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Pathogens
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Plant Virus Genome Diversity in Plant Hosts and Insect Vectors
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Plant Virus Genome Diversity in Plant Hosts and Insect Vectors

A special issue of Pathogens (ISSN 2076-0817). This special issue belongs to the section "Viral Pathogens".

Deadline for manuscript submissions: closed (10 November 2023) | Viewed by 18916

Special Issue Editors

Dr. Ralf Georg Dietzgen

E-Mail Website
Guest Editor
Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD 4072, Australia
Interests: virus evolution and epidemiology; negative-sense RNA viruses; plant virus control; virus taxonomy
Special Issues, Collections and Topics in MDPI journals
Dr. Nicolas Bejerman

E-Mail Website
Guest Editor
Unit of Phytopathology and Agricultural Modelling, CONICET-INTA, Cordoba 5119, Argentina
Interests: virus evolution; negative-sense RNA viruses; DNA viruses; virus taxonomy; virome characterization
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Viruses have been found in association with all forms of life, but their true distribution and genetic diversity remain unclear. So far, we may have discovered only the tip of the iceberg of global viral genetic diversity. The emerging knowledge of viral diversity will have significant effects on biosecurity, food security, disease control, and potential future epidemics.

Plant viruses were initially identified and characterized as causing distinct disease symptoms in crop and ornamental plants and leading to economic losses in yield and quality. High-throughput sequencing technologies have now enabled the identification of viruses in environmental samples and host transcriptomes independent of disease symptoms and without prior sequence knowledge. This has allowed the identification of plant-associated viromes consisting of both known and novel, acute and persistent viruses and has helped to refine virus classification and taxonomy.

This Special Issue aims to highlight continuing advances in our knowledge of genetic diversity and evolution of viruses associated with plant hosts, their endophytes, and fungal and arthropod vectors. We welcome original research articles, technical advances, and review articles on the identification, diagnosis, genetic diversity, phylogenetic characterization, and interactions of viruses associated with plant metagenomes.

Dr. Ralf Georg Dietzgen
Dr. Nicolas Bejerman
Guest Editors

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Keywords

  • genetic diversity
  • virus evolution
  • virus diagnostics
  • virus taxonomy
  • virus phylogeny
  • plants
  • fungi
  • arthropods
  • virus vectors

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Published Papers (7 papers)

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Research

8 pages, 627 KiB  
Communication
Evidence for Dicot Plants as Alternative Hosts of Banana Bunchy Top Virus and Its Alphasatellites in South-East Asia
by Valentin Guyot, Ngoc-Sam Ly, Tien-Dung Trieu, Oudomphone Insisiengmay, Ting Zhang, Marie-Line Iskra-Caruana, BforBB Consortium and Mikhail M. Pooggin
Pathogens 2023, 12(11), 1289; https://doi.org/10.3390/pathogens12111289 - 28 Oct 2023
Cited by 1 | Viewed by 2355
Abstract
Banana bunchy top virus is a multicomponent circular ssDNA virus (family Nanoviridae) that causes one of the most devastating diseases of cultivated bananas and plantains (family Musaceae). It is transmitted by the aphids Pentalonia nigronervosa and P. caladii among host plants of [...] Read more.
Banana bunchy top virus is a multicomponent circular ssDNA virus (family Nanoviridae) that causes one of the most devastating diseases of cultivated bananas and plantains (family Musaceae). It is transmitted by the aphids Pentalonia nigronervosa and P. caladii among host plants of Musaceae and some other families of monocots. Our Illumina sequencing reconstruction of virome components of BBTV-infected banana plants and their neighbor non-banana plants sampled in Vietnam and Laos revealed the monocot Commelina sp. (Commelinaceae) and the dicots Bidens pilosa and Chromolaena odorata (both Asteraceae) as hosts of BBTV and circular ssDNA alphasatellites (family Alphasatellitidae). Counting the proportions and relative abundances of Illumina reads representing BBTV genome components and alphasatellites suggested that Chromolaena and Commelina are poor hosts for BBTV and one to three alphasatellite species, whereas Bidens is a permissive host for BBTV and four alphasatellite species representing two genera of Alphasatellitidae. Our findings provide evidence for the dicot plants of family Asteraceae as alternative hosts of BBTV and its alphasatellites, which warrants further investigation of these and other dicots as a potential refuge and source of BBTV and multiple alphasatellites that become associated with this virus and likely affect its replication, transmission, and host range. Full article
(This article belongs to the Special Issue Plant Virus Genome Diversity in Plant Hosts and Insect Vectors)
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19 pages, 3818 KiB  
Article
Discovery and Genome Characterization of a Closterovirus from Wheat Plants with Yellowing Leaf Symptoms in Japan
by Hideki Kondo, Hitomi Sugahara, Miki Fujita, Kiwamu Hyodo, Ida Bagus Andika, Hiroshi Hisano and Nobuhiro Suzuki
Pathogens 2023, 12(3), 358; https://doi.org/10.3390/pathogens12030358 - 21 Feb 2023
Cited by 1 | Viewed by 3160
Abstract
Many aphid-borne viruses are important pathogens that affect wheat crops worldwide. An aphid-transmitted closterovirus named wheat yellow leaf virus (WYLV) was found to have infected wheat plants in Japan in the 1970s; however, since then, its viral genome sequence and occurrence in the [...] Read more.
Many aphid-borne viruses are important pathogens that affect wheat crops worldwide. An aphid-transmitted closterovirus named wheat yellow leaf virus (WYLV) was found to have infected wheat plants in Japan in the 1970s; however, since then, its viral genome sequence and occurrence in the field have not been investigated. We observed yellowing leaves in the 2018/2019 winter wheat-growing season in an experimental field in Japan where WYLV was detected five decades ago. A virome analysis of those yellow leaf samples lead to the discovery of a closterovirus together with a luteovirus (barley yellow dwarf virus PAV variant IIIa). The complete genomic sequence of this closterovirus, named wheat closterovirus 1 isolate WL19a (WhCV1-WL19a), consisted of 15,452 nucleotides harboring nine open reading frames. Additionally, we identified another WhCV1 isolate, WL20, in a wheat sample from the winter wheat-growing season of 2019/2020. A transmission test indicated that WhCV1-WL20 was able to form typical filamentous particles and transmissible by oat bird-cherry aphid (Rhopalosiphum pad). Sequence and phylogenetic analyses showed that WhCV1 was distantly related to members of the genus Closterovirus (family Closteroviridae), suggesting that the virus represents a novel species in the genus. Furthermore, the characterization of WhCV1-WL19a-derived small RNAs using high-throughput sequencing revealed highly abundant 22-nt-class small RNAs potentially derived from the 3′-terminal end of the WhCV1 negative-strand genomic RNA, indicating that this terminal end of the WhCV1 genome is likely particularly targeted for the synthesis of viral small RNAs in wheat plants. Our results provide further knowledge on closterovirus diversity and pathogenicity and suggest that the impact of WhCV1 on wheat production warrants further investigations. Full article
(This article belongs to the Special Issue Plant Virus Genome Diversity in Plant Hosts and Insect Vectors)
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13 pages, 2376 KiB  
Communication
Analysis of Hop Stunt Viroid Diversity in Grapevine (Vitis vinifera L.) in Slovakia: Coexistence of Two Particular Genetic Groups
by Peter Alaxin, Lukáš Predajňa, Adam Achs, Zdeno Šubr, Michaela Mrkvová and Miroslav Glasa
Pathogens 2023, 12(2), 205; https://doi.org/10.3390/pathogens12020205 - 28 Jan 2023
Cited by 2 | Viewed by 2283
Abstract
The hop stunt viroid (HSVd) is a widespread subviral pathogen infecting a broad spectrum of plant hosts including grapevine (Vitis vinifera L.). Despite its omnipresence in virtually all grapevine growing areas around the world, molecular data characterizing HSVd populations are missing from [...] Read more.
The hop stunt viroid (HSVd) is a widespread subviral pathogen infecting a broad spectrum of plant hosts including grapevine (Vitis vinifera L.). Despite its omnipresence in virtually all grapevine growing areas around the world, molecular data characterizing HSVd populations are missing from Slovakia. Analysis of the complete nucleotide sequences of 19 grapevine variants revealed the existence of two genetic HSVd groups in Slovakia (internally named the “6A” and “7A” groups based on the particular stretch of adenines at nucleotide positions 39–44/45, respectively). Despite their sampling at different times in various unrelated vineyards, the 6A and 7A groups are characterized by low intra-group divergence (~0.3 and 0.2%, respectively). On the other hand, inter-group divergence reached 2.2% due to several mutations, seven of which were found to be group-specific and mainly (except for one) located in the region of the pathogenic domain. Interestingly, in addition to their frequent co-existence within the same geographical location, the mixed infection of the 6A and 7A type sequence variants was also unequivocally and repeatedly proven within single grapevine plants. The RNA secondary structure analysis of representative isolates from each of these two genetic groups indicated a potential compensatory explanation of such mutations. These group-specific sites could be pointing towards the evolutionary selection linked to the necessity of the viroid to retain its structural conformational integrity, crucial for its functional biochemical ability to interact with specific grapevine cellular host factors required for HSVd propagation. Full article
(This article belongs to the Special Issue Plant Virus Genome Diversity in Plant Hosts and Insect Vectors)
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21 pages, 2268 KiB  
Article
Genetic Diversity of Viral Populations Associated with Ananas Germplasm and Improvement of Virus Diagnostic Protocols
by Adriana E. Larrea-Sarmiento, Alejandro Olmedo-Velarde, Xupeng Wang, Wayne Borth, Ryan Domingo, Tracie K. Matsumoto, Jon Y. Suzuki, Marisa M. Wall, Michael J. Melzer and John Hu
Pathogens 2022, 11(12), 1470; https://doi.org/10.3390/pathogens11121470 - 5 Dec 2022
Cited by 4 | Viewed by 2417
Abstract
Pineapple (Ananas comosus L. [Merr.]) accessions from the U.S. Tropical Plant Genetic Resources and Disease Research (TPGRDR) in Hilo, Hawaii were subjected to RNA-sequencing to study the occurrence of viral populations associated with this vegetatively propagated crop. Analysis of high-throughput sequencing data [...] Read more.
Pineapple (Ananas comosus L. [Merr.]) accessions from the U.S. Tropical Plant Genetic Resources and Disease Research (TPGRDR) in Hilo, Hawaii were subjected to RNA-sequencing to study the occurrence of viral populations associated with this vegetatively propagated crop. Analysis of high-throughput sequencing data obtained from 24 germplasm accessions and public domain transcriptome shotgun assembly (TSA) data identified two novel sadwaviruses, putatively named “pineapple secovirus C” (PSV-C) and “pineapple secovirus D” (PSV-D). They shared low amino acid sequence identity (from 34.8 to 41.3%) compared with their homologs in the Pro-pol region of the previously reported PSV-A and PSV-B. The complete genome (7485 bp) corresponding to a previously reported partial sequence of the badnavirus, pineapple bacilliform ER virus (PBERV), was retrieved from one of the datasets. Overall, we discovered a total of 69 viral sequences representing ten members within the Ampelovirus, Sadwavirus, and Badnavirus genera. Genetic diversity and recombination events were found in members of the pineapple mealybug wilt-associated virus (PMWaV) complex as well as PSVs. PMWaV-1, -3, and -6 presented recombination events across the quintuple gene block, while no recombination events were found for PMWaV-2. High recombination frequency of the RNA1 and RNA2 molecules from PSV-A and PSV-B were congruent with the diversity found by phylogenetic analyses. Here, we also report the development and improvement of RT-PCR diagnostic protocols for the specific identification and detection of viruses infecting pineapple based on the diverse viral populations characterized in this study. Given the high occurrence of recombination events, diversity, and discovery of viruses found in Ananas germplasm, the reported and validated RT-PCR assays represent an important advance for surveillance of viral infections of pineapple. Full article
(This article belongs to the Special Issue Plant Virus Genome Diversity in Plant Hosts and Insect Vectors)
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16 pages, 1746 KiB  
Article
Characterizing the Virome of Apple Orchards Affected by Rapid Decline in the Okanagan and Similkameen Valleys of British Columbia (Canada)
by Huogen Xiao, Wenjia Hao, Gavin Storoschuk, Jesse L. MacDonald and Hélène Sanfaçon
Pathogens 2022, 11(11), 1231; https://doi.org/10.3390/pathogens11111231 - 25 Oct 2022
Cited by 12 | Viewed by 2538
Abstract
Rapid apple decline disease (RAD) has been affecting orchards in the USA and Canada. Although the primary cause for RAD remains unknown, viruses may contribute to the incidence or severity of the disease. We examined the diversity and prevalence of viruses in orchards [...] Read more.
Rapid apple decline disease (RAD) has been affecting orchards in the USA and Canada. Although the primary cause for RAD remains unknown, viruses may contribute to the incidence or severity of the disease. We examined the diversity and prevalence of viruses in orchards affected by RAD in the Okanagan and Similkameen Valleys (British Columbia, Canada). Next-generation sequencing identified 20 previously described plant viruses and one viroid, as well as a new ilarvirus, which we named apple ilarvirus 2 (AIV2). AIV2 was related to subgroup 2 ilarviruses (42–71% nucleotide sequence identity). RT-PCR assays of 148 individual leaf samples revealed frequent mixed infections, with up to eight viruses or viroid detected in a single tree. AIV2 was the most prevalent, detected in 64% of the samples. Other prevalent viruses included three ubiquitous viruses from the family Betaflexiviridae and citrus concave gum-associated virus. Apple rubbery wood virus 1 and 2 and apple luteovirus 1 were also readily detected. The thirteen most prevalent viruses/viroid were detected not only in trees displaying typical RAD symptoms, but also in asymptomatic trees. When compared with reports from orchards affected by RAD in Pennsylvania, New York State, and Washington State, regional differences in relative virus prevalence were noted. Full article
(This article belongs to the Special Issue Plant Virus Genome Diversity in Plant Hosts and Insect Vectors)
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17 pages, 3500 KiB  
Article
Unlocking the Hidden Genetic Diversity of Varicosaviruses, the Neglected Plant Rhabdoviruses
by Nicolas Bejerman, Ralf G. Dietzgen and Humberto Debat
Pathogens 2022, 11(10), 1127; https://doi.org/10.3390/pathogens11101127 - 29 Sep 2022
Cited by 14 | Viewed by 2263
Abstract
The genus Varicosavirus is one of six genera of plant-infecting rhabdoviruses. Varicosaviruses have non-enveloped, flexuous, rod-shaped virions and a negative-sense, single-stranded RNA genome. A distinguishing feature of varicosaviruses, which is shared with dichorhaviruses, is a bi-segmented genome. Before 2017, a sole varicosavirus was [...] Read more.
The genus Varicosavirus is one of six genera of plant-infecting rhabdoviruses. Varicosaviruses have non-enveloped, flexuous, rod-shaped virions and a negative-sense, single-stranded RNA genome. A distinguishing feature of varicosaviruses, which is shared with dichorhaviruses, is a bi-segmented genome. Before 2017, a sole varicosavirus was known and characterized, and then two more varicosaviruses were identified through high-throughput sequencing in 2017 and 2018. More recently, the number of known varicosaviruses has substantially increased in concert with the extensive use of high-throughput sequencing platforms and data mining approaches. The novel varicosaviruses have revealed not only sequence diversity, but also plasticity in terms of genome architecture, including a virus with a tentatively unsegmented genome. Here, we report the discovery of 45 novel varicosavirus genomes which were identified in publicly available metatranscriptomic data. The identification, assembly, and curation of the raw Sequence Read Archive reads has resulted in 39 viral genome sequences with full-length coding regions and 6 with nearly complete coding regions. The highlights of the obtained sequences include eight varicosaviruses with unsegmented genomes, which are linked to a phylogenetic clade associated with gymnosperms. These findings have resulted in the most complete phylogeny of varicosaviruses to date and shed new light on the phylogenetic relationships and evolutionary landscape of this group of plant rhabdoviruses. Thus, the extensive use of sequence data mining for virus discovery has allowed us to unlock of the hidden genetic diversity of varicosaviruses, the largely neglected plant rhabdoviruses. Full article
(This article belongs to the Special Issue Plant Virus Genome Diversity in Plant Hosts and Insect Vectors)
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10 pages, 1700 KiB  
Article
Complete Genomic RNA Sequence of Tuberose Mild Mosaic Virus and Tuberose Mild Mottle Virus Acquired by High-Throughput Sequencing
by Malyaj R. Prajapati, Aakansha Manav, Pankhuri Singhal, Venkidusamy K. Sidharthan, Ujjwal Sirohi, Mukesh Kumar, Mahesh Kumar Bharti, Jitender Singh, Pankaj Kumar, Ravindra Kumar, Satya Prakash and Virendra Kumar Baranwal
Pathogens 2022, 11(8), 861; https://doi.org/10.3390/pathogens11080861 - 30 Jul 2022
Cited by 4 | Viewed by 2459
Abstract
Tuberose (Polianthes tuberosa) is an ornamental flowering crop of the Amaryllidaceae family. Tuberose mild mosaic virus (TuMMV) and tuberose mild mottle virus (TuMMoV), members of the genus Potyvirus, are ubiquitously distributed in most tuberose growing countries worldwide with low biological [...] Read more.
Tuberose (Polianthes tuberosa) is an ornamental flowering crop of the Amaryllidaceae family. Tuberose mild mosaic virus (TuMMV) and tuberose mild mottle virus (TuMMoV), members of the genus Potyvirus, are ubiquitously distributed in most tuberose growing countries worldwide with low biological incidence. Here, we report the first coding-complete genomic RNA of TuMMV and TuMMoV obtained through high-throughput sequencing (HTS) and further, the presence of both the viruses were confirmed using virus-specific primers in RT-PCR assays. Excluding the poly (A) tail, the coding-complete genomic RNA of TuMMV and TuMMoV was 9485 and 9462 nucleotides (nts) in length, respectively, and contained a single large open reading frame (ORF). Polyprotein encoded by both the viral genomes contained nine putative cleavage sites. BLASTn analysis of TuMMV and TuMMoV genomes showed 72.40–76.80% and 67.95–77% nucleotide sequence similarities, respectively, with the existing potyviral sequences. Phylogenetic analysis based on genome sequences showed that TuMMV and TuMMoV clustered in a distinct clade to other potyviruses. Further studies are required to understand the mechanism of symptom development, distribution, genetic variability, and their possible threat to tuberose production in India. Full article
(This article belongs to the Special Issue Plant Virus Genome Diversity in Plant Hosts and Insect Vectors)
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