Complete genome sequence of a novel capillovirus infecting Hevea brasiliensis in China

Li, Zhaotong; Wang, Hongxing; Zhao, Ruibai; Zhang, Ze; Zhang, Xia; Zhai, Jinling; Huang, Xi

doi:10.1007/s00705-019-04459-8

Cited by 12 publications

(10 citation statements)

References 13 publications

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“…Taxonomic assignation for each accession was annotated based on currently accepted species [12]. For accessions that correspond to not yet recognized species, taxonomic assignation was annotated based on relevant publications [6, 10, 13–38], GenBank/EMBL/DDBJ description and blast [39] analyses. Complete Rep and CP aa sequences were extracted using Geneious R8.1.9.…”

Section: Methodsmentioning

confidence: 99%

Virus classification based on in-depth sequence analyses and development of demarcation criteria using the Betaflexiviridae as a case study

Silva

Melo

Elena

et al. 2022

Journal of General Virology

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Currently, many viruses are classified based on their genome organization and nucleotide/amino acid sequence identities of their capsid and replication-associated proteins. Although biological traits such as vector specificities and host range are also considered, this later information is scarce for the majority of recently identified viruses, characterized only from genomic sequences. Accordingly, genomic sequences and derived information are being frequently used as the major, if not only, criteria for virus classification and this calls for a full review of the process. Herein, we critically addressed current issues concerning classification of viruses in the family Betaflexiviridae in the era of high-throughput sequencing and propose an updated set of demarcation criteria based on a process involving pairwise identity analyses and phylogenetics. The proposed framework has been designed to solve the majority of current conundrums in taxonomy and to facilitate future virus classification. Finally, the analyses performed herein, alongside the proposed approaches, could be used as a blueprint for virus classification at-large.

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Section: Methodsmentioning

confidence: 99%

Virus classification based on in-depth sequence analyses and development of demarcation criteria using the Betaflexiviridae as a case study

Silva

Melo

Elena

et al. 2022

Journal of General Virology

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“…To date, there have been four reports of natural viral infections in rubber trees, but the exact etiology of these viruses remains unconfirmed ( Gama et al, 1983 ; Fonseca et al, 2018 ; Li et al, 2020 ; Chen et al, 2022 ). The first documented virus to infect rubber trees, belonging to the genus Carlavirus of the family Betaflexiviridae , was found in stunted seedlings displaying inter-veinal chlorosis, suggesting an association with leaf disease ( Gama et al, 1983 ).…”

Section: Introductionmentioning

confidence: 99%

“…High-throughput RNA sequencing (RNA-seq) technologies have been applied to identify pathogenic microorganisms in affected plants ( Wu et al, 2015 ). In an effort to identify potential causal agents of TPD, a comparative transcriptome analysis of TPD-affected and healthy bark samples collected from Hainan, China, led to the discovery and identification of two viruses: Rubber tree virus 1 (RTV1) and Rubber tree latent virus 1 (RTLV1), previously annotated as Cherry virus A (CVA) and Tobacco mosaic virus (TMV), respectively ( Li et al, 2020 ; Chen et al, 2022 ). RTV1 is a member of the genus Capillovirus of family Betaflexiviridae , encoding two overlapping open reading frames (ORF) corresponding to a replicase-coat protein (CP) fusion polyprotein and a movement protein (MP), respectively.…”

Section: Introductionmentioning

confidence: 99%

“…RTV1 is a member of the genus Capillovirus of family Betaflexiviridae , encoding two overlapping open reading frames (ORF) corresponding to a replicase-coat protein (CP) fusion polyprotein and a movement protein (MP), respectively. Complete genome of RTV1 consists of 6,811 nucleotides (nt), excluding the poly(A) tail ( Li et al, 2020 ). Although both RTV1 and RTLV1 were identified from TPD-affected barks, infection of RTLV1 was considered to be asymptomatic, as it could be detected in 35 of 44 healthy trees.…”

Section: Introductionmentioning

confidence: 99%

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Identification and characterization of two closely related virga-like viruses latently infecting rubber trees (Hevea brasiliensis)

Zhao,

Su,

et al. 2023

Front. Microbiol.

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A novel virga-like virus, provisionally named Rubber tree latent virus 2 (RTLV2), was identified from rubber tree (Hevea brasiliensis). It is a close relative of the previously reported Rubber tree latent virus 1 (RTLV1). The complete genomes of RTLV1 and RTLV2 were sequenced and comparatively analyzed in terms of genome organization, putative gene products and phylogenetic relationship. Both RTLV1 and RTLV2 have positive-sense single-stranded RNA genomes that encode seven open reading frames (ORFs), forming a similar genomic layout. In phylogenetic analyses based on replicase and coat protein amino acid sequences, RTLV1 and RTLV2 were clustered with unclassified virga-like viruses. They are distinct from currently recognized plant virus families. RTLV1 and RTLV2 can be distinguished from members of Virgaviridae by the presence of a putative coat protein duplex and a poly(A) tail at the 3′-terminus. The authenticity of RTLV1 and RTLV2 as infectious viruses was confirmed through field investigations and transmissibility assays. In conclusion, RTLV1 and RTLV2 represent a novel plant virus group that does not readily fit into current virus families.

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“…RTV1 has emerged as a deleterious pathogen of the genus capillovirus in the family Betaflexiviridae. The genomic organization of the RTV1 is consisted of monopartite, linear, non-enveloped, +ssRNA molecule of 6811 nucleotides [3].…”

Section: Introductionmentioning

confidence: 99%

Computational Biology and Machine Learning Approaches to Identify the Rubber Tree (Hevea brasiliensis L.) Genome Encoded Potential MicroRNAs Targeting Rubber Tree Virus 1

Ashraf¹,

Tariq²,

Khan³

et al. 2022

Preprint

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Tapping panel dryness (TPD) syndrome is a complex disease of Rubber tree (Hevea brasiliensis L.) which causes cessation of latex drainage upon tapping of rubber tree. Rubber tree virus (RTV1) was identified as a novel pathogen associated with rubber tree and a potential causal agent of TPD. RTV1 is a monopartite RNA virus that is linear, non-enveloped and has a single-stranded (ss) positive RNA genome of approximately 6081 nucleotides and is composed of two major open reading frames (ORFs), ORF1 (polyprotein), and ORF2 (movement protein. This study aimed to investigate the possibility of rubber genome encoded tree microRNAs (miRNAs) as novel therapeutic targets against RTV1 using in silico algorithms. Mature rubber tree miRNAs are retrieved from the miRBase database and are used for hybridization of RTV1 using five different five different computational algorithms including miRanda, RNA22, RNAhybrid and psRNATarget. A total of eleven common rubber tree miRNAs were identified based on consensus genomic positions. The consensus of four algorithms predicted the hybridization sites of hbr-miR396a and hbr-miR398 at common locus positions 6676, 1840 respectively. To validate the prediction, secondary structures of the consensual rubber tree miRNAs and free energy of duplex binding were calculated using the RNAfold and RNAcofold algorithms respectively. We created a plot between rubber tree miRNAs and RTV1 ORFs by using Circos algorithm. In this study, we predicted eleven consensual rubber tree miRNAs. Among these miRNAs, hbr-miR398 was identified as the most effectual miRNA that may target the ORF1 gene of the RTV1 genome. The predicted data will be important in the development of rubber trees resistant to RTV1.

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Complete genome sequence of a novel capillovirus infecting Hevea brasiliensis in China

Cited by 12 publications

References 13 publications

Virus classification based on in-depth sequence analyses and development of demarcation criteria using the Betaflexiviridae as a case study

Virus classification based on in-depth sequence analyses and development of demarcation criteria using the Betaflexiviridae as a case study

Identification and characterization of two closely related virga-like viruses latently infecting rubber trees (Hevea brasiliensis)

Computational Biology and Machine Learning Approaches to Identify the Rubber Tree (Hevea brasiliensis L.) Genome Encoded Potential MicroRNAs Targeting Rubber Tree Virus 1

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