The comparative population genetics of Neisseria meningitidis and Neisseria gonorrhoeae
Neisseria meningitidis and N. gonorrhoeae are closely related pathogenic bacteria. To compare their population genetics, we compiled a dataset of 1,145 genes found across 20 N. meningitidis and 15 N. gonorrhoeae genomes. We find that N. meningitidis is seven-times more diverse than N. gonorrhoeae in...
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| Format: | Article |
| Language: | English |
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PeerJ Inc.
2019-06-01
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| Series: | PeerJ |
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| Online Access: | https://peerj.com/articles/7216.pdf |
| _version_ | 1827607165532110848 |
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| author | Lucile Vigué Adam Eyre-Walker |
| author_facet | Lucile Vigué Adam Eyre-Walker |
| author_sort | Lucile Vigué |
| collection | DOAJ |
| description | Neisseria meningitidis and N. gonorrhoeae are closely related pathogenic bacteria. To compare their population genetics, we compiled a dataset of 1,145 genes found across 20 N. meningitidis and 15 N. gonorrhoeae genomes. We find that N. meningitidis is seven-times more diverse than N. gonorrhoeae in their combined core genome. Both species have acquired the majority of their diversity by recombination with divergent strains, however, we find that N. meningitidis has acquired more of its diversity by recombination than N. gonorrhoeae. We find that linkage disequilibrium (LD) declines rapidly across the genomes of both species. Several observations suggest that N. meningitidis has a higher effective population size than N. gonorrhoeae; it is more diverse, the ratio of non-synonymous to synonymous polymorphism is lower, and LD declines more rapidly to a lower asymptote in N. meningitidis. The two species share a modest amount of variation, half of which seems to have been acquired by lateral gene transfer and half from their common ancestor. We investigate whether diversity varies across the genome of each species and find that it does. Much of this variation is due to different levels of lateral gene transfer. However, we also find some evidence that the effective population size varies across the genome. We test for adaptive evolution in the core genome using a McDonald–Kreitman test and by considering the diversity around non-synonymous sites that are fixed for different alleles in the two species. We find some evidence for adaptive evolution using both approaches. |
| first_indexed | 2024-03-09T06:50:35Z |
| format | Article |
| id | doaj.art-cfb1a2572e454924b32f920270a226ea |
| institution | Directory Open Access Journal |
| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T06:50:35Z |
| publishDate | 2019-06-01 |
| publisher | PeerJ Inc. |
| record_format | Article |
| series | PeerJ |
| spelling | doaj.art-cfb1a2572e454924b32f920270a226ea2023-12-03T10:29:03ZengPeerJ Inc.PeerJ2167-83592019-06-017e721610.7717/peerj.7216The comparative population genetics of Neisseria meningitidis and Neisseria gonorrhoeaeLucile Vigué0Adam Eyre-Walker1Ecole Polytechnique, Paris, FranceSchool of Life Sciences, University of Sussex, Brighton, UKNeisseria meningitidis and N. gonorrhoeae are closely related pathogenic bacteria. To compare their population genetics, we compiled a dataset of 1,145 genes found across 20 N. meningitidis and 15 N. gonorrhoeae genomes. We find that N. meningitidis is seven-times more diverse than N. gonorrhoeae in their combined core genome. Both species have acquired the majority of their diversity by recombination with divergent strains, however, we find that N. meningitidis has acquired more of its diversity by recombination than N. gonorrhoeae. We find that linkage disequilibrium (LD) declines rapidly across the genomes of both species. Several observations suggest that N. meningitidis has a higher effective population size than N. gonorrhoeae; it is more diverse, the ratio of non-synonymous to synonymous polymorphism is lower, and LD declines more rapidly to a lower asymptote in N. meningitidis. The two species share a modest amount of variation, half of which seems to have been acquired by lateral gene transfer and half from their common ancestor. We investigate whether diversity varies across the genome of each species and find that it does. Much of this variation is due to different levels of lateral gene transfer. However, we also find some evidence that the effective population size varies across the genome. We test for adaptive evolution in the core genome using a McDonald–Kreitman test and by considering the diversity around non-synonymous sites that are fixed for different alleles in the two species. We find some evidence for adaptive evolution using both approaches.https://peerj.com/articles/7216.pdfNeisseria gonorhoeaeNeisseria meningitidisPopulation genomicsRecombinationLateral gene transferHorizontal gene transfer |
| spellingShingle | Lucile Vigué Adam Eyre-Walker The comparative population genetics of Neisseria meningitidis and Neisseria gonorrhoeae PeerJ Neisseria gonorhoeae Neisseria meningitidis Population genomics Recombination Lateral gene transfer Horizontal gene transfer |
| title | The comparative population genetics of Neisseria meningitidis and Neisseria gonorrhoeae |
| title_full | The comparative population genetics of Neisseria meningitidis and Neisseria gonorrhoeae |
| title_fullStr | The comparative population genetics of Neisseria meningitidis and Neisseria gonorrhoeae |
| title_full_unstemmed | The comparative population genetics of Neisseria meningitidis and Neisseria gonorrhoeae |
| title_short | The comparative population genetics of Neisseria meningitidis and Neisseria gonorrhoeae |
| title_sort | comparative population genetics of neisseria meningitidis and neisseria gonorrhoeae |
| topic | Neisseria gonorhoeae Neisseria meningitidis Population genomics Recombination Lateral gene transfer Horizontal gene transfer |
| url | https://peerj.com/articles/7216.pdf |
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