Large-scale evaluation of experimentally determined DNA G+C contents with whole genome sequences of prokaryotes

2015 ◽  
Vol 38 (2) ◽  
pp. 79-83 ◽  
Author(s):  
Mincheol Kim ◽  
Sang-Cheol Park ◽  
Inwoo Baek ◽  
Jongsik Chun
Keyword(s):  
Large Scale ◽  
Whole Genome ◽  
Genome Sequences ◽  
Scale Evaluation

scholarly journals Introducing the first whole genomes of nationals from the United Arab Emirates

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Habiba S. AlSafar ◽  
Mariam Al-Ali ◽  
Gihan Daw Elbait ◽  
Mustafa H. Al-Maini ◽  
Dymitr Ruta ◽  
...  
Keyword(s):  
United Arab Emirates ◽  
Large Scale ◽  
Target Genes ◽  
Whole Genome ◽  
Nucleotide Polymorphisms ◽  
Genome Sequences ◽  
Therapeutic Modalities ◽  
Starting Point ◽  
Disease Associations ◽  
Medicine Quality

Abstract Whole Genome Sequencing (WGS) provides an in depth description of genome variation. In the era of large-scale population genome projects, the assembly of ethnic-specific genomes combined with mapping human reference genomes of underrepresented populations has improved the understanding of human diversity and disease associations. In this study, for the first time, whole genome sequences of two nationals of the United Arab Emirates (UAE) at >27X coverage are reported. The two Emirati individuals were predominantly of Central/South Asian ancestry. An in-house customized pipeline using BWA, Picard followed by the GATK tools to map the raw data from whole genome sequences of both individuals was used. A total of 3,994,521 variants (3,350,574 Single Nucleotide Polymorphisms (SNPs) and 643,947 indels) were identified for the first individual, the UAE S001 sample. A similar number of variants, 4,031,580 (3,373,501 SNPs and 658,079 indels), were identified for UAE S002. Variants that are associated with diabetes, hypertension, increased cholesterol levels, and obesity were also identified in these individuals. These Whole Genome Sequences has provided a starting point for constructing a UAE reference panel which will lead to improvements in the delivery of precision medicine, quality of life for affected individuals and a reduction in healthcare costs. The information compiled will likely lead to the identification of target genes that could potentially lead to the development of novel therapeutic modalities.

scholarly journals Gene Content Evolution in the Arthropods

2018 ◽  
Author(s):  
Gregg W.C. Thomas ◽  
Elias Dohmen ◽  
Daniel S.T. Hughes ◽  
Shwetha C. Murali ◽  
Monica Poelchau ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Large Scale ◽  
Gene Families ◽  
Protein Domain ◽  
Whole Genome ◽  
Genome Sequences ◽  
Arthropod Evolution ◽  
Animal Diversity ◽  
Physiological Adaptations ◽  
Protein Domain Evolution

AbstractBackgroundArthropods comprise the largest and most diverse phylum on Earth and play vital roles in nearly every ecosystem. Their diversity stems in part from variations on a conserved body plan, resulting from and recorded in adaptive changes in the genome. Dissection of the genomic record of sequence change enables broad questions regarding genome evolution to be addressed, even across hyper-diverse taxa within arthropods.ResultsUsing 76 whole genome sequences representing 21 orders spanning more than 500 million years of arthropod evolution, we document changes in gene and protein domain content and provide temporal and phylogenetic context for interpreting these innovations. We identify many novel gene families that arose early in the evolution of arthropods and during the diversification of insects into modern orders. We reveal unexpected variation in patterns of DNA methylation across arthropods and examples of gene family and protein domain evolution coincident with the appearance of notable phenotypic and physiological adaptations such as flight, metamorphosis, sociality and chemoperception.ConclusionsThese analyses demonstrate how large-scale comparative genomics can provide broad new insights into the genotype to phenotype map and generate testable hypotheses about the evolution of animal diversity.

scholarly journals Draft Genome Sequences of 510 Listeria monocytogenes Strains from Food Isolates and Human Listeriosis Cases from Northern Italy

2018 ◽  
Vol 6 (3) ◽  
Author(s):  
Sara Lomonaco ◽  
Silvia Gallina ◽  
Virginia Filipello ◽  
Maria Sanchez Leon ◽  
George John Kastanis ◽  
...  
Keyword(s):  
Listeria Monocytogenes ◽  
Genome Sequencing ◽  
Molecular Typing ◽  
Large Scale ◽  
Draft Genome ◽  
Northern Italy ◽  
Whole Genome ◽  
Genome Sequences ◽  
Sequencing Studies ◽  
Different Sources

ABSTRACT Listeriosis outbreaks are frequently multistate/multicountry outbreaks, underlining the importance of molecular typing data for several diverse and well-characterized isolates. Large-scale whole-genome sequencing studies on Listeria monocytogenes isolates from non-U.S. locations have been limited. Herein, we describe the draft genome sequences of 510 L. monocytogenes isolates from northern Italy from different sources.

0306 Exploring the feasibility of using copy number variants as genetic markers through large-scale whole genome sequencing experiments

2016 ◽  
Vol 94 (suppl_5) ◽  
pp. 146-146
Author(s):  
D. M. Bickhart ◽  
L. Xu ◽  
J. L. Hutchison ◽  
J. B. Cole ◽  
D. J. Null ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genetic Markers ◽  
Genome Sequencing ◽  
Copy Number ◽  
Large Scale ◽  
Copy Number Variants ◽  
Whole Genome

scholarly journals Molecular Epidemiology and Whole-Genome Analysis of Bovine Foamy Virus in Japan

Viruses ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 1017
Author(s):  
Hirohisa Mekata ◽  
Tomohiro Okagawa ◽  
Satoru Konnai ◽  
Takayuki Miyazawa
Keyword(s):  
Phylogenetic Analyses ◽  
Foamy Virus ◽  
Pcr Analysis ◽  
Whole Genome ◽  
Genome Sequences ◽  
Whole Genome Analysis ◽  
Virus Family ◽  
Bovine Foamy Virus ◽  
Novel Genotype

Bovine foamy virus (BFV) is a member of the foamy virus family in cattle. Information on the epidemiology, transmission routes, and whole-genome sequences of BFV is still limited. To understand the characteristics of BFV, this study included a molecular survey in Japan and the determination of the whole-genome sequences of 30 BFV isolates. A total of 30 (3.4%, 30/884) cattle were infected with BFV according to PCR analysis. Cattle less than 48 months old were scarcely infected with this virus, and older animals had a significantly higher rate of infection. To reveal the possibility of vertical transmission, we additionally surveyed 77 pairs of dams and 3-month-old calves in a farm already confirmed to have BFV. We confirmed that one of the calves born from a dam with BFV was infected. Phylogenetic analyses revealed that a novel genotype was spread in Japan. In conclusion, the prevalence of BFV in Japan is relatively low and three genotypes, including a novel genotype, are spread in Japan.

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