Population Genomics of Plant Viruses

Pagán, Israel; García‐Arenal, Fernando

doi:10.1007/13836_2018_15

Cited by 19 publications

(17 citation statements)

References 201 publications

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“…In the past few years, tools have been developed for the genetic characterization of virus populations. This has broadened current knowledge on the mechanisms that generate genetic diversity and the evolutionary forces that shape the genetic structure and dynamics of virus populations [36]. HTS has allowed for the discovery of novel viruses across a vast array of sample types, but due to large numbers of host/non-viral reads, gaining adequate coverage of full viral genomes within a sample in order to look at population structure is difficult [14].…”

Section: Discussionmentioning

confidence: 99%

The population structure of Rose rosette virus in the USA

Katsiani

Stainton

Lamour

et al. 2020

Journal of General Virology

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Rose rosette virus (RRV) (genus Emaravirus) is the causal agent of the homonymous disease, the most destructive malady of roses in the USA. Although the importance of the disease is recognized, little sequence information and no full genomes are available for RRV, a multi-segmented RNA virus. To better understand the population structure of the virus we implemented a Hi-Plex PCR amplicon high-throughput sequencing approach to sequence all 7 segments and to quantify polymorphisms in 91 RRV isolates collected from 16 states in the USA. Analysis revealed insertion/deletion (indel) polymorphisms primarily in the 5′ and 3′ non-coding, but also within coding regions, including some resulting in changes of protein length. Phylogenetic analysis showed little geographical structuring, suggesting that topography does not have a strong influence on virus evolution. Overall, the virus populations were homogeneous, possibly because of regular movement of plants, the recent emergence of RRV and/or because the virus is under strong purification selection to preserve its integrity and biological functions.

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Section: Discussionmentioning

confidence: 99%

The population structure of Rose rosette virus in the USA

Katsiani

Stainton

Lamour

et al. 2020

Journal of General Virology

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“…Populations of viruses can exist as a quasispecies, that is, a haplotype collection, whose consensus sequence might not be infectious. Third‐generation sequencers produce (extra) long reads that allow reconstruction of full‐length viral haplotypes (Ameur et al ., ; Pagán and García‐Arenal, ). Chemical synthesis of selected haplotypes would generate variant clones with faithful linkage between mutations and that are more likely to be infectious than consensus clones.…”

Section: From Clone Assembly To De Novo Synthesismentioning

confidence: 99%

“…Plant viruses can exist as populations, and mixtures of different species are common in nature (Elena et al ., ; Pagán and García‐Arenal, ). The use of synthetic multispecies communities is an emerging trend to augment microbiome systems for industrial and environmental biotechnology (Johns et al ., ).…”

Section: Synthetic Virus Populations and Consortiamentioning

confidence: 99%

Harnessed viruses in the age of metagenomics and synthetic biology: an update on infectious clone assembly and biotechnologies of plant viruses

Pasin

Menzel

Daròs

2019

Plant Biotechnology Journal

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Summary Recent metagenomic studies have provided an unprecedented wealth of data, which are revolutionizing our understanding of virus diversity. A redrawn landscape highlights viruses as active players in the phytobiome, and surveys have uncovered their positive roles in environmental stress tolerance of plants. Viral infectious clones are key tools for functional characterization of known and newly identified viruses. Knowledge of viruses and their components has been instrumental for the development of modern plant molecular biology and biotechnology. In this review, we provide extensive guidelines built on current synthetic biology advances that streamline infectious clone assembly, thus lessening a major technical constraint of plant virology. The focus is on generation of infectious clones in binary T‐ DNA vectors, which are delivered efficiently to plants by Agrobacterium . We then summarize recent applications of plant viruses and explore emerging trends in microbiology, bacterial and human virology that, once translated to plant virology, could lead to the development of virus‐based gene therapies for ad hoc engineering of plant traits. The systematic characterization of plant virus roles in the phytobiome and next‐generation virus‐based tools will be indispensable landmarks in the synthetic biology roadmap to better crops.

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“…The maximum clade credibility tree (MCCT) from the beast analysis, using the uncorrelated lognormal relaxed‐clock model, showed similar groups to those of the previously obtained phylogenetic tree. The analysis of the spatiotemporal diffusion process of PRSV‐P isolates (American continent and the Caribbean islands) showed a most recent common ancestor (mean) in 1942 (HPD 95% = 1911–1967), with a substitution rate of 7.7 × 10 −4 substitutions per site per year (HPD 95% = 4.6 × 10 −4 to 1.1 × 10 −3 ), which is equivalent to those of plant viruses (Pagán & García‐Arenal, ). The spatiotemporal diffusion analysis proposed Mexico as an ancestral area for the American continent and the Caribbean islands (posterior probability of the ancestral state (PPAS) = 0.91; Fig.…”

Section: Resultsmentioning

confidence: 97%

Distribution and phylodynamics of papaya ringspot virus on Carica papaya in Cuba

et al. 2018

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Orchard and garden papaya crops grown in 47 Cuban municipalities were surveyed from 2008 to 2013, revealing the widespread distribution of papaya ringspot virus (PRSV) in Cuba. Phylodynamic analyses performed with the partial coat protein gene of all Cuban PRSV‐P isolates (34 sequences) and 107 sequences of isolates from the American continent and the Caribbean islands showed a most recent common ancestor in 1942 (95% highest posterior density, HPD 95% = 1911–1967). The substitution rate was estimated to be 7.7 × 10−4 substitutions per site per year (HPD 95% = 4.6 × 10−4 to 1.1 × 10−3), which is equivalent to those detected in other RNA viruses. Demographic reconstruction of PRSV showed that viral diversity increased in the 1985–1990 period, which coincides with the implementation of extensive production practices. Moreover in Cuba, viral dispersion occurred from Mexico and other unknown ancestral locations. The spatiotemporal diffusion analysis proposed Mexico as an ancestral area for the origin of diversification in the American continent and suggests new dispersion events between American and Caribbean isolates. The observed widespread distribution, clear geographic grouping of Cuban isolates, virus growth and genetic diversity provide strong evidence of the PRSV dispersion patterns, which has implications for the control strategies of PRSV.

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Population Genomics of Plant Viruses

Cited by 19 publications

References 201 publications

The population structure of Rose rosette virus in the USA

The population structure of Rose rosette virus in the USA

Harnessed viruses in the age of metagenomics and synthetic biology: an update on infectious clone assembly and biotechnologies of plant viruses

Distribution and phylodynamics of papaya ringspot virus on Carica papaya in Cuba

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