Discovery and comparative genomic analysis of elk circovirus (ElkCV), a novel circovirus species and the first reported from a cervid host

Abstract The complete genome sequence of a novel circovirus (elk circovirus (ElkCV) Banff/2019) was determined via high throughput sequencing of liver tissue from a euthanized Rocky Mountain elk (Cervus canadensis nelsoni) from Alberta, Canada. The genome is circular and 1,787 nucleotides long, with two major ORFs encoding predicted proteins. Comparative genomic analysis to 4,164 publicly available complete and near complete circovirus genomes showed that ElkCV shares approximately 65% pairwise genome-wide nucleotide identity with the most closely related circovirus species, porcine circoviruses (PCV) 1 and 2 and bat-associated circovirus (BatACV) 11. ElkCV features a stem-loop within the origin of replication region characteristic of circoviruses. However, it differs from those found in PCV1, PCV2 and BatACV11 since it has a longer stem and contains hexamer repeats that overlap the stem in opposing orientations. Interestingly, stem-loop structures of similar length featuring repeats in a similar position and orientation are also seen in some avian circoviruses. Based on the demarcation threshold established by the International Committee on Taxonomy of Viruses (ICTV) for members of Circoviridae (80% pairwise genome-wide nucleotide identity), ElkCV represents a novel species and is the first complete circovirus genome reported from a cervid host.

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Comparative Genomic Analysis Provides Insights into the Evolution and Genetic Diversity of Community-Genotype Sequence Type 72 Staphylococcus aureus Isolates

mSystems ◽

10.1128/msystems.00986-21 ◽

2021 ◽

Author(s):

Wangxiao Zhou ◽

Ye Jin ◽

Yanzi Zhou ◽

Yuan Wang ◽

Luying Xiong ◽

...

Keyword(s):

Genetic Diversity ◽

Staphylococcus Aureus ◽

Genomic Analysis ◽

Comparative Genomic Analysis ◽

Sequence Type ◽

Comparative Genomic ◽

Health Issues ◽

Content Type ◽

Genome Wide Analysis ◽

Genome Wide

Understanding the evolution and dissemination of community-genotype ST72 Staphylococcus aureus isolates is important, as isolates of this lineage have rapidly spread into hospital settings and caused serious health issues. In this study, we first carried out genome-wide analysis of 107 global ST72 isolates to characterize the evolution and genetic diversity of the ST72 lineage.

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Genome-wide SNP identification for the construction of a high-resolution genetic map of Japanese flounder (Paralichthys olivaceus): applications to QTL mapping of Vibrio anguillarum disease resistance and comparative genomic analysis

DNA Research ◽

10.1093/dnares/dsv001 ◽

2015 ◽

Vol 22 (2) ◽

pp. 161-170 ◽

Cited By ~ 77

Author(s):

C. Shao ◽

Y. Niu ◽

P. Rastas ◽

Y. Liu ◽

Z. Xie ◽

...

Keyword(s):

Disease Resistance ◽

High Resolution ◽

Qtl Mapping ◽

Paralichthys Olivaceus ◽

Vibrio Anguillarum ◽

Genomic Analysis ◽

Comparative Genomic Analysis ◽

Japanese Flounder ◽

Comparative Genomic ◽

Genome Wide

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Comparative genomics reveal shared genomic changes in syngnathid fishes and signatures of genetic convergence with placental mammals

National Science Review ◽

10.1093/nsr/nwaa002 ◽

2020 ◽

Vol 7 (6) ◽

pp. 964-977 ◽

Cited By ~ 4

Author(s):

Yan-Hong Zhang ◽

Vydianathan Ravi ◽

Geng Qin ◽

He Dai ◽

Hui-Xian Zhang ◽

...

Keyword(s):

Amino Acid ◽

Comparative Genomics ◽

Embryonic Development ◽

Evolutionary Rate ◽

Genomic Analysis ◽

Comparative Genomic Analysis ◽

Comparative Genomic ◽

Amino Acid Substitutions ◽

Genomic Changes ◽

Genome Wide

Abstract Syngnathids (seahorses, pipefishes and seadragons) exhibit an array of morphological innovations including loss of pelvic fins, a toothless tubular mouth and male pregnancy. They comprise two subfamilies: Syngnathinae and Nerophinae. Genomes of three Syngnathinae members have been analyzed previously. In this study, we have sequenced the genome of a Nerophinae member, the Manado pipefish (Microphis manadensis), which has a semi-enclosed brood pouch. Comparative genomic analysis revealed that the molecular evolutionary rate of the four syngnathids is higher than that of other teleosts. The loss of all but one P/Q-rich SCPP gene in the syngnathids suggests a role for the lost genes in dentin and enameloid formation in teleosts. Genome-wide comparison identified a set of 118 genes with parallel identical amino acid substitutions in syngnathids and placental mammals. Association of some of these genes with placental and embryonic development in mammals suggests a role for them in syngnathid pregnancy.

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Comparative genomic analysis of Mycobacterium tuberculosis reveals evolution and genomic instability within Uganda I sub-lineage

10.1101/2020.10.24.353425 ◽

2020 ◽

Author(s):

Stephen Kanyerezi ◽

Patricia Nabisubi

Keyword(s):

Mycobacterium Tuberculosis ◽

Core Genome ◽

Variant Calling ◽

Genomic Analysis ◽

Comparative Genomic Analysis ◽

Genome Wide Association ◽

Comparative Genomic ◽

Pan Genome ◽

Genome Wide

AbstractIntroductionTuberculosis (TB) is the leading cause of morbidity and mortality globally, responsible for an estimated annual 10.0 million new cases and 1.3 million deaths among infectious diseases with Africa contributing a quarter of these cases in 2019. Classification of Mycobacterium tuberculosis (MTB) strains is important in understanding their geographical predominance and pathogenicity. Different studies have gone ahead to classify MTB using different methods. Some of these include; RFLP, spoligotyping, MIRU-VNTR and SNP set based phylogeny. The SNP set based classification has been found to be in concordance with the region of difference (RD) analysis of MTB complex classification system. In Uganda, the most common cause of pulmonary tuberculosis (PTB) is Uganda genotype of MTB and accounts for up to 70 % of isolates.MethodsSequenced MTB genome samples were retrieved from NCBI and others from local sequencing projects. The genomes were subjected to snippy (a rapid haploid variant calling and core genome alignment) to call variants and annotate them. Outputs from snippy were used to classify the isolates into Uganda genotypes and Non Ugandan genotypes based on 62 SNP set. The Ugandan genotype isolates were later subjected to 413 SNP set and then to a pan genome wide association analysis.Results6 Uganda genotype isolates were found not to classify as either Uganda I or II genotypes based on the 62 SNP set. Using the 413 SNP set, the 6 Uganda genotype isolates were found to have only one SNP out of the 7 SNPs that classify the Uganda I genotypes. They were also found to have both missense and frameshift mutations within the ctpH gene whereas the rest of Uganda I that had a mutation within this gene, was a missense.ConclusionAmong the Uganda genotypes genomes, Uganda I genomes are unstable. We used publicly available datasets to perform analysis like mapping, variant calling, mixed infection, pan-genome analysis to investigate and compare evolution of the Ugandan genotype.

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