scholarly journals Long read sequencing reveals Poxvirus evolution through rapid homogenization of gene arrays

2018 ◽  
Author(s):  
Thomas A. Sasani ◽  
Kelsey R. Cone ◽  
Aaron R. Quinlan ◽  
Nels C. Elde
Keyword(s):  
Copy Number ◽  
Gene Copy Number ◽  
Gene Copy ◽  
Single Nucleotide Variants ◽  
Sequencing Platform ◽  
Sequencing Technologies ◽  
Gene Copy Number Variation ◽  
Large Gene ◽  
Long Read ◽  
Number Variation

AbstractLarge DNA viruses rapidly evolve to defeat host defenses. Poxvirus adaptation can involve combinations of recombination-driven gene copy number variation and beneficial single nucleotide variants (SNVs) at the same locus, yet how these distinct mechanisms of genetic diversification might simultaneously facilitate adaptation to immune blocks is unknown. We performed experimental evolution with a vaccinia virus population harboring a SNV in a gene actively undergoing copy number amplification. Comparisons of virus genomes using the Oxford Nanopore Technologies sequencing platform allowed us to phase SNVs within large gene copy arrays for the first time, and uncovered a mechanism of adaptive SNV homogenization reminiscent of gene conversion, which is actively driven by selection. Our work reveals a new mechanism for the fluid gain of beneficial mutations in genetic regions undergoing active recombination in viruses, and illustrates the value of long read sequencing technologies for investigating complex genome dynamics in diverse biological systems.

scholarly journals Long read sequencing reveals poxvirus evolution through rapid homogenization of gene arrays

eLife ◽  
2018 ◽  
Vol 7 ◽  
Author(s):  
Thomas A Sasani ◽  
Kelsey R Cone ◽  
Aaron R Quinlan ◽  
Nels C Elde
Keyword(s):  
Copy Number ◽  
Gene Copy Number ◽  
Gene Copy ◽  
Single Nucleotide Variants ◽  
Sequencing Technologies ◽  
Gene Copy Number Variation ◽  
Large Gene ◽  
Oxford Nanopore ◽  
Long Read ◽  
Number Variation

Poxvirus adaptation can involve combinations of recombination-driven gene copy number variation and beneficial single nucleotide variants (SNVs) at the same loci. How these distinct mechanisms of genetic diversification might simultaneously facilitate adaptation to host immune defenses is unknown. We performed experimental evolution with vaccinia virus populations harboring a SNV in a gene actively undergoing copy number amplification. Using long sequencing reads from the Oxford Nanopore Technologies platform, we phased SNVs within large gene copy arrays for the first time. Our analysis uncovered a mechanism of adaptive SNV homogenization reminiscent of gene conversion, which is actively driven by selection. This study reveals a new mechanism for the fluid gain of beneficial mutations in genetic regions undergoing active recombination in viruses and illustrates the value of long read sequencing technologies for investigating complex genome dynamics in diverse biological systems.

Genetic variability of CYP2D6, CYP3A4 and CYP3A5 among the Egyptian population

2021 ◽  
Author(s):  
Thuraya M Mutawi ◽  
Mohamed M Zedan ◽  
Raida S Yahya ◽  
Mahmoud M Zakria ◽  
Mamdouh R El-Sawi ◽  
...  
Keyword(s):  
Genetic Variability ◽  
Copy Number Variation ◽  
Copy Number ◽  
Middle Eastern ◽  
Gene Copy Number ◽  
Gene Copy ◽  
Allelic Variants ◽  
Gene Copy Number Variation ◽  
Number Variation ◽  
Study Participants

Aim: This study investigated major allelic variants of CYP2D6, CYP3A4 and CYP3A5 in Egyptians, an Arabic population for which there is little information regarding these important pharmacogenes. Patients & methods: CYP2D6*2, *4, *5, *10, *41 and gene copy number variation, as well as CYP3A4*22 and CYP3A5*3 were determined with commercially available TaqMan assays in 145 healthy study participants. Results: The CYP2D6 alleles identified suggest that the prevalence of poor metabolizers is low as none were found among the 145 subjects investigated. The frequency for CYP3A5 nonexpressers was 74.5% and the CYP3A4*22 allele frequency was low at 2.0%. Conclusion: These preliminary findings indicate that pharmacogene variation in Egyptians is different from those of other Middle Eastern/Arabic populations and warrants further investigation.

Gene copy number variation and common human disease

2010 ◽  
Vol 77 (3) ◽  
pp. 201-213 ◽  
Author(s):  
M Fanciulli ◽  
E Petretto ◽  
TJ Aitman
Keyword(s):  
Copy Number Variation ◽  
Human Disease ◽  
Copy Number ◽  
Gene Copy Number ◽  
Gene Copy ◽  
Gene Copy Number Variation ◽  
Number Variation

Gene copy number variation in schizophrenia

2007 ◽  
Vol 96 (1-3) ◽  
pp. 93-99 ◽  
Author(s):  
S SUTRALA ◽  
D GOOSSENS ◽  
N WILLIAMS ◽  
L HEYRMAN ◽  
R ADOLFSSON ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Copy Number ◽  
Gene Copy Number ◽  
Gene Copy ◽  
Gene Copy Number Variation ◽  
Number Variation

scholarly journals Gene copy number variation and its significance in cyanobacterial phylogeny

2012 ◽  
Vol 12 (1) ◽  
pp. 177 ◽  
Author(s):  
Bettina E Schirrmeister ◽  
Daniel A Dalquen ◽  
Maria Anisimova ◽  
Homayoun C Bagheri
Keyword(s):  
Copy Number Variation ◽  
Copy Number ◽  
Gene Copy Number ◽  
Gene Copy ◽  
Gene Copy Number Variation ◽  
Number Variation
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