Plant Virus Adaptation to New Hosts: A Multi-scale Approach

Elena, Santiago F.; García‐Arenal, Fernando

doi:10.1007/978-3-031-15640-3_5

Cited by 4 publications

(3 citation statements)

References 181 publications

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“…Overall, our findings underscored the critical impact of TDRP in estimating long-term evolutionary history of viruses and offered a new perspective on the possible long-term virus-host associations within the Sobemovirus genus. This is exemplified by host range evolution, a pivotal aspect of plant virus emergence that has garnered significant attention in recent years (see [ 36 , 37 ] for recent reviews).…”

Section: Discussionmentioning

confidence: 99%

Revisiting the origins of the Sobemovirus genus: A case for ancient origins of plant viruses

Ghafari,

Sõmera,

Sarmiento

et al. 2024

PLoS Pathog

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The discrepancy between short- and long-term rate estimates, known as the time-dependent rate phenomenon (TDRP), poses a challenge to extrapolating evolutionary rates over time and reconstructing evolutionary history of viruses. The TDRP reveals a decline in evolutionary rate estimates with the measurement timescale, explained empirically by a power-law rate decay, notably observed in animal and human viruses. A mechanistic evolutionary model, the Prisoner of War (PoW) model, has been proposed to address TDRP in viruses. Although TDRP has been studied in animal viruses, its impact on plant virus evolutionary history remains largely unexplored. Here, we investigated the consequences of TDRP in plant viruses by applying the PoW model to reconstruct the evolutionary history of sobemoviruses, plant pathogens with significant importance due to their impact on agriculture and plant health. Our analysis showed that the Sobemovirus genus dates back over four million years, indicating an ancient origin. We found evidence that supports deep host jumps to Poaceae, Fabaceae, and Solanaceae occurring between tens to hundreds of thousand years ago, followed by specialization. Remarkably, the TDRP-corrected evolutionary history of sobemoviruses was extended far beyond previous estimates that had suggested their emergence nearly 9,000 years ago, a time coinciding with the Neolithic period in the Near East. By incorporating sequences collected through metagenomic analyses, the resulting phylogenetic tree showcases increased genetic diversity, reflecting a deep history of sobemovirus species. We identified major radiation events beginning between 4,600 to 2,000 years ago, which aligns with the Neolithic period in various regions, suggesting a period of rapid diversification from then to the present. Our findings make a case for the possibility of deep evolutionary origins of plant viruses.

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Section: Discussionmentioning

confidence: 99%

Revisiting the origins of the Sobemovirus genus: A case for ancient origins of plant viruses

Ghafari,

Sõmera,

Sarmiento

et al. 2024

PLoS Pathog

View full text Add to dashboard Cite

show abstract

Section: Discussionmentioning

confidence: 99%

Revisiting the origins of theSobemovirusgenus: a case for ancient origins of plant viruses

Ghafari,

Somera,

Sarmiento

et al. 2023

Preprint

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The discrepancy between short- and long-term rate estimates, known as the time-dependent rate phenomenon (TDRP), poses a challenge to extrapolating evolutionary rates over time and reconstructing evolutionary history of viruses. The TDRP reveals a decline in evolutionary rate estimates with the measurement timescale, explained empirically by a power-law rate decay, notably observed in animal and human viruses. A mechanistic evolutionary model, the Prisoner of War (PoW) model, has been proposed to address TDRP in viruses. Although TDRP has been studied in animal viruses, its impact on plant virus evolutionary history remains largely unexplored. Here, we investigated the consequences of TDRP in plant viruses by applying the PoW model to reconstruct the evolutionary history of sobemoviruses, plant pathogens with significant importance due to their impact on agriculture and plant health. Our analysis showed that theSobemovirusgenus dates back over four million years, indicating an ancient origin. We found evidence that supports deep host jumps to Poaceae, Fabaceae, and Solanaceae occurring between tens to hundreds of thousand years ago, followed by specialization. Remarkably, the TDRP-corrected evolutionary history of sobemoviruses was extended far beyond previous estimates that had suggested their emergence during the Neolithic period. By incorporating sequences collected through metagenomic analyses, the resulting phylogenetic tree showcases increased genetic diversity, reflecting a deep history of sobemovirus species with major radiation events taking place during the Neolithic period, suggesting rapid diversification in that period. Our findings make a case for the possibility of deep evolutionary origins of plant viruses.

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“…Similar trends have also been reported in other Latin American countries such as Ecuador and Mexico (Galarza et al, 2016;Brito et al, 2016 andCardona &Bolaños, 2019;Torres et al, 2023). Unfortunately, the uncontrolled expansion of a crop also increases the probability of dispersion and emergence of plant diseases, thus compromising the future productivity and longevity of fields (Jones, 2009;Ristaino et al, 2021 andGarcía-Arenal, 2023).…”

Section: Introductionmentioning

confidence: 99%

A global analysis of the Rubus virome using public transcriptome data

Higuita,

Pérez,

Gallo

et al. 2023

Preprint

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Viruses are the causal agent of some of the most limiting diseases in Rubus crops. In this regard, a detailed knowledge of the Rubus virome is essential for the successful implementation of mitigation strategies and to assess the risk of emergence of novel viral diseases. Fortunately, the widespread use of RNA sequencing to characterize diverse aspects about the biology of Rubus species can also be a valuable source of data on viruses associated with these hosts. Here, we present a meta-analysis of the Rubus virome based on the re-examination of public RNAseq data from nine Rubus species and 23 hybrid cultivars across the world. As a result, we identified 23 viruses and one viroid associated with the genus Rubus. Detected viruses are part of eleven families and 26 genera. We a provide evidence for existence of a second species in the genus Brambyvirus, and a novel member of the family Virgaviridae. Our data also revealed raspberry bushy dwarf virus (RBDV) to be the most prevalent and generalist Rubus virus across the world. In terms of number of species, the genus Ilarvirus and the family Closteroviridae were the most diverse taxonomic rank affecting Rubus. Network analysis revealed distinct Rubus viromes in different countries and analysis of coinfections revealed three main viral communities infecting these plant species across the world. We also provide information on virus variants from new locations across the world and data on potential emergent viruses from other plant hosts.

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Plant Virus Adaptation to New Hosts: A Multi-scale Approach

Cited by 4 publications

References 181 publications

Revisiting the origins of the Sobemovirus genus: A case for ancient origins of plant viruses

Revisiting the origins of the Sobemovirus genus: A case for ancient origins of plant viruses

Revisiting the origins of theSobemovirusgenus: a case for ancient origins of plant viruses

A global analysis of the Rubus virome using public transcriptome data

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