From Spatial Metagenomics to Molecular Characterization of Plant Viruses: A Geminivirus Case Study

Claverie, Sohini; Bernardo, Pauline; Kraberger, Simona; Hartnady, Penelope; Lefeuvre, Pierre; Lett, Jean‐Michel; Galzi, Serge; Harkins, Gordon William; Varsani, Arvind; Martin, Darren P.; Filloux, Denis

doi:10.1016/bs.aivir.2018.02.003

Cited by 37 publications

(31 citation statements)

References 113 publications

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“…However, different population-based or taxonomy-based terms are often used in these analyses, such as virus species, isolates, strains, operational taxonomic unit (OTU) or quasispecies, while their definition has been discussed by virologists (Van Regenmortel, 2007;Adams et al, 2013;Peterson, 2014) and these terms have sometimes been inconsistently used in the literature. The crucial point is thus to define clearly the fundamental unit used for diversity estimation (Claverie et al, 2018). In recent geometagenomics work (Bernardo et al, 2018), virus family was for example defined as the base "individual" unit enumerated to evaluate virus richness per sample, i.e., the number of virus families represented (if any) as determined by BLAST matches of viral contigs.…”

Section: Drawbacksmentioning

confidence: 99%

Illuminating an Ecological Blackbox: Using High Throughput Sequencing to Characterize the Plant Virome Across Scales

et al. 2020

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The ecology of plant viruses began to be explored at the end of the 19th century. Since then, major advances have revealed mechanisms of virus-host-vector interactions in various environments. These advances have been accelerated by new technlogies for virus detection and characterization, most recently including high throughput sequencing (HTS). HTS allows investigators, for the first time, to characterize all or nearly all viruses in a sample without a priori information about which viruses might be present. This powerful approach has spurred new investigation of the viral metagenome (virome). The rich virome datasets accumulated illuminate important ecological phenomena such as virus spread among host reservoirs (wild and domestic), effects of ecosystem simplification caused by human activities (and agriculture) on the biodiversity and the emergence of new viruses in crops. To be effective, however, HTS-based virome studies must successfully navigate challenges and pitfalls at each procedural step, from plant sampling to library preparation and bioinformatic analyses. This review summarizes major advances in plant virus ecology associated with technological developments, and then presents important considerations and best practices for HTS use in virome studies.

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Section: Drawbacksmentioning

confidence: 99%

Illuminating an Ecological Blackbox: Using High Throughput Sequencing to Characterize the Plant Virome Across Scales

et al. 2020

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“…Although geminiviruses have been intensively studied since the 1970s [ 1 , 2 ], it is only since the recent development and application of viral metagenomics-based approaches that the true diversity of this group of viruses is starting to become apparent [ 3 , 4 ]. The genus Capulavirus is just one of several new genera in the family Geminiviridae that have been established to accommodate some of the novel and diverse geminiviruses that have been discovered over the past ten years [ 5 ].…”

Section: Introductionmentioning

confidence: 99%

The Westward Journey of Alfalfa Leaf Curl Virus

Davoodi

Bejerman

Richet

et al. 2018

Viruses

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Alfalfa leaf curl virus (ALCV), which causes severe disease symptoms in alfalfa (Medicago sativa L.) and is transmitted by the widespread aphid species, Aphis craccivora Koch, has been found throughout the Mediterranean basin as well as in Iran and Argentina. Here we reconstruct the evolutionary history of ALCV and attempt to determine whether the recent discovery and widespread detection of ALCV is attributable either to past diagnostic biases or to the emergence and global spread of the virus over the past few years. One hundred and twenty ALCV complete genome sequences recovered from ten countries were analyzed and four ALCV genotypes (ALCV-A, ALCV-B, ALCV-C, and ALCV-D) were clearly distinguished. We further confirm that ALCV isolates are highly recombinogenic and that recombination has been a major determinant in the origins of the various genotypes. Collectively, the sequence data support the hypothesis that, of all the analyzed locations, ALCV likely emerged and diversified in the Middle East before spreading to the western Mediterranean basin and Argentina.

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“…The impacts of these technologies on plant virus discovery are evident within the family Geminiviridae, a family of plant viruses for which HTS-based virus discovery projects are uncovering a growing number of divergent lineages. In addition to the nine recognized geminivirus genera-Becurtovirus, Begomovirus, Capulavirus, Curtovirus, Eragrovirus, Grablovirus, Mastrevirus, Topocuvirus and Turncurtovirus; [21,22]-four of which were established based on viruses discovered in large-scale HTS-based virus discovery projects, it is likely that multiple new genera will need to be formed to accommodate 12 other, currently unassigned, divergent geminivirus lineages [23][24][25][26][27][28][29][30][31][32].…”

Section: Introductionmentioning

confidence: 99%

Diverse genomoviruses representing twenty-nine species identified associated with plants

et al. 2020

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Cactaceae comprise a diverse and iconic group of flowering plants which are almost exclusively indigenous to the New World. The wide variety of growth forms found amongst the cacti have led to the trafficking of many species throughout the world as ornamentals. Despite the evolution and physiological properties of these plants having been extensively studied, little research has focused on cactus-associated viral communities. While only single-stranded RNA viruses had ever

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From Spatial Metagenomics to Molecular Characterization of Plant Viruses: A Geminivirus Case Study

Cited by 37 publications

References 113 publications

Illuminating an Ecological Blackbox: Using High Throughput Sequencing to Characterize the Plant Virome Across Scales

Illuminating an Ecological Blackbox: Using High Throughput Sequencing to Characterize the Plant Virome Across Scales

The Westward Journey of Alfalfa Leaf Curl Virus

Diverse genomoviruses representing twenty-nine species identified associated with plants

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