Population Genomic Analysis of 962 Whole Genome Sequences of Humans Reveals Natural Selection in Non-Coding Regions

Although G2P[4] rotaviruses are common causes of acute childhood diarrhoea in Africa, to date there are no reports on whole genomic analysis of African G2P[4] strains. In this study, the nearly complete genome sequences of two Kenyan G2P[4] strains, AK26 and D205, detected in 1982 and 1989, respectively, were analysed. Strain D205 exhibited a DS-1-like genotype constellation, whilst strain AK26 appeared to be an intergenogroup reassortant with a Wa-like NSP2 genotype on the DS-1-like genotype constellation. The VP2-4, VP6-7, NSP1, NSP3 and NSP5 genes of strain AK26 and the VP2, VP4, VP7 and NSP1–5 genes of strain D205 were closely related to those of the prototype or other human G2P[4] strains. In contrast, their remaining genes were distantly related, and, except for NSP2 of AK26, appeared to originate from or share a common origin with rotavirus genes of artiodactyl (ruminant and camelid) origin. These observations highlight the complex evolutionary dynamics of African G2P[4] rotaviruses.

Download Full-text

Whole-Genome Sequences and Classification of Streptococcus agalactiae Strains Isolated from Laboratory-Reared Long-Evans Rats (Rattus norvegicus)

Genome Announcements ◽

10.1128/genomea.01435-16 ◽

2017 ◽

Vol 5 (1) ◽

Cited By ~ 4

Author(s):

C. Bodi Winn ◽

J. Dzink-Fox ◽

Y. Feng ◽

Z. Shen ◽

V. Bakthavatchalu ◽

...

Keyword(s):

Streptococcus Agalactiae ◽

Genomic Analysis ◽

Opportunistic Pathogen ◽

Comparative Genomic ◽

Whole Genome ◽

Genome Sequences ◽

Content Type ◽

Long Evans ◽

Fatal Septicemia

ABSTRACT In collaboration with the CDC’s Streptococcus Laboratory, we report here the whole-genome sequences of seven Streptococcus agalactiae bacteria isolated from laboratory-reared Long-Evans rats. Four of the S. agalactiae isolates were associated with morbidity accompanied by endocarditis, metritis, and fatal septicemia, providing an opportunity for comparative genomic analysis of this opportunistic pathogen.

Download Full-text

Morphological and Population Genomic Analysis Demonstrates that Natural Selection and Neutral Evolutionary Processes Contributed to the Evolution of the Human Skeleton

The FASEB Journal ◽

10.1096/fasebj.29.1_supplement.343.3 ◽

2015 ◽

Vol 29 (S1) ◽

Author(s):

Charles Roseman

Keyword(s):

Natural Selection ◽

Genomic Analysis ◽

Evolutionary Processes ◽

Human Skeleton ◽

Population Genomic

Download Full-text

Antimicrobial Susceptibility and Genomic Analysis of Aliarcobacter cibarius and Aliarcobacter thereius, Two Rarely Detected Aliarcobacter Species

Frontiers in Cellular and Infection Microbiology ◽

10.3389/fcimb.2021.532989 ◽

2021 ◽

Vol 11 ◽

Author(s):

Ingrid Hänel ◽

Eva Müller ◽

Belén González Santamarina ◽

Herbert Tomaso ◽

Helmut Hotzel ◽

...

Keyword(s):

Amino Acid ◽

Foodborne Pathogens ◽

Antimicrobial Susceptibility ◽

Amino Acid Change ◽

Genomic Analysis ◽

Whole Genome ◽

Genome Sequences ◽

Phenotypic Analysis ◽

Phenotypic Resistance ◽

Reference Strains

Aliarcobacter cibarius and Aliarcobacter thereius are two rarely detected Aliarcobacter species. In the study, we analyzed the antimicrobial susceptibility and provide detailed insights into the genotype and phylogeny of both species using whole-genome sequencing. Thermophilic Campylobacter species are the most common bacterial foodborne pathogens causing gastroenteritis in humans worldwide. The genus Aliarcobacter is part of the Campylobacteraceae family and includes the species Aliarcobacter butzleri, Aliarcobacter cryaerophilus, Aliarcobacter skirrowii, and the rarely described Aliarcobacter cibarius, Aliarcobacter faecis, Aliarcobacter lanthieri, Aliarcobacter thereius, and Acrobarter trophiarum. Aliarcobacter are emergent enteropathogens and potential zoonotic agents. Here, we generated, analyzed, and characterized whole-genome sequences of Aliarcobacter cibarius and Aliarcobacter thereius. They were isolated from water poultry farms in Germany, cultured and identified by MALDI-TOF MS. With PCR the identity was verified. Antibiotic susceptibility testing was carried out with erythromycin, ciprofloxacin, doxycycline, tetracycline, gentamicin, streptomycin, ampicillin, and cefotaxime using the gradient strip method (E-test). Whole-genome sequences were generated including those of reference strains. Complete genomes for six selected strains are reported. These provide detailed insights into the genotype. With these, we predicted in silico known AMR genes, virulence-associated genes, and plasmid replicons. Phenotypic analysis of resistance showed differences between the presence of resistance genes and the prediction of phenotypic resistance profiles. In Aliarcobacter butzleri, the nucleotide sequence of the gyrA gene (DQ464331) can show a signature mutation resulting in an amino acid change T85>I. Acrobarter cibarius and Acrobarter thereius showed the same gene as assessed by similarity annotation of the mutations 254C>G. Most of the isolates were found to be sensitive to ciprofloxacin. The ciprofloxacin-resistant Aliarcobacter thereius isolate was associated with the amino acid change T85>I. But this was not predicted with antibiotic resistance databases, before. Ultimately, a phylogenetic analysis was done to facilitate in future outbreak analysis.

Download Full-text

Evolutionary and genomic analysis of four SARS-CoV-2 isolates circulating in March 2020 in Sri Lanka; Additional evidence on multiple introduction and further transmission

Epidemiology and Infection ◽

10.1017/s0950268821000583 ◽

2021 ◽

Vol 149 ◽

Author(s):

Dilan Amila Satharasinghe ◽

Parakatawella Mudiyanselage Shalini Daupadi Kumari Parakatawella ◽

Jayasekara Mudiyanselage Krishanthi Jayarukshi Kumari Premarathne ◽

L. J. P. Anura P. Jayasooriya ◽

Gamika A. Prathapasinghe ◽

...

Keyword(s):

Sri Lanka ◽

Disease Transmission ◽

Genomic Analysis ◽

Virus Evolution ◽

Control Measures ◽

The Other ◽

Whole Genome ◽

Genome Sequences ◽

Main Cluster ◽

Multiple Introduction

Abstract The molecular epidemiology of the virus and mapping helps understand the epidemics' evolution and apply quick control measures. This study provides genomic evidence of multiple severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) introductions into Sri Lanka and virus evolution during circulation. Whole-genome sequences of four SARS-CoV-2 strains obtained from coronavirus disease 2019 (COVID-19) positive patients reported in Sri Lanka during March 2020 were compared with sequences from Europe, Asia, Africa, Australia and North America. The phylogenetic analysis revealed that the sequence of the sample of the first local patient collected on 10 March, who contacted tourists from Italy, was clustered with SARS-CoV-2 strains collected from Italy, Germany, France and Mexico. Subsequently, the sequence of the isolate obtained on 19 March also clustered in the same group with the samples collected in March and April from Belgium, France, India and South Africa. The other two strains of SARS-CoV-2 were segregated from the main cluster, and the sample collected from 16 March clustered with England and the sample collected on 30 March showed the highest genetic divergence to the isolate of Wuhan, China. Here we report the first molecular epidemiological study conducted on circulating SARS-CoV-2 in Sri Lanka. The finding provides the robustness of molecular epidemiological tools and their application in tracing possible exposure in disease transmission during the pandemic.

Download Full-text

CNCDatabase: a database of non-coding cancer drivers

10.1101/2020.04.29.069047 ◽

2020 ◽

Author(s):

Eric Minwei Liu ◽

Alexander Martinez-Fundichely ◽

Rajesh Bollapragada ◽

Maurice Spiewack ◽

Ekta Khurana

Keyword(s):

Gene Expression ◽

Luciferase Reporter ◽

Whole Genome ◽

Gene Promoters ◽

Genome Sequences ◽

Coding Regions ◽

Cancer Types ◽

Cancer Drivers ◽

Non Coding Rnas ◽

Experimental Validations

ABSTRACTMost mutations in cancer genomes occur in the non-coding regions with unknown impact to tumor development. Although the increase in number of cancer whole-genome sequences has revealed numerous putative non-coding cancer drivers, their information is dispersed across multiple studies and thus it is difficult to bridge the understanding of non-coding alterations, the genes they impact and the supporting evidence for their role in tumorigenesis across multiple cancer types. To address this gap, we have developed CNCDatabase, Cornell Non-Coding Cancer driver Database (https://cncdatabase.med.cornell.edu/) that contains detailed information about predicted non-coding drivers at gene promoters, 5’ and 3’ UTRs (untranslated regions), enhancers, CTCF insulators and non-coding RNAs. CNCDatabase documents 1,111 protein-coding genes and 90 non-coding RNAs with reported drivers in their non-coding regions from 32 cancer types by computational predictions of positive selection in whole-genome sequences; differential gene expression in samples with and without mutations; or another set of experimental validations including luciferase reporter assays and genome editing. The database can be easily modified and scaled as lists of non-coding drivers are revised in the community with larger whole-genome sequencing studies, CRISPR screens and further experimental validations. Overall, CNCDatabase provides a helpful resource for researchers to explore the pathological role of non-coding alterations and their associations with gene expression in human cancers.

Download Full-text

Comparative genomics of two Shewanella xiamenensis strains isolated from a pilgrim before and during travels to the Hajj

Gut Pathogens ◽

10.1186/s13099-021-00404-w ◽

2021 ◽

Vol 13 (1) ◽

Author(s):

Thongpan Leangapichart ◽

Linda Hadjadj ◽

Philippe Gautret ◽

Jean-Marc Rolain

Keyword(s):

Genome Size ◽

Pathogenic Bacteria ◽

Capsular Polysaccharide ◽

Draft Genome ◽

Water Environment ◽

Antibiotic Resistance Genes ◽

Genomic Analysis ◽

Comparative Genomic ◽

Whole Genome ◽

Genome Sequences

Abstract Background Shewanella xiamenensis has been reported in water environment and in patients and can act as the originator of oxacillinase in gram-negative bacteria. In order to assess genome plasticity and its functional properties related diarrhea symptoms in pilgrim, comparisons of draft genome sequences of the two isolates were conducted with other closely related genomes. Results We isolated S. xiamenensis 111B and 111D strains from a pilgrim before travels to the Hajj and during travels with diarrhea symptom, respectively. Whole-genome sequencing showed that draft genome size of 111B strain was 5,008,191 bp, containing 49 kb of a putative plasmid. The genome size of 111D was 4,964,295 bp containing 225 kb of a putative plasmid that shared the backbone sequences with the hospital wastewater strain T17. Comparatively, two Hajj strains are identical at 97.3% identity and 98.7% coverage. They are closely related to river water strain, AS58 by SNPs analysis. Notably, a novel blaOXA-48 allele blaOXA-547 was identified in 111D, sharing 99.5% identity with blaOXA-546 and blaOXA-894. Multiple copies of virulence specific genes, such as capsular polysaccharide biosynthesis, O-antigen and lasB (vibriolysin related gene) have been identified specifically in 111D, but absent in 111B strain. Conclusions The whole genome sequences of S. xiamenensis strain 111B and 111D, including comparative genomic analysis, highlight here the potential for virulence factors that might be related to the cause of diarrhea in humans and also indicate the possible acquisition of pathogenic bacteria, including antibiotic resistance genes or plasmids during the Hajj.

Download Full-text

Evolutionary and genomic analysis of four SARS-CoV-2 isolates circulating in March 2020 in Sri Lanka; Additional evidence on multiple introduction and further transmission

10.21203/rs.3.rs-44134/v1 ◽

2020 ◽

Author(s):

Dilan Amila Satharasinghe ◽

Parakatawella Mudiyanselage Shalini Daupadi Kumari Parakatawella ◽

Jayasekara Mudiyanselage Krishanthi Jayarukshi Kumari Premarathne ◽

L. J.P. Anura P. Jayasooriya ◽

Gamika A. Prathapasinghe ◽

...

Keyword(s):

Sri Lanka ◽

Disease Transmission ◽

Genomic Analysis ◽

Virus Evolution ◽

Control Measures ◽

The Other ◽

Whole Genome ◽

Genome Sequences ◽

Main Cluster ◽

Multiple Introduction

Abstract The molecular epidemiology of the virus, and mapping help to understand the evolution of the epidemics and apply quick control measures. The study genomic evidence of multiple SARS-CoV-2 introductions into Sri Lanka and virus evolution during circulation. Whole-genome sequences of four SARS-CoV-2 strains obtained from COVID-19 positive patients reported in Sri Lanka during March 2020 were compared with sequences from Europe and elsewhere. The phylogenetic analysis revealed that the sequence of the sample of first local patient collected on 10th March, who contacted tourists from Italy, was clustered with SARS-CoV-2 strains collected from Italy, Germany, France and Mexico. Subsequently, the sequence of the isolate obtained on 19th March also clustered in the same group with the samples collected in March and April from Belgium, France, India, and South Africa. The other two strains of SARS-CoV-2 were segregated from the main cluster, and the sample collected from 16th March clustered with England and the sample collected on 30th March showed the highest genetic divergent to the isolate of Wuhan, China. Here we report the first molecular epidemiological study conducted on circulating SARS-CoV-2 in Sri Lanka. The finding provides the robustness of molecular epidemiological tools and its application in tracing possible exposure in disease transmission during the pandemic.

Download Full-text

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

F1000Research ◽

10.12688/f1000research.17620.2 ◽

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.

Download Full-text

Historical Introgression from Wild Relatives Enhanced Climatic Adaptation and Resistance to Pneumonia in Sheep

Molecular Biology and Evolution ◽

10.1093/molbev/msaa236 ◽

2020 ◽

Author(s):

Yin-Hong Cao ◽

Song-Song Xu ◽

Min Shen ◽

Ze-Hui Chen ◽

Lei Gao ◽

...

Keyword(s):

Genomic Analysis ◽

Wild Relatives ◽

Domestic Sheep ◽

Whole Genome ◽

Genome Sequences ◽

Climatic Adaptation ◽

Genome Wide ◽

Genetic Mechanisms ◽

Mechanisms Of Adaptation ◽

Thinhorn Sheep

Abstract How animals, particularly livestock, adapt to various climates and environments over short evolutionary time is of fundamental biological interest. Further, understanding the genetic mechanisms of adaptation in indigenous livestock populations is important for designing appropriate breeding programs to cope with the impacts of changing climate. Here, we conducted a comprehensive genomic analysis of diversity, interspecies introgression, and climate-mediated selective signatures in a global sample of sheep and their wild relatives. By examining 600K and 50K genome-wide single nucleotide polymorphism data from 3,447 samples representing 111 domestic sheep populations and 403 samples from all their seven wild relatives (argali, Asiatic mouflon, European mouflon, urial, snow sheep, bighorn, and thinhorn sheep), coupled with 88 whole-genome sequences, we detected clear signals of common introgression from wild relatives into sympatric domestic populations, thereby increasing their genomic diversities. The introgressions provided beneficial genetic variants in native populations, which were significantly associated with local climatic adaptation. We observed common introgression signals of alleles in olfactory-related genes (e.g., ADCY3 and TRPV1) and the PADI gene family including in particular PADI2, which is associated with antibacterial innate immunity. Further analyses of whole-genome sequences showed that the introgressed alleles in a specific region of PADI2 (chr2: 248,302,667–248,306,614) correlate with resistance to pneumonia. We conclude that wild introgression enhanced climatic adaptation and resistance to pneumonia in sheep. This has enabled them to adapt to varying climatic and environmental conditions after domestication.

Download Full-text