Genomic analysis unveils important aspects of population structure, virulence, and antimicrobial resistance inKlebsiella aerogenes

ABSTRACTKlebsiella aerogenesis an important pathogen in healthcare-associated infections. Nevertheless, in comparison to other clinically important pathogens,K. aerogenespopulation structure, genetic diversity, and pathogenicity remain poorly understood. Here, we elucidateK. aerogenesclonal complexes (CCs) and genomic features associated with resistance and virulence. We present a detailed description of the population structure ofK. aerogenesbased on 97 publicly available genomes by using both, multilocus sequence typing and single nucleotide polymorphisms extracted from core genome. We also assessed virulence and resistance profiles using VFDB and CARD, respectively. We show thatK. aerogeneshas an open pangenome and a large effective population size, which account for its high genomic diversity and support that negative selection prevents fixation of most deleterious alleles. The population is structured in at least ten CCs, including two novel ones identified here, CC9 and CC10. The repertoires of resistance genes comprise a high number of antibiotic efflux proteins as well as narrow and extended spectrum β-lactamases. Regarding the population structure, we identified two clusters based on virulence profile due to the presence of the toxin-encodingclboperon and the siderophore production genes,irpandybt.Notably, CC3 comprises the majority ofK. aerogenesisolates associated with hospital outbreaks, emphasizing the importance of its constant monitoring. Collectively, our results can be useful in the development of new therapeutic and surveillance strategies worldwide.

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Genome-Wide Diversity, Population Structure and Demographic History of Dromedaries in the Central Desert of Iran

Genes ◽

10.3390/genes11060599 ◽

2020 ◽

Vol 11 (6) ◽

pp. 599 ◽

Cited By ~ 1

Author(s):

Morteza Bitaraf Sani ◽

Javad Zare Harofte ◽

Ahmad Bitaraf ◽

Saeid Esmaeilkhanian ◽

Mohammad Hossein Banabazi ◽

...

Keyword(s):

Population Structure ◽

Population Size ◽

Balancing Selection ◽

Demographic History ◽

Genomic Analysis ◽

Genotyping By Sequencing ◽

Genomic Diversity ◽

Nucleotide Polymorphisms ◽

Effective Population ◽

Genome Wide

The development of camel husbandry for good production in a desert climate is very important, thus we need to understand the genetic basis of camels and give attention to genomic analysis. We assessed genome-wide diversity, linkage disequilibrium (LD), effective population size (Ne) and relatedness in 96 dromedaries originating from five different regions of the central desert of Iran using genotyping-by-sequencing (GBS). A total of 14,522 Single Nucleotide Polymorphisms (SNPs) with an average minor allele frequency (MAF) of 0.19 passed quality control and filtering steps. The average observed heterozygosity in the population was estimated at 0.25 ± 0.03. The mean of LD at distances shorter than 40 kb was low (r2 = 0.089 ± 0.234). The camels sampled from the central desert of Iran exhibited higher relatedness than Sudanese and lower than Arabian Peninsula dromedaries. Recent Ne of Iran’s camels was estimated to be 89. Predicted Tajima’s D (1.28) suggested a bottleneck or balancing selection in dromedary camels in the central desert of Iran. A general decrease in effective and census population size poses a threat for Iran’s dromedaries. This report is the first SNP calling report on nearly the chromosome level and a first step towards understanding genomic diversity, population structure and demography in Iranian dromedaries.

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Genome-Wide Single Nucleotide Polymorphisms are Robust in Resolving Fine-Scale Population Genetic Structure of the Small Brown Planthopper, Laodelphax striatellus (Fallén) (Hemiptera: Delphacidae)

Journal of Economic Entomology ◽

10.1093/jee/toz145 ◽

2019 ◽

Vol 112 (5) ◽

pp. 2362-2368

Author(s):

Yan Liu ◽

Lei Chen ◽

Xing-Zhi Duan ◽

Dian-Shu Zhao ◽

Jing-Tao Sun ◽

...

Keyword(s):

Population Structure ◽

Discriminant Analysis ◽

Genetic Structure ◽

Population Genetic ◽

Brown Planthopper ◽

Fine Scale ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Small Brown Planthopper ◽

Scale Population

Abstract Deciphering genetic structure and inferring migration routes of insects with high migratory ability have been challenging, due to weak genetic differentiation and limited resolution offered by traditional genotyping methods. Here, we tested the ability of double digest restriction-site associated DNA sequencing (ddRADseq)-based single nucleotide polymorphisms (SNPs) in revealing the population structure relative to 13 microsatellite markers by using four small brown planthopper populations as subjects. Using ddRADseq, we identified 230,000 RAD loci and 5,535 SNP sites, which were present in at least 80% of individuals across the four populations with a minimum sequencing depth of 10. Our results show that this large SNP panel is more powerful than traditional microsatellite markers in revealing fine-scale population structure among the small brown planthopper populations. In contrast to the mixed population structure suggested by microsatellites, discriminant analysis of principal components (DAPC) of the SNP dataset clearly separated the individuals into four geographic populations. Our results also suggest the DAPC analysis is more powerful than the principal component analysis (PCA) in resolving population genetic structure of high migratory taxa, probably due to the advantages of DAPC in using more genetic variation and the discriminant analysis function. Together, these results point to ddRADseq being a promising approach for population genetic and migration studies of small brown planthopper.

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Genomic diversity in Mycobacterium avium: Single nucleotide polymorphisms between the S and C strains of M. avium subsp. paratuberculosis and with M. a. avium

Molecular and Cellular Probes ◽

10.1016/j.mcp.2006.08.002 ◽

2007 ◽

Vol 21 (1) ◽

pp. 66-75 ◽

Cited By ~ 22

Author(s):

I.B. Marsh ◽

R.J. Whittington

Keyword(s):

Single Nucleotide Polymorphisms ◽

Mycobacterium Avium ◽

Genomic Diversity ◽

Nucleotide Polymorphisms ◽

Single Nucleotide

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Population Structure and Genetic Diversity in Korean Cowpea Germplasm Based on SNP Markers

Plants ◽

10.3390/plants9091190 ◽

2020 ◽

Vol 9 (9) ◽

pp. 1190 ◽

Cited By ~ 1

Author(s):

Eunju Seo ◽

Kipoong Kim ◽

Tae-Hwan Jun ◽

Jinsil Choi ◽

Seong-Hoon Kim ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Principal Component ◽

Snp Markers ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Useful Knowledge ◽

Population Structure Analysis ◽

Group 3 ◽

Genetic Diversity Study

Cowpea is one of the most essential legume crops providing inexpensive dietary protein and nutrients. The aim of this study was to understand the genetic diversity and population structure of global and Korean cowpea germplasms. A total of 384 cowpea accessions from 21 countries were genotyped with the Cowpea iSelect Consortium Array containing 51,128 single-nucleotide polymorphisms (SNPs). After SNP filtering, a genetic diversity study was carried out using 35,116 SNPs within 376 cowpea accessions, including 229 Korean accessions. Based on structure and principal component analysis, a total of 376 global accessions were divided into four major populations. Accessions in group 1 were from Asia and Europe, those in groups 2 and 4 were from Korea, and those in group 3 were from West Africa. In addition, 229 Korean accessions were divided into three major populations (Q1, Jeonra province; Q2, Gangwon province; Q3, a mixture of provinces). Additionally, the neighbor-joining tree indicated similar results. Further genetic diversity analysis within the global and Korean population groups indicated low heterozygosity, a low polymorphism information content, and a high inbreeding coefficient in the Korean cowpea accessions. The population structure analysis will provide useful knowledge to support the genetic potential of the cowpea breeding program, especially in Korea.

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RAD-seq-Based High-Density Linkage Map Construction and QTL Mapping of Biomass-Related Traits in Sorghum using the Japanese Landrace Takakibi NOG

Plant and Cell Physiology ◽

10.1093/pcp/pcaa056 ◽

2020 ◽

Vol 61 (7) ◽

pp. 1262-1272

Author(s):

Hiromi Kajiya-Kanegae ◽

Hideki Takanashi ◽

Masaru Fujimoto ◽

Motoyuki Ishimori ◽

Norikazu Ohnishi ◽

...

Keyword(s):

Linkage Map ◽

High Density ◽

Genomic Diversity ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Genetic Traits ◽

Map Construction ◽

Days To Heading ◽

High Density Linkage Map ◽

Sorghum Bicolor L

Abstract Sorghum [Sorghum bicolor (L.) Moench] grown locally by Japanese farmers is generically termed Takakibi, although its genetic diversity compared with geographically distant varieties or even within Takakibi lines remains unclear. To explore the genomic diversity and genetic traits controlling biomass and other physiological traits in Takakibi, we focused on a landrace, NOG, in this study. Admixture analysis of 460 sorghum accessions revealed that NOG belonged to the subgroup that represented Asian sorghums, and it was only distantly related to American/African accessions including BTx623. In an attempt to dissect major traits related to biomass, we generated a recombinant inbred line (RIL) from a cross between BTx623 and NOG, and we constructed a high-density linkage map based on 3,710 single-nucleotide polymorphisms obtained by restriction-site-associated DNA sequencing of 213 RIL individuals. Consequently, 13 fine quantitative trait loci (QTLs) were detected on chromosomes 2, 3, 6, 7, 8 and 9, which included five QTLs for days to heading, three for plant height (PH) and total shoot fresh weight and two for Brix. Furthermore, we identified two dominant loci for PH as being identical to the previously reported dw1 and dw3. Together, these results corroborate the diversified genome of Japanese Takakibi, while the RIL population and high-density linkage map generated in this study will be useful for dissecting other important traits in sorghum.

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Genomic surveillance of COVID-19 cases in Beijing

Nature Communications ◽

10.1038/s41467-020-19345-0 ◽

2020 ◽

Vol 11 (1) ◽

Cited By ~ 2

Author(s):

Pengcheng Du ◽

Nan Ding ◽

Jiarui Li ◽

Fujie Zhang ◽

Qi Wang ◽

...

Keyword(s):

Single Nucleotide Polymorphisms ◽

High Frequency ◽

Epidemiological Data ◽

Genomic Diversity ◽

Nucleotide Polymorphisms ◽

Genomic Evolution ◽

Single Nucleotide ◽

Imported Cases ◽

Single Nucleotide Variations ◽

Local Transmission

Abstract The spread of SARS-CoV-2 in Beijing before May, 2020 resulted from transmission following both domestic and global importation of cases. Here we present genomic surveillance data on 102 imported cases, which account for 17.2% of the total cases in Beijing. Our data suggest that all of the cases in Beijing can be broadly classified into one of three groups: Wuhan exposure, local transmission and overseas imports. We classify all sequenced genomes into seven clusters based on representative high-frequency single nucleotide polymorphisms (SNPs). Genomic comparisons reveal higher genomic diversity in the imported group compared to both the Wuhan exposure and local transmission groups, indicating continuous genomic evolution during global transmission. The imported group show region-specific SNPs, while the intra-host single nucleotide variations present as random features, and show no significant differences among groups. Epidemiological data suggest that detection of cases at immigration with mandatory quarantine may be an effective way to prevent recurring outbreaks triggered by imported cases. Notably, we also identify a set of novel indels. Our data imply that SARS-CoV-2 genomes may have high mutational tolerance.

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The efficacy of short tandem repeat polymorphisms versus single-nucleotide polymorphisms for resolving population structure

BMC Genetics ◽

10.1186/1471-2156-6-s1-s84 ◽

2005 ◽

Vol 6 (Suppl 1) ◽

pp. S84 ◽

Cited By ~ 4

Author(s):

John SK Kauwe ◽

Sarah Bertelsen ◽

Laura Bierut ◽

Gerald Dunn ◽

Anthony L Hinrichs ◽

...

Keyword(s):

Population Structure ◽

Single Nucleotide Polymorphisms ◽

Tandem Repeat ◽

Short Tandem Repeat ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Short Tandem

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Complete Genome Sequence of Yersinia pestis Strains Antiqua and Nepal516: Evidence of Gene Reduction in an Emerging Pathogen

Journal of Bacteriology ◽

10.1128/jb.00124-06 ◽

2006 ◽

Vol 188 (12) ◽

pp. 4453-4463 ◽

Cited By ~ 114

Author(s):

Patrick S. G. Chain ◽

Ping Hu ◽

Stephanie A. Malfatti ◽

Lyndsay Radnedge ◽

Frank Larimer ◽

...

Keyword(s):

Single Nucleotide Polymorphisms ◽

Yersinia Pestis ◽

Yersinia Pseudotuberculosis ◽

Open Reading Frames ◽

Genomic Diversity ◽

Avirulent Strain ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Protein Coding ◽

Definition Of

ABSTRACT Yersinia pestis, the causative agent of bubonic and pneumonic plagues, has undergone detailed study at the molecular level. To further investigate the genomic diversity among this group and to help characterize lineages of the plague organism that have no sequenced members, we present here the genomes of two isolates of the “classical” antiqua biovar, strains Antiqua and Nepal516. The genomes of Antiqua and Nepal516 are 4.7 Mb and 4.5 Mb and encode 4,138 and 3,956 open reading frames, respectively. Though both strains belong to one of the three classical biovars, they represent separate lineages defined by recent phylogenetic studies. We compare all five currently sequenced Y. pestis genomes and the corresponding features in Yersinia pseudotuberculosis. There are strain-specific rearrangements, insertions, deletions, single nucleotide polymorphisms, and a unique distribution of insertion sequences. We found 453 single nucleotide polymorphisms in protein-coding regions, which were used to assess the evolutionary relationships of these Y. pestis strains. Gene reduction analysis revealed that the gene deletion processes are under selective pressure, and many of the inactivations are probably related to the organism's interaction with its host environment. The results presented here clearly demonstrate the differences between the two biovar antiqua lineages and support the notion that grouping Y. pestis strains based strictly on the classical definition of biovars (predicated upon two biochemical assays) does not accurately reflect the phylogenetic relationships within this species. A comparison of four virulent Y. pestis strains with the human-avirulent strain 91001 provides further insight into the genetic basis of virulence to humans.

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