副溶血弧菌:一种海洋病原体的流行性克隆、海洋基因库和生态连锁失衡研究
  • 本研究把有性繁殖种群的分析理念和方法应用于副溶血弧菌,根据全基因组变异重建其精细种群结构,发现该物种的独特海域性基因库;通过建模计算,提出“生态连锁失衡”是其主要进化推动力,并鉴定出具有与生物膜形成和六型分泌系统相关的上位相互作用区。该研究为高频重组细菌进化分析提供了全新范例。
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Epidemic Clones, Oceanic Gene Pools, and Eco-LD in the Free Living Marine Pathogen Vibrio parahaemolyticus

10.1093/molbev/msv009

2015-01-19, Article

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We investigated global patterns of variation in 157 whole-genome sequences of Vibrio parahaemolyticus, a free-living and seafood associated marine bacterium. Pandemic clones, responsible for recent outbreaks of gastroenteritis in humans, have spread globally. However, there are oceanic gene pools, one located in the oceans surrounding Asia and another in the Mexican Gulf. Frequent recombination means that most isolates have acquired the genetic profile of their current location. We investigated the genetic structure in the Asian gene pool by calculating the effective population size in two different ways. Under standard neutral models, the two estimates should give similar answers but we found a 27-fold difference. We propose that this discrepancy is caused by the subdivision of the species into a hundred or more ecotypes which are maintained stably in the population. To investigate the genetic factors involved, we used 51 unrelated isolates to conduct a genome-wide scan for epistatically interacting loci. We found a single example of strong epistasis between distant genome regions. A majority of strains had a type VI secretion system associated with bacterial killing. The remaining strains had genes associated with biofilm formation and regulated by cyclic dimeric GMP signaling. All strains had one or other of the two systems and none of isolate had complete complements of both systems, although several strains had remnants. Further "top down" analysis of patterns of linkage disequilibrium within frequently recombining species will allow a detailed understanding of how selection acts to structure the pattern of variation within natural bacterial populations.

First Authors:
Yujun Cui,Xianwei Yang

Correspondence Authors:
Ruifu Yang

All Authors:
Yujun Cui,Xianwei Yang,Xavier Didelot,Chenyi Guo,Dongfang Li,Yanfeng Yan,Yiquan Zhang,Yanting Yuan,Huanming Yang,Jian Wang,Jun Wang,Yajun Song,Dongsheng Zhou,Daniel Falush,Ruifu Yang

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