used to define intra-species units has not been evaluated yet. Whole-genome comparisons among members of 1,016 bacteriophage (Caudoviricetes) species revealed a region of low frequency of ANI values around 99.2%–99.8%, showing threefold or fewer pairs than expected for an even distribution. This second gap is prevalent in viruses infecting various cultured or uncultured hosts from a variety of environments, although a few exceptions to this pattern were also observed (3.7% of total species) and are likely attributed to cultivation biases or other factors. Similar results were observed for a limited set of eukaryotic viruses that are adequately sampled, including SARS-CoV-2, whose ANI-based clusters matched well with the WHO-defined variants of concern, indicating that our findings from bacteriophages might be more broadly applicable and the ANI-based clusters may represent functionally and/or ecologically distinct units. These units appear to be predominantly driven by (high) ecological cohesiveness coupled to either frequent recombination for bacteriophages or selection and clonal evolution for other viruses such as SARS-CoV-2, indicating that fundamentally different underlying mechanisms could lead to similar diversity patterns. Accordingly, we propose the ANI gap approach outlined above for defining viral intra-species units, for which we propose the term genomovars. ; This work has been supported, in part, by the US National Science Foundation (Award No. 1759831 and 2129823) to K.T.K. and the METACIRCLE projects (PID2021-126114NB-C41 and PID2021-126114NB-C42) funded by the Spanish Ministry of Science and Innovation to J.A. ... |
| نوع الوثيقة: | article in journal/newspaper |
| اللغة: | English |
| تدمد: | 2150-7511 |
| Relation: | https://doi.org/10.1128/mbio.01536-24; info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2021-2023/PID2021-126114NB-C41; info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2021-2023/PID2021-126114NB-C42; info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2021-2023/RED2022-134837-T; mBio. 2024, 15(8): e01536-24. https://doi.org/10.1128/mbio.01536-24; http://hdl.handle.net/10045/145691 |
| DOI: | 10.1128/mbio.01536-24 |
| الاتاحة: | http://hdl.handle.net/10045/145691 https://doi.org/10.1128/mbio.01536-24 |
| Rights: | © 2024 Aldeguer-Riquelme et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license. ; info:eu-repo/semantics/openAccess |
| رقم الانضمام: | edsbas.EB846F78 |
| قاعدة البيانات: | BASE |
Full Text Finder | تدمد: | 21507511 |
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| DOI: | 10.1128/mbio.01536-24 |