scholarly journals Phylogeographic separation and formation of sexually discrete lineages in a global population of Yersinia pseudotuberculosis

2017 ◽  
Author(s):  
Tristan Seecharran ◽  
Laura Kalin-Mänttäri ◽  
Katja A. Koskela ◽  
Simo Nikkari ◽  
Benjamin Dickins ◽  
...  
Keyword(s):  
Large Scale ◽  
Yersinia Pseudotuberculosis ◽  
Genomic Analysis ◽  
Genetic Exchange ◽  
Evolutionary Trajectory ◽  
Population Genomic ◽  
The World ◽  
Genomic Studies ◽  
Lineage Structure ◽  
Global Population

AbstractYersinia pseudotuberculosis is a Gram negative intestinal pathogen of humans and has been responsible for several nation-wide gastro-intestinal outbreaks. Large-scale population genomic studies have been performed on the other human pathogenic Yersinia, Y. pestis and Y. enterocolitica allowing a high-resolution understanding of the ecology, evolution and dissemination of these pathogens. However, to date no large-scale global population genomic analysis of Y. pseudotuberculosis has been performed. Here we present analyses of the genomes of 134 strains of Y. pseudotuberculosis isolated from around the world, from multiple ecosystems since 1960’s. Our data display a phylogeographic split within the population, with an Asian ancestry and subsequent dispersal of successful clonal lineages into Europe and the rest of the world. These lineages can be differentiated by CRISPR cluster arrays, and we show that the lineages are limited with respect to inter-lineage genetic exchange. This restriction of genetic exchange maintains the discrete lineage structure in the population despite co-existence of lineages for thousands of years in multiple countries. Our data highlights how CRISPR can be informative of the evolutionary trajectory of bacterial lineages, and merits further study across bacteria.

scholarly journals Population genomic analysis of Cryptococcus Brazilian isolates reveals an African type subclade distribution

2021 ◽  
Author(s):  
Corinne Maufrais ◽  
Luciana de Oliveira ◽  
Rafael W Bastos ◽  
Frédérique Moyrand ◽  
Flavia C G Reis ◽  
...  
Keyword(s):  
Population Structure ◽  
South America ◽  
Genomic Analysis ◽  
Opportunistic Pathogen ◽  
South American ◽  
Brazilian Isolate ◽  
Population Genomic ◽  
The World ◽  
Lineage Specificity ◽  
Global Population

Abstract The genomes of a large number of Cryptococcus neoformans isolates have been sequenced and analyzed in recent years. These genomes have been used to understand the global population structure of this opportunistic pathogen. However, only a small number of South American isolates have been considered in these studies, and the population structure of C. neoformans in this part of the world remains elusive. Here, we analyzed the genomic sequences of 53 Brazilian Cryptococcus isolates and deciphered the C. neoformans population structure in this country. Our data reveal an African-like structure that suggested repeated intercontinental transports from Africa to South America. We also identified a mutator phenotype in one VNBII Brazilian isolate, exemplifying how fast-evolving isolates can shape the Cryptococcus population structure. Finally, phenotypic analyses revealed wide diversity but not lineage specificity in the expression of classical virulence traits within the set of isolates.

scholarly journals Population Genomic Analysis of Cryptococcus Brazilian Strains Reveals an African Type Subclades Distribution

2021 ◽  
Author(s):  
Corinne Maufrais ◽  
Luciana de Oliveira ◽  
Rafael W. Bastos ◽  
Frédérique Moyrand ◽  
Flavia C. G. Reis ◽  
...  
Keyword(s):  
Population Structure ◽  
South America ◽  
Genomic Analysis ◽  
Opportunistic Pathogen ◽  
South American ◽  
Brazilian Isolate ◽  
Population Genomic ◽  
The World ◽  
Lineage Specificity ◽  
Global Population

AbstractThe genome of a large number of Cryptococcus neoformans isolates has been sequenced and analyzed in recent years. These genomes have been used to understand the global population structure of this opportunistic pathogen. However, only a small number of South American isolates have been considered in these studies, and the population structure of C. neoformans in this part of the world remains evasive. Here, we analyzed the genomic sequences of 53 Brazilian Cryptococcus isolates and deciphered the C. neoformans population structure in this country. Our data reveal an African-like structure that suggesting repeated and privileged intercontinental transports from Africa to South America. We also identified a mutator phenotype in one VNBII Brazilian isolate, exemplifying how fast-evolving isolates can shape the Cryptococcus population structure. Finally, phenotypic analyses revealed wide diversity but not lineage specificity in the expression of classical virulence traits within the set of isolates.

scholarly journals The presence and impact of reference bias on population genomic studies of prehistoric human populations

2018 ◽  
Author(s):  
Torsten Günther ◽  
Carl Nettelblad
Keyword(s):  
Ancient Dna ◽  
Sequence Data ◽  
Genomic Analysis ◽  
Genomic Research ◽  
Human Populations ◽  
Reference Allele ◽  
Population Genomic ◽  
Genomic Studies ◽  
Reference Bias ◽  
The Impact

AbstractHigh quality reference genomes are an important resource in genomic research projects. A consequence is that DNA fragments carrying the reference allele will be more likely to map suc-cessfully, or receive higher quality scores. This reference bias can have effects on downstream population genomic analysis when heterozygous sites are falsely considered homozygous for the reference allele.In palaeogenomic studies of human populations, mapping against the human reference genome is used to identify endogenous human sequences. Ancient DNA studies usually operate with low sequencing coverages and fragmentation of DNA molecules causes a large proportion of the sequenced fragments to be shorter than 50 bp – reducing the amount of accepted mismatches, and increasing the probability of multiple matching sites in the genome. These ancient DNA specific properties are potentially exacerbating the impact of reference bias on downstream analyses, especially since most studies of ancient human populations use pseudohaploid data, i.e. they randomly sample only one sequencing read per site.We show that reference bias is pervasive in published ancient DNA sequence data of pre-historic humans with some differences between individual genomic regions. We illustrate that the strength of reference bias is negatively correlated with fragment length. Reference bias can cause differences in the results of downstream analyses such as population affinities, heterozygosity estimates and estimates of archaic ancestry. These spurious results highlight how important it is to be aware of these technical artifacts and that we need strategies to mitigate the effect. Therefore, we suggest some post-mapping filtering strategies to resolve reference bias which help to reduce its impact substantially.

scholarly journals Large scale and significant expression from pseudogenes in Sodalis glossinidius - a facultative bacterial endosymbiont

2017 ◽  
Author(s):  
Ian Goodhead ◽  
Frances Blow ◽  
Philip Brownridge ◽  
Margaret Hughes ◽  
John Kenny ◽  
...  
Keyword(s):  
Single Molecule ◽  
Translational Control ◽  
Large Scale ◽  
Evolutionary Relationship ◽  
Genomic Analysis ◽  
Proteome Analysis ◽  
Comparative Genomic ◽  
Intracellular Bacteria ◽  
Evolutionary Trajectory ◽  
Sodalis Glossinidius

AbstractThe majority of bacterial genomes have high coding efficiencies, but there are some genomes of intracellular bacteria that have low gene density. The genome of the endosymbiont Sodalis glossinidius contains almost 50% pseudogenes containing mutations that putatively silence them at the genomic level. We have applied multiple ‘omic strategies, combining: Illumina and Pacific Biosciences Single-Molecule Real Time DNA-sequencing and annotation; stranded RNA-sequencing; and proteome analysis to better understand the transcriptional and translational landscape of Sodalis pseudogenes, and potential mechanisms for their control. Between 53% and 74% of the Sodalis transcriptome remains active in cell-free culture. Mean sense transcription from Coding Domain Sequences (CDS) is four-times greater than that from pseudogenes. Comparative genomic analysis of six Illumina-sequenced Sodalis isolates from different host Glossina species shows pseudogenes make up ~40% of the 2,729 genes in the core genome, suggesting that they are stable and/or Sodalis is a recent introduction across the Glossina genus as a facultative symbiont. These data further shed light on the importance of transcriptional and translational control in deciphering host-microbe interactions. The combination of genomics, transcriptomics and proteomics give a multidimensional perspective for studying prokaryotic genomes with a view to elucidating evolutionary adaptation to novel environmental niches.ImportanceBacterial genes are generally 1Kb in length, organized efficiently (i.e. with few gaps between genes or operons), and few open reading frames (ORFs) lack any predicted function. Intracellular bacteria have been removed from extracellular selection pressures acting on pathways of declining importance to fitness and thus, these bacteria tend to delete redundant genes in favour of smaller functional repertoires. In the genomes of endosymbionts with a recent evolutionary relationship with their host, however, this process of genome reduction is not complete; Genes and pathways may be at an intermediate stage, undergoing mutation linked to reduced selection and small population numbers being vertically transmitted from mother to offspring in their hosts, resulting in an increase in abundance of pseudogenes and reduced coding capacities. A greater knowledge of the genomic architecture of persistent pseudogenes, with respect to their DNA structure, mRNA transcription and even putative translation to protein products, will lead to a better understanding of the evolutionary trajectory of endosymbiont genomes, many of which have important roles in arthropod ecology.

Genomic analysis of hepatocellular carcinoma (HCC) with active hepatitis B virus (HBV) replication.

2019 ◽  
Vol 37 (15_suppl) ◽  
pp. e15593-e15593
Author(s):  
Huat Chye Lim ◽  
John Dozier Gordan
Keyword(s):  
Large Scale ◽  
Somatic Mutations ◽  
Genomic Analysis ◽  
Enrichment Analysis ◽  
Gene Set Enrichment Analysis ◽  
State Transitions ◽  
Rna Seq ◽  
Hbv Replication ◽  
Gene Sets ◽  
Genomic Studies

e15593 Background: HBV replication contributes to HCC initiation and is associated with worse patient outcomes. Prior tumor genomic studies of HBV-positive and -negative (HBV+/-) HCC have used detection of HBV surface antigen (HBsAg) in serum to annotate HBV status. However, a substantial proportion of HBsAg+ patients lack HBV replication in tumor, suggesting a potentially distinct patient subset. In this study, we determined HBV status by measuring tumor HBV RNA, a proxy for active replication. We then investigated HBV RNA+/- association with somatic mutations, gene sets, homologous recombination deficiency (HRD) and tumor mutation burden (TMB). Methods: RNA-Seq data for 371 HCC tumors were obtained from TCGA. Tumors were classified as HBV RNA+ if they harbored more than 1 HBV RNA read per million human reads, as measured using GATK PathSeq software. Associations between HBV RNA status and somatic mutations, gene sets, HRD and TMB were investigated. HRD score was calculated as the sum of 3 independent HRD measures (large scale state transitions, loss of heterozygosity and telomeric allelic imbalance). Results: HBV RNA+ status was associated with a higher rate of nonsynonymous somatic mutations in multiple genes, including the tumor suppressors TP53, CDKN2A, CHD5 and TET1, as well as AXIN2 and the proto-oncogene BCL11A ( p < 0.05 for all), while HBV RNA- status was associated with a higher rate of nonsynonymous mutations in the chromatin modifier BAP1 ( p = 0.03). In gene set enrichment analysis of normalized RNA-Seq expression data, HBV RNA+ status was associated with increased transcription of DNA repair genes, as well as genes upregulated by mTORC1 and MYC (FDR < 0.03 for all). HBV RNA status was also associated with HRD score (22.19 for HBV RNA+ vs. 15.97 for HBV RNA-, p = 1e-6), but not with TMB. A substantial subset of HBV RNA+ patients (33/100) were not annotated as HBV+ in the TCGA clinical database. Conclusions: HBV status based on tumor HBV RNA detection identifies a genetically distinct subset within all HBV-infected HCC patients that is associated with nonsynonymous somatic mutations in several genes and differential transcription of gene sets, some of which have not been previously reported, as well as with HRD score. These findings suggest potential for differential responsiveness to targeted therapies.

scholarly journals Large scale enterohemorrhagic E coli population genomic analysis using whole genome typing reveals recombination clusters and potential drug target

F1000Research ◽  
2019 ◽  
Vol 8 ◽  
pp. 33
Author(s):  
DJ Darwin Bandoy
Keyword(s):  
Drug Discovery ◽  
Drug Target ◽  
Large Scale ◽  
Genomic Analysis ◽  
Wide Distribution ◽  
Whole Genome ◽  
Potential Drug Target ◽  
Potential Drug ◽  
New Paradigm ◽  
Population Genomic

Enterohemorrhagic Escherichia coli continues to be a significant public health risk. With the onset of next generation sequencing, whole genome sequences require a new paradigm of analysis relevant for epidemiology and drug discovery. A large-scale bacterial population genomic analysis was applied to 702 isolates of serotypes associated with EHEC resulting in five pangenome clusters. Serotype incongruence with pangenome types suggests recombination clusters. Core genome analysis was performed to determine the population wide distribution of sdiA as potential drug target. Protein modelling revealed nonsynonymous variants are notably absent in the ligand binding site for quorum sensing, indicating that population wide conservation of the sdiA ligand site can be targeted for potential prophylactic purposes. Applying pathotype-wide pangenomics as a guide for determining evolution of pharmacophore sites is a potential approach in drug discovery.

scholarly journals Large scale genomic analysis of 3067 SARS-CoV-2 genomes reveals a clonal geo-distribution and a rich genetic variations of hotspots mutations

PLoS ONE ◽  
2020 ◽  
Vol 15 (11) ◽  
pp. e0240345 ◽  
Author(s):  
Meriem Laamarti ◽  
Tarek Alouane ◽  
Souad Kartti ◽  
M. W. Chemao-Elfihri ◽  
Mohammed Hakmi ◽  
...  
Keyword(s):  
Genetic Variants ◽  
Large Scale ◽  
Genomic Analysis ◽  
Geographic Locations ◽  
Synonymous Mutations ◽  
Global Pandemic ◽  
Recurrent Mutations ◽  
Epidemic Period ◽  
The World ◽  
First Time

In late December 2019, an emerging viral infection COVID-19 was identified in Wuhan, China, and became a global pandemic. Characterization of the genetic variants of SARS-CoV-2 is crucial in following and evaluating it spread across countries. In this study, we collected and analyzed 3,067 SARS-CoV-2 genomes isolated from 55 countries during the first three months after the onset of this virus. Using comparative genomics analysis, we traced the profiles of the whole-genome mutations and compared the frequency of each mutation in the studied population. The accumulation of mutations during the epidemic period with their geographic locations was also monitored. The results showed 782 variants sites, of which 512 (65.47%) had a non-synonymous effect. Frequencies of mutated alleles revealed the presence of 68 recurrent mutations, including ten hotspot non-synonymous mutations with a prevalence higher than 0.10 in this population and distributed in six SARS-CoV-2 genes. The distribution of these recurrent mutations on the world map revealed that certain genotypes are specific to geographic locations. We also identified co-occurring mutations resulting in the presence of several haplotypes. Moreover, evolution over time has shown a mechanism of mutation co-accumulation which might affect the severity and spread of the SARS-CoV-2. The phylogentic analysis identified two major Clades C1 and C2 harboring mutations L3606F and G614D, respectively and both emerging for the first time in China. On the other hand, analysis of the selective pressure revealed the presence of negatively selected residues that could be taken into considerations as therapeutic targets. We have also created an inclusive unified database (http://covid-19.medbiotech.ma) that lists all of the genetic variants of the SARS-CoV-2 genomes found in this study with phylogeographic analysis around the world.

scholarly journals Integrated population genomic analysis and numerical simulation to estimate larval dispersal of Acanthaster cf. solaris between Ogasawara and other Japanese regions

2021 ◽  
Author(s):  
Mizuki Horoiwa ◽  
Takashi Nakamura ◽  
Hideaki Yuasa ◽  
Rei Kajitani ◽  
Yosuke Ameda ◽  
...  
Keyword(s):  
Larval Dispersal ◽  
Large Scale ◽  
Genomic Analysis ◽  
Connectivity Matrix ◽  
Larval Recruitment ◽  
Population Genomic ◽  
Population Outbreak ◽  
Japanese Regions ◽  
The Kuroshio ◽  
Kuroshio Region

AbstractThe estimation of larval dispersal of marine species occurring on an ecological timescale is significant for conservation. In 2018, a semi-population outbreak of crown of thorns starfish, Acanthaster cf. solaris was observed on a relatively isolated oceanic island, Ogasawara. The aim of this study was to assess whether this population outbreak was caused by large-scale larval recruitment (termed secondary outbreak) from the Kuroshio region. We estimated larval dispersal of the coral predator A. cf. solaris between the Kuroshio and Ogasawara regions using both population genomic analysis and oceanographic dispersal simulation. Population genomic analysis revealed overall genetically homogenized patterns among Ogasawara and other Japanese populations, suggesting that the origin of the populations in the two regions is the same. In contrast, a simulation of 26-year oceanographic dispersal indicated that larvae are mostly self-seeded in Ogasawara populations and have difficulty reaching Ogasawara from the Kuroshio region within one generation. However, a connectivity matrix produced by the larval dispersal simulation assuming a Markov chain indicated gradual larval dispersal migration from the Kuroshio region to Ogasawara in a stepping-stone manner over multiple years. These results suggest that, while large-scale larval dispersal from an outbreak of the Kuroshio population spreading to the Ogasawara population within one generation is unlikely. This study also highlighted the importance of using both genomic and oceanographic methods to estimate larval dispersal, which provides significant insight into larval dispersal that occurs on ecological and evolutionary timescales.

scholarly journals Integrated Population Genomic Analysis and Numerical Simulation to Estimate Larval Dispersal of Acanthaster cf. solaris Between Ogasawara and Other Japanese Regions

2022 ◽  
Vol 8 ◽  
Author(s):  
Mizuki Horoiwa ◽  
Takashi Nakamura ◽  
Hideaki Yuasa ◽  
Rei Kajitani ◽  
Yosuke Ameda ◽  
...  
Keyword(s):  
Larval Dispersal ◽  
Large Scale ◽  
Genomic Analysis ◽  
Connectivity Matrix ◽  
Larval Recruitment ◽  
Population Genomic ◽  
Population Outbreak ◽  
Japanese Regions ◽  
The Kuroshio ◽  
Kuroshio Region

The estimation of larval dispersal on an ecological timescale is significant for conservation of marine species. In 2018, a semi-population outbreak of crown-of-thorns sea star, Acanthaster cf. solaris, was observed on a relatively isolated oceanic island, Ogasawara. The aim of this study was to assess whether this population outbreak was caused by large-scale larval recruitment (termed secondary outbreak) from the Kuroshio region. We estimated larval dispersal of the coral predator A. cf. solaris between the Kuroshio and Ogasawara regions using both population genomic analysis and simulation of oceanographic dispersal. Population genomic analysis revealed overall genetically homogenized patterns among Ogasawara and other Japanese populations, suggesting that the origin of the populations in the two regions is the same. In contrast, a simulation of 26-year oceanographic dispersal indicated that larvae are mostly self-seeded in Ogasawara populations and have difficulty reaching Ogasawara from the Kuroshio region within one generation. However, a connectivity matrix produced by the larval dispersal simulation assuming a Markov chain indicated gradual larval dispersal migration from the Kuroshio region to Ogasawara in a stepping-stone manner over multiple years. These results suggest that the 2018 outbreak was likely the result of self-seeding, including possible inbreeding (as evidenced by clonemate analysis), as large-scale larval dispersal from the Kurishio population to the Ogasawara population within one generation is unlikely. Instead, the population in Ogasawara is basically sustained by self-seedings, and the outbreak in 2018 was also most likely caused by successful self-seedings including possible inbreeding, as evidenced by clonemate analysis. This study also highlighted the importance of using both genomic and oceanographic methods to estimate larval dispersal, which provides significant insight into larval dispersal that occurs on ecological and evolutionary timescales.

scholarly journals Large scale enterohemorrhagic E coli population genomic analysis using whole genome typing reveals recombination clusters and potential drug target

F1000Research ◽  
2020 ◽  
Vol 8 ◽  
pp. 33
Author(s):  
DJ Darwin Bandoy
Keyword(s):  
Drug Discovery ◽  
Drug Target ◽  
Large Scale ◽  
Genomic Analysis ◽  
Wide Distribution ◽  
Whole Genome ◽  
Potential Drug Target ◽  
Potential Drug ◽  
New Paradigm ◽  
Population Genomic

Enterohemorrhagic Escherichia coli continues to be a significant public health risk. With the onset of next generation sequencing, whole genome sequences require a new paradigm of analysis relevant for epidemiology and drug discovery. A large-scale bacterial population genomic analysis was applied to 702 isolates of serotypes associated with EHEC resulting in five pangenome clusters. Serotype incongruence with pangenome types suggests recombination clusters. Core genome analysis was performed to determine the population wide distribution of sdiA as potential drug target. Protein modelling revealed nonsynonymous variants are notably absent in the ligand binding site for quorum sensing, indicating that population wide conservation of the sdiA ligand site can be targeted for potential prophylactic purposes. Applying pathotype-wide pangenomics as a guide for determining evolution of pharmacophore sites is a potential approach in drug discovery.

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