Gene amplification and adaptive evolution in bacteria, Annu. Rev. Genet, vol.43, pp.167-195, 2009. ,
Site-directed mutations in the potyvirus HC-PRO gene affect helper component activity, virus accumulation, and symptom expression in infected tobacco plants, Virology, vol.191, pp.106-111, 1992. ,
Stability of Tobacco etch virus infectious clones in plasmid vectors, Virus Res, vol.149, pp.234-240, 2010. ,
The evolution of genome compression and genomic novelty in RNA viruses, Genome Res, vol.17, pp.1496-1504, 2007. ,
Pacing a small cage: mutation and RNA viruses, Trends Ecol. Evol, vol.23, pp.188-193, 2008. ,
Kotonkan and Obodhiang viruses: African ephemeroviruses with large and complex genomes, Virology, vol.425, pp.143-153, 2012. ,
Coat protein gene duplication in a filamentous RNA virus of plants, Proc. Natl Acad. Sci. U S A, vol.89, pp.9156-9160, 1992. ,
Viral genome size distribution does not correlate with the antiquity of the host lineages, Front. Ecol. Evol, vol.3, p.143, 2015. ,
A real-time RTPCR assay for quantifying the fitness of Tobacco etch virus in competition experiments, J. Virol. Methods, vol.139, pp.181-188, 2007. ,
Internal cleavage and trans-proteolytic activities of the VPg-proteinase (NIa) of Tobacco etch potyvirus in vivo, J. Virol, vol.67, pp.6995-7000, 1993. ,
Long-distance movement factor: a transport function of the potyvirus helper component proteinase, Plant Cell, vol.7, pp.549-559, 1995. ,
Spontaneous mutagenesis of a plant potyvirus genome after insertion of a foreign gene, J. Virol, vol.67, pp.5968-5975, 1993. ,
Mechanisms of genetic robustness in RNA viruses, EMBO Rep, vol.7, pp.168-173, 2006. ,
Golden gate shuffling: a one-pot DNA shuffling method based on type IIs restriction enzymes, PLoS One, vol.4, p.5553, 2009. ,
Nucleotide sequence and organization of ten open reading frames in the genome of grapevine leafroll-associated virus 1 and identification of three subgenomic RNAs, J. Gen. Virol, vol.81, pp.605-615, 2000. ,
A tandem repeat gene in a picornavirus, Nucleic Acids Res, vol.10, pp.6441-6450, 1982. ,
Ngaingan virus, a macropod-associated rhabdovirus, contains a second glycoprotein gene and seven novel open reading frames, Virology, vol.399, pp.98-108, 2010. ,
Error thresholds and the constraints to RNA virus evolution, Trends Microbiol, vol.11, pp.543-546, 2003. ,
Evidence for genomic rearrangements mediated by human endogenous retroviruses during primate evolution, Nat. Genet, vol.29, pp.487-489, 2001. ,
Complete nucleotide sequence of an endogenous retrovirus from the amphibian, Xenopus laevis, Virology, vol.311, pp.1-6, 2003. ,
VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing, Genome Res, vol.22, pp.568-576, 2012. ,
Complete genome sequence and analyses of the subgenomic RNAs of Sweet potato chlorotic stunt virus reveal several new features for the genus Crinivirus, J. Virol, vol.76, pp.9260-9270, 2002. ,
Fast gapped-read alignment with Bowtie 2, Nat. Methods, vol.9, pp.357-359, 2012. ,
Sequence and transcriptional analyses of the fish retroviruses walleye epidermal hyperplasia virus types 1 and 2: evidence for a gene duplication, J. Virol, vol.73, pp.9393-9403, 1999. ,
The sequence alignment/map format and SAMtools, Bioinformatics, vol.25, pp.2078-2079, 2009. ,
Streamlining and simplification of microbial genome architecture, Annu. Rev. Microbiol, vol.60, pp.327-349, 2006. ,
Relocation of the NIb gene in the Tobacco etch potyvirus genome, J. Virol, vol.88, pp.4586-4590, 2014. ,
Dynamics of a plant RNA virus intracellular accumulation: stamping machine vs. geometric replication, Genetics, vol.188, pp.637-646, 2011. ,
R: A language and environment for statistical computing. R Core Team, 2014. ,
Molecular biology of potyviruses, Adv. Virus Res, vol.92, pp.101-199, 2015. ,
The distribution of fitness effects caused by single-nucleotide substitutions in an RNA virus, Proc. Natl Acad. Sci. U S A, vol.101, pp.8396-8401, 2004. ,
Viral mutation rates, J. Virol, vol.84, pp.9733-9748, 2010. ,
Quality control and preprocessing of metagenomic datasets, Bioinformatics, vol.27, pp.863-864, 2011. ,
The evolution of large DNA viruses: combining genomic information of viruses and their hosts, Trends Microbiol, vol.12, pp.458-465, 2004. ,
Gene duplication is infrequent in the recent evolutionary history of RNA viruses, Mol. Biol. Evol, vol.30, pp.1263-1269, 2013. ,
Red Queen dynamics, competition and critical points in a model of RNA virus quasispecies, J. Theor. Biol, vol.198, pp.47-59, 1998. ,
Performance of common analysis methods for detecting low-frequency single nucleotide variants in targeted nextgeneration sequence data, J. Mol. Diagn, vol.16, pp.75-88, 2014. ,
Gene and genome duplication in Acanthamoeba polyphaga Mimivirus, J. Virol, vol.79, pp.14095-14101, 2005. ,
Comparative sequence of the helper component (HC) region of Potato virus Y and a HC-defective strain, Potato virus C, Virology, vol.178, pp.573-578, 1990. ,
Origin of vpx in lentiviruses, Nature, vol.347, pp.341-342, 1990. ,
Within-host spatiotemporal dynamics of plant virus infection at the cellular level, PLoS Genet, vol.10, p.1004186, 2014. ,
Estimation of the in vivo recombination rate for a plant RNA virus, J. Gen. Virol, vol.95, pp.724-732, 2014. ,
Sex and the evolution of intrahost competition in RNA virus phi6, Genetics, vol.150, pp.523-532, 1998. ,
Strawberry chlorotic fleck: identification and characterization of a novel Closterovirus associated with the disease, Virus Res, vol.124, pp.88-94, 2007. ,
Characterization of a Novel Member of the Family Closteroviridae from Mentha spp, Phytopathology, vol.95, pp.1043-1048, 2005. ,
Recombination and gene duplication in the evolutionary diversification of P1 proteins in the family Potyviridae, J. Gen. Virol, vol.88, pp.1016-1028, 2007. ,
The genome of Bovine ephemeral fever rhabdovirus contains two related glycoprotein genes, Virology, vol.191, pp.49-61, 1992. ,
Multiple barriers to the evolution of alternative gene orders in a positive-strand RNA virus, Genetics, vol.202, pp.1503-1521, 2016. ,
Evolution by gene duplication: an update, Trends Ecol. Evol, vol.18, pp.292-298, 2003. ,
One is enough: in vivo effective population size is dose-dependent for a plant RNA virus, PLoS Pathog, vol.7, p.1002122, 2011. ,
Effects of potyvirus effective population size in inoculated leaves on viral accumulation and the onset of symptoms, J. Virol, vol.86, pp.9737-9747, 2012. ,
Experimental evolution of pseudogenization and gene loss in a plant RNA virus, Mol. Biol. Evol, vol.31, pp.121-134, 2014. ,