Whole-genome sequence variation, population structure and demographic history of the Dutch population

Background: Typhoid fever, a systemic infection caused by Salmonella enterica serovar Typhi, remains a considerable public health threat in impoverished regions within many low- and middle-income settings. However, we still lack a detailed understanding of the emergence, population structure, molecular mechanisms of antimicrobial resistance (AMR), and transmission dynamics of S. Typhi across many settings, particularly throughout the Asia-Pacific islands. Here we present a comprehensive whole genome sequence (WGS) based overview of S. Typhi populations circulating in Papua New Guinea (PNG) over 30 years. Principle findings: Bioinformatic analysis of 86 S. Typhi isolates collected between 1980-2010 demonstrated that the population structure of PNG is dominated by a single genotype (2.1.7) that appears to have emerged in the Indonesian archipelago in the mid-twentieth century with very limited evidence of inter-country transmission. Genotypic and phenotypic data demonstrated that the PNG S. Typhi population appears to be susceptible to former first line drugs for treating typhoid fever (chloramphenicol, ampicillin and co-trimoxazole), as well as fluoroquinolones, third generation cephalosporins, and macrolides. PNG genotype 2.1.7 was genetically conserved, with very few deletions, and no evidence of plasmid or prophage acquisition. Genetic variation among this population was attributed to either single point mutations, or homologous recombination adjacent to repetitive ribosomal RNA operons. Significance: Antimicrobials remain an effective option for the treatment of typhoid fever in PNG, along with other intervention strategies including improvements to water, sanitation and hygiene (WaSH) related infrastructure and potentially the introduction of Vi-conjugate vaccines. However, continued genomic surveillance is warranted to monitor for the emergence of AMR within local populations, or the introduction of AMR associated genotypes of S. Typhi in this setting.

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Whole genome sequence analyses of Western Central African Pygmy hunter-gatherers reveal a complex demographic history and identify candidate genes under positive natural selection

10.1101/022194 ◽

2015 ◽

Author(s):

PingHsun Hsieh ◽

Krishna R Veeramah ◽

Joseph Lachance ◽

Sarah A Tishkoff ◽

Jeffrey D Wall ◽

...

Keyword(s):

Gene Flow ◽

Natural Selection ◽

Muscle Development ◽

Demographic History ◽

Single Pulse ◽

Whole Genome Sequence ◽

Whole Genome ◽

Anatomically Modern Humans ◽

History Of ◽

African Pygmies

African Pygmies practicing a mobile hunter-gatherer lifestyle are phenotypically and genetically diverged from other anatomically modern humans, and they likely experienced strong selective pressures due to their unique lifestyle in the Central African rainforest. To identify genomic targets of adaptation, we sequenced the genomes of four Biaka Pygmies from the Central African Republic and jointly analyzed these data with the genome sequences of three Baka Pygmies from Cameroon and nine Yoruba famers. To account for the complex demographic history of these populations that includes both isolation and gene flow, we fit models using the joint allele frequency spectrum and validated them using independent approaches. Our two best-fit models both suggest ancient divergence between the ancestors of the farmers and Pygmies, 90,000 or 150,000 years ago. We also find that bi-directional asymmetric gene-flow is statistically better supported than a single pulse of unidirectional gene flow from farmers to Pygmies, as previously suggested. We then applied complementary statistics to scan the genome for evidence of selective sweeps and polygenic selection. We found that conventional statistical outlier approaches were biased toward identifying candidates in regions of high mutation or low recombination rate. To avoid this bias, we assigned P-values for candidates using whole-genome simulations incorporating demography and variation in both recombination and mutation rates. We found that genes and gene sets involved in muscle development, bone synthesis, immunity, reproduction, cell signaling and development, and energy metabolism are likely to be targets of positive natural selection in Western African Pygmies or their recent ancestors.

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Mycoplasma genitalium: whole genome sequence analysis, recombination and population structure

BMC Genomics ◽

10.1186/s12864-017-4399-6 ◽

2017 ◽

Vol 18 (1) ◽

Cited By ~ 13

Author(s):

Maria C. Fookes ◽

James Hadfield ◽

Simon Harris ◽

Surendra Parmar ◽

Magnus Unemo ◽

...

Keyword(s):

Population Structure ◽

Sequence Analysis ◽

Genome Sequence ◽

Mycoplasma Genitalium ◽

Whole Genome Sequence ◽

Whole Genome ◽

Genome Sequence Analysis

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The genome of Mekong tiger perch (Datnioides undecimradiatus) provides insights into the phylogenic position of Lobotiformes and biological conservation

10.1101/787077 ◽

2019 ◽

Author(s):

Shuai Sun ◽

Yue Wang ◽

Xiao Du ◽

Lei Li ◽

Xiaoning Hong ◽

...

Keyword(s):

Demographic History ◽

Whole Genome Sequence ◽

Biological Conservation ◽

Whole Genome ◽

Effective Population ◽

Phylogenetic Tree Analysis ◽

Pigment Synthesis ◽

Long Time ◽

History Of ◽

Immune Related Genes

AbstractMekong tiger perch (Datnioides undecimradiatus) is one ornamental fish and a vulnerable species, which belongs to order Lobotiformes. Here, we report a ∼595 Mb D. undecimradiatus genome, which is the first whole genome sequence in the order Lobotiformes. Based on this genome, the phylogenetic tree analysis suggested that Lobotiformes and Sciaenidae are closer than Tetraodontiformes, resolving a long-time dispute. We depicted the pigment synthesis pathway in Mekong tiger perch and result confirmed that this pathway had evolved from the shared whole genome duplication. We also estimated the demographic history of Mekong tiger perch, showing the effective population size suffered a continuous reduction possibly related to the contraction of immune-related genes. Our study provided a reference genome resource for the Lobotiformes, as well as insights into the phylogeny of Eupercaria and biological conservation.

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A genome-wide resource of intron spanning primers compatible for quantitative PCR and intron length polymorphism in rice

Indian Journal of Genetics and Plant Breeding (The) ◽

10.31742/ijgpb.79.2.15 ◽

2019 ◽

Vol 79 (02) ◽

Author(s):

Humira Sonah ◽

Hasthi Ram ◽

Bikram Pratap Singh ◽

Jawaharlal Katara ◽

Radha Chopra ◽

...

Keyword(s):

Quantitative Pcr ◽

Genome Sequence ◽

Sequence Variation ◽

Whole Genome Sequence ◽

Pcr Analysis ◽

Sequence Information ◽

Whole Genome ◽

Intron Length Polymorphism ◽

Genome Wide ◽

A Genome

Whole genome sequence availability in rice has provided several advantages for genomics as well as other omics assisted applications. Genome-wide molecular markers are one of such availability that has exceptional importance in modern plant breeding. In the present study, a resource of intron-spanning primers (ISPs) was developed using whole genome sequence information of two rice subspecies, japonica (cv. Nipponbare) and indica (cv. 93-11). The ISPs were designed in a way that the PCR using a cDNA template will yield 60 to 100 base pair size amplicon ideal for the quantitative PCR analysis. Whereas, PCR using genomic DNA will amplify the introns, which are more prone to sequence variation. The sequence variation in the intron serves as an excellent marker resource. The application of ISPs was demonstrated by characterizing 12 diverse rice cultivars. A total of eight out of ten ISPs were found to be polymorphic. The resource will be helpful for the rice molecular biologist and breeder community.

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Development and Validation of Polymorphic Microsatellite Loci for the NA2 Lineage of Phytophthora ramorum from Whole Genome Sequence Data

Plant Disease ◽

10.1094/pdis-11-16-1586-re ◽

2017 ◽

Vol 101 (5) ◽

pp. 666-673 ◽

Cited By ~ 10

Author(s):

Marie-Claude Gagnon ◽

Nicolas Feau ◽

Angela L. Dale ◽

Braham Dhillon ◽

Richard C. Hamelin ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Genome Sequence ◽

Sequence Data ◽

Ornamental Plants ◽

Phytophthora Ramorum ◽

Whole Genome Sequence ◽

Whole Genome ◽

Genome Sequence Data ◽

And Migration

Phytophthora ramorum is the causal agent of sudden oak death and sudden larch death, and is also responsible for causing ramorum blight on woody ornamental plants. Many microsatellite markers are available to characterize the genetic diversity and population structure of P. ramorum. However, only two markers are polymorphic in the NA2 lineage, which is predominant in Canadian nurseries. Microsatellite motifs were mined from whole-genome sequence data of six P. ramorum NA2 isolates. Of the 43 microsatellite primer pairs selected, 13 loci displayed different allele sizes among the four P. ramorum lineages, 10 loci displayed intralineage variation in the EU1, EU2, and/or NA1 lineages, and 12 microsatellites displayed polymorphism in the NA2 lineage. Genotyping of 272 P. ramorum NA2 isolates collected in nurseries in British Columbia, Canada, from 2004 to 2013 revealed 12 multilocus genotypes (MLGs). One MLG was dominant when examined over time and across sampling locations, and only a few mutations separated the 12 MLGs. The NA2 population observed in Canadian nurseries also showed no signs of sexual recombination, similar to what has been observed in previous studies. The markers developed in this study can be used to assess P. ramorum inter- and intralineage genetic diversity and generate a better understanding of the population structure and migration patterns of this important plant pathogen, especially for the lesser-characterized NA2 lineage.

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