Complete genome sequence of cnidium virus 1, a novel betanucleorhabdovirus infecting Cnidium officinale

Belete, Mesele Tilahun; Igori, Davaajargal; Kim, Se Eun; Lee, Su-Heon; Moon, Jae Sun

doi:10.1007/s00705-021-05348-9

Cited by 9 publications

(13 citation statements)

References 7 publications

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“…Total RNA was extracted from pooled asymptomatic and dwarfed samples as previously described [ 3 , 4 ]. An easy-spin™ Total RNA Isolation Kit (iNtRON Biotechnology, Sangdaewon-dong, South Korea) was used to extract RNA according to the manufacturer’s protocol.…”

Section: Methodsmentioning

confidence: 99%

“…Trimmomatic (v0.38) and the sliding window method [ 44 ] were used to remove including adapter sequences and low-quality reads (Phred < 30) [ 45 ]. The de novo assembly of the trimmed reads was performed using Trinity (vr20140717) [ 4 ]. The trimmed reads for each library were mapped to the assembled reference sequence ( https://www.ncbi.nlm.nih.gov/genomes/GenomesGroup.cgi?taxid=10239 ; retrieved in July 2021) using Bowtie 1.1.2 [ 44 ].…”

Section: Methodsmentioning

confidence: 99%

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Deciphering the virome of Chunkung (Cnidium officinale) showing dwarfism-like symptoms via a high-throughput sequencing analysis

Belete,

Kim,

Gudeta

et al. 2024

Virol J

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Background Viruses have notable effects on agroecosystems, wherein they can adversely affect plant health and cause problems (e.g., increased biosecurity risks and economic losses). However, our knowledge of their diversity and interactions with specific host plants in ecosystems remains limited. To enhance our understanding of the roles that viruses play in agroecosystems, comprehensive analyses of the viromes of a wide range of plants are essential. High-throughput sequencing (HTS) techniques are useful for conducting impartial and unbiased investigations of plant viromes, ultimately forming a basis for generating further biological and ecological insights. This study was conducted to thoroughly characterize the viral community dynamics in individual plants. Results An HTS-based virome analysis in conjunction with proximity sampling and a tripartite network analysis were performed to investigate the viral diversity in chunkung (Cnidium officinale) plants. We identified 61 distinct chunkung plant-associated viruses (27 DNA and 34 RNA viruses) from 21 known genera and 6 unclassified genera in 14 known viral families. Notably, 12 persistent viruses (7 DNA and 5 RNA viruses) were exclusive to dwarfed chunkung plants. The detection of viruses from the families Partitiviridae, Picobirnaviridae, and Spinareoviridae only in the dwarfed plants suggested that they may contribute to the observed dwarfism. The co-infection of chunkung by multiple viruses is indicative of a dynamic and interactive viral ecosystem with significant sequence variability and evidence of recombination. Conclusions We revealed the viral community involved in chunkung. Our findings suggest that chunkung serves as a significant reservoir for a variety of plant viruses. Moreover, the co-infection rate of individual plants was unexpectedly high. Future research will need to elucidate the mechanisms enabling several dozen viruses to co-exist in chunkung. Nevertheless, the important insights into the chunkung virome generated in this study may be relevant to developing effective plant viral disease management and control strategies.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Deciphering the virome of Chunkung (Cnidium officinale) showing dwarfism-like symptoms via a high-throughput sequencing analysis

Belete,

Kim,

Gudeta

et al. 2024

Virol J

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“…• Betanucleorhabdovirus asclepiadis for Asclepias syriaca virus 2 (AscSyV2) discovered by HTS in common milkweed (apocynaceaen Asclepias syriaca L.) sampled in Illinois, USA [29]; • Betanucleorhabdovirus cnidii for Cnidium virus 1 (CnV1) discovered by HTS in apiaceaen Cnidium officinale Makino plants sampled in South Korea [32]; • Betanucleorhabdovirus plectranthi for Plectranthus aromaticus virus 1 (PleArV1) discovered by HTS in Cuban oregano (lamiaceaen Coleus amboinicus Lour.) sampled in Malaysia [29]; and • Betanucleorhabdovirus rhododendri for Rhododendon delavayi virus 1 (RhoDeV1) discovered by HTS in red rhododendron (ericaceaen Rhododendron arboreum delavayi Franchet) sampled in Yúnnán Province (云南省), China [29].…”

Section: Family Rhabdoviridaementioning

confidence: 99%

Annual (2023) taxonomic update of RNA-directed RNA polymerase-encoding negative-sense RNA viruses (realm Riboviria: kingdom Orthornavirae: phylum Negarnaviricota)

Kuhn

Abe

Adkins

et al. 2023

Journal of General Virology

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In April 2023, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. The phylum was expanded by one new family, 14 new genera, and 140 new species. Two genera and 538 species were renamed. One species was moved, and four were abolished. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV.

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“…To date, six viruses have been identified in Cnidium officinale ( 3 – 7 ). However, the first published South Korean ASGV isolate recovered from C. officinale has only been partially sequenced (GenBank accession numbers MW889883 and MW889884 ).…”

Section: Announcementmentioning

confidence: 99%

Complete Genome Sequences of Two Apple Stem Grooving Viruses in Cnidium officinale in Korea

Lee

Kim

et al. 2023

Microbiol Resour Announc

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Complete genome sequence of cnidium virus 1, a novel betanucleorhabdovirus infecting Cnidium officinale

Cited by 9 publications

References 7 publications

Deciphering the virome of Chunkung (Cnidium officinale) showing dwarfism-like symptoms via a high-throughput sequencing analysis

Deciphering the virome of Chunkung (Cnidium officinale) showing dwarfism-like symptoms via a high-throughput sequencing analysis

Annual (2023) taxonomic update of RNA-directed RNA polymerase-encoding negative-sense RNA viruses (realm Riboviria: kingdom Orthornavirae: phylum Negarnaviricota)

Complete Genome Sequences of Two Apple Stem Grooving Viruses in Cnidium officinale in Korea

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