High‐throughput sequencing allowed the completion of the genome of grapevine Red Globe virus and revealed recurring co‐infection with other tymoviruses in grapevine

Cretazzo, Enrico; Velasco, L.

doi:10.1111/ppa.12669

Cited by 17 publications

(21 citation statements)

References 29 publications

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“…Higher number of 21-nt class vsiRNAs populations with respect to 22-nt support the prevalence of a Dicer like protein 4 (DCL4) in the production of vsiRNAs in beans, as has been suggested in others plants [ 54 , 55 ]. 21- and 22-nt vsiRNAs populations, showed the same preference for sense or antisense polarity in RNA1 and RNA2, indicating that the mechanisms responsible for strand polarity are not dependent on the preference of DCL enzymes but on other factors specific to this virus species.…”

Section: Discussionmentioning

confidence: 55%

First natural crossover recombination between two distinct species of the family Closteroviridae leads to the emergence of a new disease

et al. 2018

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Lettuce chlorosis virus-SP (LCV-SP) (family Closteroviridae, genus Crinivirus), is a new strain of LCV which is able to infect green bean plants but not lettuce. In the present study, high-throughput and Sanger sequencing of RNA was used to obtain the LCV-SP full-length sequence. The LCV-SP genome comprises 8825 nt and 8672 nt long RNA1 and RNA2 respectively. RNA1 of LCV-SP contains four ORFs, the proteins encoded by the ORF1a and ORF1b are closely related to LCV RNA1 from California (FJ380118) whereas the 3´ end encodes proteins which share high amino acid sequence identity with RNA1 of Bean yellow disorder virus (BnYDV; EU191904). The genomic sequence of RNA2 consists of 8 ORFs, instead of 10 ORFs contained in LCV-California isolate. The distribution of vsiRNA (virus-derived small interfering RNA) along the LCV-SP genome suggested the presence of subgenomic RNAs corresponding with HSP70, P6.4 and P60. Results of the analysis using RDP4 and Simplot programs are the proof of the evidence that LCV-SP is the first recombinant of the family Closteroviridae by crossover recombination of intact ORFs, being the LCV RNA1 (FJ380118) and BnYDV RNA1 (EU191904) the origin of the new LCV strain. Genetic diversity values of virus isolates in the recombinant region obtained after sampling LCV-SP infected green bean between 2011 and 2017 might suggest that the recombinant virus event occurred in the area before this period. The presence of LCV-SP shows the role of recombination as a driving force of evolution within the genus Crinivirus, a globally distributed, emergent genus.

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Section: Discussionmentioning

confidence: 55%

First natural crossover recombination between two distinct species of the family Closteroviridae leads to the emergence of a new disease

et al. 2018

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“…Higher number of 21-nt class vsiRNAs populations with respect to 22-nt support the prevalence of a Dicer like protein 4 (DCL4) in the production of vsiRNAs in beans, as has been suggested in others plants [52,53]. 21− and 22-nt vsiRNAs populations, showed the same preference for sense or antisense polarity in RNA1 and RNA2, indicating that the mechanisms responsible for strand polarity are not dependent on the preference of DCL enzymes but on other factors specific to this virus species.…”

Section: Resultsmentioning

confidence: 63%

First natural crossover recombination of intact ORFs between two distinct species of the familyClosteroviridae

Ruiz

Simon

García

et al. 2018

Preprint

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18Lettuce chlorosis virus-SP (LCV-SP) (family Closteroviridae, genus Crinivirus), is a 19 new strain of LCV which is able to infect green bean plants and incapable of infecting 20 lettuce crops. In the present study, high throughput and Sanger sequencing of RNA 21 was used to obtain the LCV-SP full-length sequence. The LCV-SP genome comprises 22 8825 nt and 8672 nt equivalent with RNA1 and RNA2 respectively. RNA1 of LCV-SP 23 contains four ORFs, the proteins encoded by the ORF1a and ORF1b are closely related 24 to LCV RNA1 from California (FJ380118) whereas the 3´ end encodes proteins which 25 share high amino acid sequence identity with RNA1 of BnYDV (EU191904). The 26 genomic sequence of RNA2 consists of 8 ORFs, instead of 10 ORFs contained in LCV-27 California isolate. The distribution of vsiRNA (virus-derived small interfering RNA) along 28 the LCV-SP genome suggested the presence of subgenomic RNAs corresponding with 29 HSP70, P6.4 and P60. Results of the analysis using RDP4 and Simplot programs are the 30 proof of the evidence that LCV-SP is the first recombinant of the family Closteroviridae 31 by crossover recombination of intact ORFs, being the LCV RNA1 (FJ380118) and BnYDV 32 RNA1 (EU191904) the origin of the new LCV strain. Genetic diversity values of virus 33 isolates in the recombinant region obtained after sampling LCV-SP infected green bean 34 between 2011 and 2017 might suggest that the recombinant virus event occurred in 35 the area before this period. The presence of LCV-SP shows the role of recombination 36 as a driving force of evolution within the genus Crinivirus, a globally distributed, 37 emergent genus. 38 39 Introduction 3 40 Lettuce chlorosis virus (LCV) belongs to the genus Crinivirus, family 41 Closteroviridae. Viruses included in this family are the largest among the known plant 42 viruses and present ssRNA, positive-sense genome [1]. Family Closteroviridae has been 43 classified in three genera based on vector transmission and phylogenetic relationships: 44 Closterovirus, Ampelovirus, and Crinivirus. Recently, a new genus named Velarivirus 45 has been proposed [2]. All members of genus Crinivirus include segmented genomes, 46 are whitefly-transmitted and limited to the phloem [3]. 47 Many members of genus Crinivirus are considered emerging epidemics worldwide [4]. 48 LCV was described in the 1990´s in California, transmitted by the whitefly Bemisia 49 tabaci and affecting lettuce and sugar beet crops [5]. The complete sequence and the 50 genomic organization of LCV were described in 2009 by [6] and comprises a bipartite 51 genome formed by RNA1 and RNA2. LCV RNA1 contains the replication module (ORFs 52 1a and 1b), which encodes conserved domains of a papain-like leader proteinase (P-53 PRo), a methyltransferase (MTR), helicase (HEL) and RNA-dependent RNA polymerase 54 (RdRp), ORF2 encodes a putative 8-kDa protein (P8), and ORF3 encodes a 22.9-kDa 55 protein (P23) recently described as viral suppressor of RNA silencing [7]. LCV RNA2 56 contains the hallmark Closterovirus gene array ...

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“…On the other hand, negative-sense vsiRNAs prevailed over positive ones in all populations aligning to EnHV1. This is in contrast with most plant virus examples ( Donaire et al, 2009 ; Velasco et al, 2015 ; Cretazzo and Velasco, 2017 ).…”

Section: Discussionmentioning

confidence: 73%

A Novel Hypovirus Species From Xylariaceae Fungi Infecting Avocado

et al. 2018

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The white rot root disease caused by Rosellinia necatrix is a major concern for avocado cultivation in Spain. Healthy escapes of avocado trees surrounded by diseased trees prompted us to hypothesize the presence of hypovirulent R. necatrix due to mycovirus infections. Recently, we reported the presence of another fungal species, Entoleuca sp., belonging to the Xylariaceae, that was also found in healthy avocado trees and frequently co-infecting the same roots than R. necatrix. We investigated the presence of mycoviruses that might explain the hypovirulence. For that, we performed deep sequencing of dsRNAs from two isolates of Entoleuca sp. that revealed the simultaneous infection of several mycoviruses, not described previously. In this work, we report a new member of the Hypoviridae, tentatively named Entoleuca hypovirus 1 (EnHV1). The complete genome sequence was obtained for two EnHV1 strains, which lengths resulted to be 14,958 and 14,984 nt, respectively, excluding the poly(A) tails. The genome shows two ORFs separated by a 32-nt inter-ORF, and both 5′- and 3′-UTRs longer than any other hypovirus reported to date. The analysis of virus-derived siRNA populations obtained from Entoleuca sp. demonstrated antiviral silencing activity in this fungus. We screened a collection of Entoleuca sp. and R. necatrix isolates and found that EnHV1 was present in both fungal species. A genetic population analysis of EnHV1 strains revealed the presence of two main clades, each of them including members from both Entoleuca sp. and R. necatrix, which suggests intra- and interspecific virus transmission in the field. Several attempts failed to cure Entoleuca sp. from EnHV1. However, all Entoleuca sp. isolates collected from avocado, whether harboring the virus or not, showed hypovirulence. Conversely, all R. necatrix isolates were pathogenic to that crop, regardless of being infected by EnHV1.

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High‐throughput sequencing allowed the completion of the genome of grapevine Red Globe virus and revealed recurring co‐infection with other tymoviruses in grapevine

Cited by 17 publications

References 29 publications

First natural crossover recombination between two distinct species of the family Closteroviridae leads to the emergence of a new disease

First natural crossover recombination between two distinct species of the family Closteroviridae leads to the emergence of a new disease

First natural crossover recombination of intact ORFs between two distinct species of the familyClosteroviridae

A Novel Hypovirus Species From Xylariaceae Fungi Infecting Avocado

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