Relating ecological diversity to genetic discontinuity across bacterial species
Abstract Background Genetic discontinuity represents abrupt breaks in genomic identity among species. Advances in genome sequencing have enhanced our ability to track and characterize genetic discontinuity in bacterial populations. However, exploring the degree to which bacterial diversity exists as...
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| Format: | Article |
| Language: | English |
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BMC
2025-01-01
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| Series: | Genome Biology |
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| Online Access: | https://doi.org/10.1186/s13059-024-03443-z |
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| author | Hemanoel Passarelli-Araujo Thiago M. Venancio William P. Hanage |
| author_facet | Hemanoel Passarelli-Araujo Thiago M. Venancio William P. Hanage |
| author_sort | Hemanoel Passarelli-Araujo |
| collection | DOAJ |
| description | Abstract Background Genetic discontinuity represents abrupt breaks in genomic identity among species. Advances in genome sequencing have enhanced our ability to track and characterize genetic discontinuity in bacterial populations. However, exploring the degree to which bacterial diversity exists as a continuum or sorted into discrete and readily defined species remains a challenge in microbial ecology. Here, we aim to quantify the genetic discontinuity ( $$\delta$$ δ ) and investigate how this metric is related to ecology. Results We harness a dataset comprising 210,129 genomes to systematically explore genetic discontinuity patterns across several distantly related species, finding clear breakpoints which vary depending on the taxa in question. By delving into pangenome characteristics, we uncover a significant association between pangenome saturation and genetic discontinuity. Closed pangenomes are associated with more pronounced breaks, exemplified by Mycobacterium tuberculosis. Additionally, through a machine learning approach, we detect key features such as gene conservation patterns and functional annotations that significantly impact genetic discontinuity prediction. Conclusions Our study clarifies bacterial genetic patterns and their ecological impacts, enhancing the delineation of species boundaries and deepening our understanding of microbial diversity. |
| format | Article |
| id | doaj-art-053c8eadd87342dbab475fd88c7faaf8 |
| institution | Kabale University |
| issn | 1474-760X |
| language | English |
| publishDate | 2025-01-01 |
| publisher | BMC |
| record_format | Article |
| series | Genome Biology |
| spelling | doaj-art-053c8eadd87342dbab475fd88c7faaf82025-01-12T12:25:59ZengBMCGenome Biology1474-760X2025-01-0126111410.1186/s13059-024-03443-zRelating ecological diversity to genetic discontinuity across bacterial speciesHemanoel Passarelli-Araujo0Thiago M. Venancio1William P. Hanage2Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard TH Chan School of Public HealthLaboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy RibeiroCenter for Communicable Disease Dynamics, Department of Epidemiology, Harvard TH Chan School of Public HealthAbstract Background Genetic discontinuity represents abrupt breaks in genomic identity among species. Advances in genome sequencing have enhanced our ability to track and characterize genetic discontinuity in bacterial populations. However, exploring the degree to which bacterial diversity exists as a continuum or sorted into discrete and readily defined species remains a challenge in microbial ecology. Here, we aim to quantify the genetic discontinuity ( $$\delta$$ δ ) and investigate how this metric is related to ecology. Results We harness a dataset comprising 210,129 genomes to systematically explore genetic discontinuity patterns across several distantly related species, finding clear breakpoints which vary depending on the taxa in question. By delving into pangenome characteristics, we uncover a significant association between pangenome saturation and genetic discontinuity. Closed pangenomes are associated with more pronounced breaks, exemplified by Mycobacterium tuberculosis. Additionally, through a machine learning approach, we detect key features such as gene conservation patterns and functional annotations that significantly impact genetic discontinuity prediction. Conclusions Our study clarifies bacterial genetic patterns and their ecological impacts, enhancing the delineation of species boundaries and deepening our understanding of microbial diversity.https://doi.org/10.1186/s13059-024-03443-zPangenomeMachine learningSpeciationGenetic Rate of ChangeBacterial ecology |
| spellingShingle | Hemanoel Passarelli-Araujo Thiago M. Venancio William P. Hanage Relating ecological diversity to genetic discontinuity across bacterial species Genome Biology Pangenome Machine learning Speciation Genetic Rate of Change Bacterial ecology |
| title | Relating ecological diversity to genetic discontinuity across bacterial species |
| title_full | Relating ecological diversity to genetic discontinuity across bacterial species |
| title_fullStr | Relating ecological diversity to genetic discontinuity across bacterial species |
| title_full_unstemmed | Relating ecological diversity to genetic discontinuity across bacterial species |
| title_short | Relating ecological diversity to genetic discontinuity across bacterial species |
| title_sort | relating ecological diversity to genetic discontinuity across bacterial species |
| topic | Pangenome Machine learning Speciation Genetic Rate of Change Bacterial ecology |
| url | https://doi.org/10.1186/s13059-024-03443-z |
| work_keys_str_mv | AT hemanoelpassarelliaraujo relatingecologicaldiversitytogeneticdiscontinuityacrossbacterialspecies AT thiagomvenancio relatingecologicaldiversitytogeneticdiscontinuityacrossbacterialspecies AT williamphanage relatingecologicaldiversitytogeneticdiscontinuityacrossbacterialspecies |