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

ELife
Thomas A SasaniNels C Elde

Abstract

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.

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Citations

Nov 2, 2018·Wiley Interdisciplinary Reviews. RNA·Nathan MeadeDerek Walsh
Nov 11, 2020·Viruses·Emmanuel AlakunleMalachy Ifeanyi Okeke
May 10, 2021·Journal of Virological Methods·Rosario N BrancaccioTarik Gheit
Apr 30, 2021·Journal of Virology·Greg ValléeDavid H Evans

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Datasets Mentioned

BETA
M35027.1
SRP128569
SRP128573
SRP013146

Methods Mentioned

BETA
genotyping
PCR
Illumina sequencing
gene array
Assay
electrophoresis

Software Mentioned

BLAST
Metrichor cloud suite
freebayes
ONT
Albacore
GraphPad Prism
poretools
nanopolish
BWA
MEM

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