The comparative population genetics of Neisseria meningitidis and Neisseria gonorrhoeae

PeerJ

article

Lucile Vigué¹  Adam Eyre-Walker² 

[1] Ecole Polytechnique;School of Life Sciences, University of Sussex

关键词: Neisseria gonorhoeae;    Neisseria meningitidis;    Population genomics;    Recombination;    Lateral gene transfer;    Horizontal gene transfer;    Adaptive evolution;    Linkage disequilibrium;   

DOI  :  10.7717/peerj.7216

学科分类：社会科学、人文和艺术（综合）

来源: Inra

【 摘 要 】

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.

【 授权许可】

CC BY