The Study On Population Genomics Of Vibrio Parahaemolyticus

Vibrio parahaemolyticus is a Gram-negative halophilic bacterium that is widely distributed in estuarial,coastal and marine environments,and in a variety of aquatic products.Consumption of aquatic products contaminated by V.parahaemolyticus can cause acute gastroenteritis in humans;and in recent years,the infections caused by V.parahaemolyticus keep increasing,making it the leading cause of bacterial gastroenteritis worldwide.V.parahaemolyticus can also cause acute hepatopancreatic necrosis disease of shrimp,which leads to serious losses on aquaculture.The study on population genomics of V.parahaemolyticus can promote our understanding on its evolution and transmission,which is helpful for the source tracking and prevention of this pathogen.V.parahaemolyticus exhibits high rates of homologous recombination.Frequent homologous recombinations disturb the boundary between variations introduced by horizontal recombination events and the spontaneous mutations that represent vertical genetic signals.Therefore,classical population genetics approaches,such as phylogenybased analysis,are not suitable for deciphering population structure of bacterial species with high recombination rates.Currently,the theory and tool in the field of bacterial recombination study is lacking,and hence hinders the evolutionary study of bacterial species with high recombination rates.Studying the evolution of V.parahaemolyticus can provide insights into the above issues in the evolutionary study of frequently recombining bacteria.In this study,by using V.parahaemolyticus as a model,we aim to solve two major challenges in the evolutionary study of frequently recombining bacteria: population structure reconstruction and evolutionary forces of recombination.We analyzed the whole genome sequences of 1,103 V.parahaemolyticus strains from 24 countries and regions in Asia,America,Europe and Africa,to perform the study with three sections:(1)Population structure and transoceanic spread of V.parahaemolyticusPopulation structure reconstruction is a difficult issue in the evolutionary study of frequently recombining bacteria.We adjusted the population structure analysis tools of sexual reproduction species and applied them into V.parahaemolyticus.We successfully constructed the global population structure of this species.By analyzing the whole genome sequences of 1,103 global strains,we show that V.parahaemolyticus is composed of four diverse populations: Vpp US1,Vpp US2,Vpp X and Vpp Asia.The first two are largely restricted to the North America and Northern Europe,while the others are found worldwide,with Vpp Asia making up the great majority of isolates in the seas around Asia.Patterns of diversity within and between the populations are consistent with them having arisen by progressive divergence via genetic drift during geographical isolation.However,we find that there is substantial overlap in their current distribution,but hybrids are rare,which is qualitatively inconsistent with “migration-drift equilibrium”.These observations can be reconciled without requiring genetic barriers to exchange between populations if dispersal between oceans has increased dramatically in the recent past.In order to test this hypothesis,we compare the ancestry of Vpp Asia isolates and find that Vpp Asia isolates from the North America have an average of 1.01% more shared ancestry with Vpp US1 and Vpp US2 isolates than Vpp Asia isolates from Asia itself.We further estimate that recombination affects about 0.017% of the genome per year,implying that the genetic mixture has taken place for approximately 60 years,indicating that population mixing takes place recently,which is consistent with our hypothesis.These results suggest that human activity,such as shipping and aquatic products trade,has disrupted long-standing barriers to genetic exchange in the oceans,allowing bacteria to disperse between continents,which will eventually affect the bacterial population structure and evolutionary patterns.(2)The landscape of coadaptation in V.parahaemolyticusThe evolutionary driving force of recombination,that is,whether recombination can be affected by natural selection,is another problem in the evolutionary study of frequently recombining bacteria.In recent years,the emerging genome-wide coadaptation(epistasis)studies provide novel insights into this problem.V.parahaemolyticus has the population structure that approximates panmixia,hence,we take advantage of this structure to perform a genome-wide screen for coadapted genetic elements in the core and accessory genome.We identify 90 coadaptation networks,including 1,936 SNPs in 110 core genes and 1,593 accessory genome elements.Based on the relationships between genome elements,we divide the coadaptation networks into three types: “genome island-like”,“incompatibility” and “complex”(combination of the former two).The great majority of interactions that we detected are between accessory genes,which belong to the genome island-like type(56%)and incompatibility type(29%),including genes involved in carbohydrate transport and metabolism.Few coadaptation networks(9%)include core genes,providing evidence for a “plug and play-like” architecture,in which elements have evolved to be functional immediately on arrival in a new genome.The most complex coadaptation networks(complex type)include 62 core genes and 152 accessory genes,encoding genes involved in lateral flagella and cell wall biogenesis.The complexity of the coadaptation network indicates that it has different stages of development.Based on all the identified networks,we summarize the development of coadaptation networks into four stages: namely casual,going steady,getting married and moving out together.Our results confirm that recombination can be influenced by natural selection in the form of coadaptation,and push the bacterial genome-wide coadaptation study to a more comprehensive stage.(3)Recombination-scaled effective population size of V.parahaemolyticusHomologous recombination progressively breaks down non-random associations between genomic loci.Under neutral model of evolution,linkage equilibrium is expected between all pairs of genomic sites in frequently recombining bacterial populations,making the genetic distance of random paired-strains approximately equal and showing the population structure of panmixia.Although there are many bacterial species with high recombination rates,panmixia is rare in bacteria.We propose a potential resolution for this paradox in this section.Firstly,we simulate bacterial populations under different evolution scenarios and show that recombination-scaled effective population size 0)(0)refers to the effective population size, refers to recombination rate)does not correlate with nucleotide diversity ,and 0) is a more effective parameter to quantify the levels of population structure of frequently recombining bacteria.Subsequently,we estimate the 0) of 21 bacterial species(6,355 genomes)with medium or high recombination rates,and find that only V.parahaemolyticus and Helicobacter pylori have estimates substantially over 100,which are consistent with approximate panmixia;while the other 19 bacterial species have 0) values of less than 100,proving that panmixia is indeed rare in bacteria.Further analysis indicates that V.parahaemolyticus and H.pylori are far from demographic equilibrium,with diversity predicted to increase more than 30 fold in V.parahaemolyticus if the current value of 0) was maintained,to values much higher than found in any known bacterial species.Therefore,we propose that panmixia is unstable in bacteria because high diversity tends to suppress recombination through mechanisms such as ecotype differentiation,mismatch repair,and epistatic interactions.The low 0) values of the other 19 bacterial species suggest that they may have evolved barriers to genetic exchange,which act to prevent a continuous increase in diversity and disrupt the previous panmixia structure.Our results further prove that bacterial recombinations are not neutral,highlight the dynamic nature of genetic diversity and population structure of bacteria,which provide insights into one of the basic questions of population genetics-factors determining the amount of diversity within species.Conclusion:In this study,we not only provide the methods for analyzing the population structure of frequently recombining bacteria(Chapter 2),but also confirm that bacterial recombination can be influenced by natural selection(Chapters 3 and 4),providing novel insights into the two major challenges in the evolutionary study of frequently recombining bacteria.All three parts are in a deep sense about the V.parahaemolyticus evolution on different timescales,including short-term evolution(the last few decades of population migration and mixing,Chapter 2),medium/long-term evolution(the dynamic process from coadaptation to speciation,Chapter 3)and long-term evolution(long-term accumulation of genetic diversity will suppress recombination,Chapter 4).Each part stands alone,while together being significantly more than the sum of them.Our "trilogy" provide fresh insights into the evolution of V.parahaemolyticus,which not only provide a theoretical basis for the prevention and control of this important foodborne pathogen,but also further promote our understanding on the evolutionary pattern of bacterial recombination.