Deep Sequencing Analysis of RNAs from Citrus Plants Grown in a Citrus Sudden Death-Affected Area Reveals Diverse Known and Putative  Novel Viruses

Matsumura, Emilyn E.; Coletta-Filho, Helvécio Della; Nouri, Shahideh; Falk, Bryce W.; Nerva, Luca; Oliveira, Tiago Silva; Dorta, Silvia O; Machado, Marcos Antônio

doi:10.3390/v9040092

Cited by 57 publications

(57 citation statements)

References 27 publications

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“…To further strengthen these results, CSDaV consensus sequences were obtained from transcriptome sequencing, conducted for both symptomatic and asymptomatic plants by using Illumina next generation sequencing (NGS) technology [22]. The coding regions studied here were accessed in these consensus sequences and included in the phylogenetic analysis.…”

Section: Resultsmentioning

confidence: 99%

Genetic Structure and Molecular Variability Analysis of Citrus sudden death-associated virus Isolates from Infected Plants Grown in Brazil

Matsumura

Coletta-Filho²,

Dorta³

et al. 2016

Viruses

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Citrus sudden death-associated virus (CSDaV) is a monopartite positive-sense single-stranded RNA virus that was suggested to be associated with citrus sudden death (CSD) disease in Brazil. Here, we report the first study of the genetic structure and molecular variability among 31 CSDaV isolates collected from both symptomatic and asymptomatic trees in CSD-affected areas. Analyses of partial nucleotide sequences of five domains of the CSDaV genomic RNA, including those encoding for the methyltransferase, the multi-domain region (MDR), the helicase, the RNA-dependent RNA polymerase and the coat protein, showed that the MDR coding region was the most diverse region assessed here, and a possible association between this region and virus adaption to different host or plant tissues is considered. Overall, the nucleotide diversity (π) was low for CSDaV isolates, but the phylogenetic analyses revealed the predominance of two main groups, one of which showed a higher association with CSD-symptomatic plants. Isolates obtained from CSD-symptomatic plants, compared to those obtained from asymptomatic plants, showed higher nucleotide diversity, nonsynonymous and synonymous substitution rates and number of amino acid changes on the coding regions located closer to the 5’ end region of the genomic RNA. This work provides new insights into the genetic diversity of the CSDaV, giving support for further epidemiological studies.

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Section: Resultsmentioning

confidence: 99%

Genetic Structure and Molecular Variability Analysis of Citrus sudden death-associated virus Isolates from Infected Plants Grown in Brazil

Matsumura

Coletta-Filho²,

Dorta³

et al. 2016

Viruses

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“…Ribosomal RNA (rRNAs) was depleted with the Ribo‐Zero™ Gold kit (Epicentre, Madison, USA), and after library assembly, samples were sequenced in a single lane of Illumina NovaSeq (100 M, 100 bp, paired‐end reads). The raw reads were then mapped against reference genomes using BWA (Li and Durbin, ) and SAMtools (Li et al ., ) as previously described (Matsumura et al ., ). Integrative genomics viewer was used for data visualization and exploration (Thorvaldsdottir et al ., ).…”

Section: Methodsmentioning

confidence: 97%

Mycoviruses mediate mycotoxin regulation in Aspergillus ochraceus

Nerva

Chitarra

Siciliano

et al. 2018

Environmental Microbiology

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Summary To date, no demonstration of a direct correlation between the presence of mycoviruses and the quantitative or qualitative modulation of mycotoxins has been shown. In our study, we transfected a virus‐free ochratoxin A (OTA)‐producing isolate of Aspergillus ochraceus with purified mycoviruses from a different A. ochraceus isolate and from Penicillium aurantiogriseum. Among the mycoviruses tested, only Aspergillus ochraceus virus (AoV), a partitivirus widespread in A. ochraceus, caused a specific interaction that led to an overproduction of OTA, which is regulated by the European Commission and is the second most important contaminant of food and feed commodities. Gene expression analysis failed to reveal a specific viral upregulation of the mRNA of genes considered to play a role in the OTA biosynthetic pathway. Furthermore, AoOTApks1, a polyketide synthase gene considered essential for OTA production, is surprisingly absent in the genome of our OTA‐producing isolate. The possible biological and evolutionary implications of the mycoviral regulation of mycotoxin production are discussed.

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“…The sequences of such EPRVs are known to be integrated in high copy numbers in the genome of many citrus species (Geering et al, 2014;Diop et al, 2018). In 2017, using an HTS approach to study putative viruses associated with CSD, Matsumura et al (2017) identified multiple viruses in CSD-affected citrus plants and also confirmed the presence of CitPRV sequences.…”

Section: Conclusion Of Pest Categorisation (Section 4)mentioning

confidence: 93%

Pest categorisation of ‘Blight and blight‐like’ diseases of citrus

Jeger¹,

Bragard²,

Caffier³

et al. 2018

EFS2

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The EFSA Panel on Plant Health performed a pest categorisation of 'Blight and blight-like' for the EU territory. Blight is a major disease of citrus. Similar 'blight-like' diseases are also known (e.g. declinio, declinamiento) and are addressed simultaneously with Blight in the present categorisation. The causal agent(s) remain(s) unknown and the potential role of a recently identified citrus endogenous pararetrovirus (Citrus Blight-associated pararetrovirus, CBaPRV) remains to be established. Transmissibility and ability to produce consistent (although poorly specific) symptoms have been demonstrated and a combination of indirect approaches is used, with limits, for diagnosis. There are large uncertainties on the biology of the causal agent(s) and on the epidemiology of the disease, including the transmission mechanism(s) responsible for the observed field spread. Blight has been reported from North, Central and South America, Africa and Oceania but is not known to occur in the EU. It is listed in Annex IIA of Directive 2000/29EC. It has the potential to enter, establish and spread in the EU territory. The main entry pathway (citrus plants for planting) is closed by existing legislation and entry is only possible on minor pathways (such as illegal import). Blight is a severe disease and a negative impact is expected should it be introduced in the EU, but the magnitude of this negative impact is very difficult to estimate. 'Blight and blight like' satisfies all criteria evaluated by EFSA to qualify as a Union quarantine pest. It does not meet the criterion of being present in the EU to qualify as a Union regulated non-quarantine pest (RNQP). Since the identity of the causal agent(s) of the Blight and blight-like disease(s) and the existence and efficiency of natural spread mechanism(s) remain unknown, large uncertainties affect all aspects of the present pest categorisation.

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Deep Sequencing Analysis of RNAs from Citrus Plants Grown in a Citrus Sudden Death-Affected Area Reveals Diverse Known and Putative Novel Viruses

Cited by 57 publications

References 27 publications

Genetic Structure and Molecular Variability Analysis of Citrus sudden death-associated virus Isolates from Infected Plants Grown in Brazil

Genetic Structure and Molecular Variability Analysis of Citrus sudden death-associated virus Isolates from Infected Plants Grown in Brazil

Mycoviruses mediate mycotoxin regulation in Aspergillus ochraceus

Pest categorisation of ‘Blight and blight‐like’ diseases of citrus

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