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Padmanabhan C, Nunziata S, Leon M. G, Rivera Y, Mavrodieva VA, Nakhla MK, Roy A. High-throughput sequencing application in the detection and discovery of viruses associated with the regulated citrus leprosis disease complex. FRONTIERS IN PLANT SCIENCE 2023; 13:1058847. [PMID: 36762187 PMCID: PMC9907091 DOI: 10.3389/fpls.2022.1058847] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 11/24/2022] [Indexed: 06/18/2023]
Abstract
Citrus leprosis (CiL) is one of the destructive emerging viral diseases of citrus in the Americas. Leprosis syndrome is associated with two taxonomically distinct groups of Brevipalpus-transmitted viruses (BTVs), that consist of positive-sense Cilevirus, Higrevirus, and negative-sense Dichorhavirus. The localized CiL symptoms observed in multiple citrus species and other alternate hosts indicates that these viruses might have originated from the mites and eventually adopted citrus as a secondary host. Genetic diversity in the genomes of viruses associated with the CiL disease complex have complicated current detection and diagnostic measures that prompted the application of High-Throughput Sequencing (HTS) protocols for improved detection and diagnosis. Two cileviruses are known to infect citrus, and among them only citrus leprosis virus C2 (CiLV-C2) hibiscus strain (CiLV-C2H) has been reported in hibiscus and passion fruit in the US. Based on our current CiL disease complex hypothesis, there is a high probability that CiL disease is associated with more viruses/strains that have not yet been identified but exist in nature. To protect the citrus industry, a Ribo-Zero HTS protocol was utilized for detection of cileviruses infecting three different hosts: Citrus spp., Swinglea glutinosa, and Hibiscus rosa-sinensis. Real-time RT-PCR assays were used to identify plants infected with CiLV-C2 or CiLV-C2H or both in mixed infection in all the above-mentioned plant genera. These results were further confirmed by bioinformatic analysis using HTS generated data. In this study, we utilized HTS assay in confirmatory diagnostics to screen BTVs infecting Dieffenbachia sp. (family: Araceae), Passiflora edulis (Passifloraceae), and Smilax auriculata (Smilacaceae). Through the implementation of HTS and downstream data analysis, we detected not only the known cileviruses in the studied hosts but also discovered a new strain of CiLV-C2 in hibiscus from Colombia. Phylogenetically, the new hibiscus strain is more closely related to CiLV-C2 than the known hibiscus strain, CiLV-C2H. We propose this strain to be named as CiLV-C2 hibiscus strain 2 (CiLV-C2H2). The findings from the study are critical for citrus growers, industry, regulators, and researchers. The possible movement of CiLV-C2H2 from hibiscus to citrus by the Brevipalpus spp. warrants further investigation.
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Affiliation(s)
- Chellappan Padmanabhan
- United States Department of Agriculture (USDA), Animal Plant Health Inspection Service, Plant Protection and Quarantine, Science and Technology, Plant Pathogen Confirmatory Diagnostics Laboratory, Laurel, MD, United States
| | - Schyler Nunziata
- United States Department of Agriculture (USDA), Animal Plant Health Inspection Service, Plant Protection and Quarantine, Science and Technology, Plant Pathogen Confirmatory Diagnostics Laboratory, Laurel, MD, United States
| | | | - Yazmín Rivera
- United States Department of Agriculture (USDA), Animal Plant Health Inspection Service, Plant Protection and Quarantine, Science and Technology, Plant Pathogen Confirmatory Diagnostics Laboratory, Laurel, MD, United States
| | - Vessela A. Mavrodieva
- United States Department of Agriculture (USDA), Animal Plant Health Inspection Service, Plant Protection and Quarantine, Science and Technology, Plant Pathogen Confirmatory Diagnostics Laboratory, Laurel, MD, United States
| | - Mark K. Nakhla
- United States Department of Agriculture (USDA), Animal Plant Health Inspection Service, Plant Protection and Quarantine, Science and Technology, Plant Pathogen Confirmatory Diagnostics Laboratory, Laurel, MD, United States
| | - Avijit Roy
- United States Department of Agriculture (USDA), Animal Plant Health Inspection Service, Plant Protection and Quarantine, Science and Technology, Plant Pathogen Confirmatory Diagnostics Laboratory, Laurel, MD, United States
- United States Department of Agriculture (USDA), Agricultural Research Service, Molecular Plant Pathology Laboratory, Beltsville Agricultural Research Center, Beltsville, MD, United States
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2
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Malmstrom CM, Martin MD, Gagnevin L. Exploring the Emergence and Evolution of Plant Pathogenic Microbes Using Historical and Paleontological Sources. ANNUAL REVIEW OF PHYTOPATHOLOGY 2022; 60:187-209. [PMID: 35483672 DOI: 10.1146/annurev-phyto-021021-041830] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Biotechnological advances now permit broad exploration of past microbial communities preserved in diverse substrates. Despite biomolecular degradation, high-throughput sequencing of preserved materials can yield invaluable genomic and metagenomic data from the past. This line of research has expanded from its initial human- and animal-centric foci to include plant-associated microbes (viruses, archaea, bacteria, fungi, and oomycetes), for which historical, archaeological, and paleontological data illuminate past epidemics and evolutionary history. Genetic mechanisms underlying the acquisition of microbial pathogenicity, including hybridization, polyploidization, and horizontal gene transfer, can now be reconstructed, as can gene-for-gene coevolution with plant hosts. Epidemiological parameters, such as geographic origin and range expansion, can also be assessed. Building on published case studies with individual phytomicrobial taxa, the stage is now set for broader, community-wide studies of preserved plant microbiomes to strengthen mechanistic understanding of microbial interactions and plant disease emergence.
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Affiliation(s)
- Carolyn M Malmstrom
- Department of Plant Biology and Program in Ecology, Evolution, and Behavior, Michigan State University, East Lansing, Michigan, USA
| | - Michael D Martin
- Department of Natural History, University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Lionel Gagnevin
- Plant Health Institute of Montpellier, CIRAD, Montpellier, France;
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3
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Nishimura L, Fujito N, Sugimoto R, Inoue I. Detection of Ancient Viruses and Long-Term Viral Evolution. Viruses 2022; 14:v14061336. [PMID: 35746807 PMCID: PMC9230872 DOI: 10.3390/v14061336] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 06/15/2022] [Accepted: 06/16/2022] [Indexed: 12/22/2022] Open
Abstract
The COVID-19 outbreak has reminded us of the importance of viral evolutionary studies as regards comprehending complex viral evolution and preventing future pandemics. A unique approach to understanding viral evolution is the use of ancient viral genomes. Ancient viruses are detectable in various archaeological remains, including ancient people's skeletons and mummified tissues. Those specimens have preserved ancient viral DNA and RNA, which have been vigorously analyzed in the last few decades thanks to the development of sequencing technologies. Reconstructed ancient pathogenic viral genomes have been utilized to estimate the past pandemics of pathogenic viruses within the ancient human population and long-term evolutionary events. Recent studies revealed the existence of non-pathogenic viral genomes in ancient people's bodies. These ancient non-pathogenic viruses might be informative for inferring their relationships with ancient people's diets and lifestyles. Here, we reviewed the past and ongoing studies on ancient pathogenic and non-pathogenic viruses and the usage of ancient viral genomes to understand their long-term viral evolution.
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Affiliation(s)
- Luca Nishimura
- Human Genetics Laboratory, National Institute of Genetics, Mishima 411-8540, Japan; (L.N.); (N.F.); (R.S.)
- Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Mishima 411-8540, Japan
| | - Naoko Fujito
- Human Genetics Laboratory, National Institute of Genetics, Mishima 411-8540, Japan; (L.N.); (N.F.); (R.S.)
- Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Mishima 411-8540, Japan
| | - Ryota Sugimoto
- Human Genetics Laboratory, National Institute of Genetics, Mishima 411-8540, Japan; (L.N.); (N.F.); (R.S.)
| | - Ituro Inoue
- Human Genetics Laboratory, National Institute of Genetics, Mishima 411-8540, Japan; (L.N.); (N.F.); (R.S.)
- Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Mishima 411-8540, Japan
- Correspondence: ; Tel.: +81-55-981-6795
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Dey K, Velez-Climent M, Padmanabhan C, Nunziata S, Rivera Y, McVay J, Roy A. Smilax auriculata: A new host for Orchid fleck dichorhavirus identified in Florida, USA. PLANT DISEASE 2021; 106:2271. [PMID: 34931891 DOI: 10.1094/pdis-09-21-2085-pdn] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
In June 2020, Orchid fleck virus (OFV) was detected in a species of Liriope in Leon and Alachua County, Florida (Fife et al; 2021). In October of the same year, four adjacent dune/ear-leaf greenbrier vines, Smilax auriculata (Smilaceae: Liliales), showed yellowing and mottling symptoms (Figure 1). Infected and healthy S. auriculata leaves samples were collected in Alachua County by the Florida Department of Agriculture and Consumer Services, Gainesville, Florida. OFV primers successfully detected in four Smilax samples by conventional RT-PCR assay. Amplicon sequences (Acc. No. MZ645935 and MZ645938) shared 99% nucleotide identity with OFV infecting orchids (LC222629) and citrus (MK522804). The OFV subgroup I (OFV-Orc1) and subgroup II (OFV-Orc2) specific primers (Kondo et al 2017) were utilized to confirm the presence of OFV type strains infecting Smilax. Sanger sequencing of subgroup I specific amplicons (MZ645934) shared 99% nucleotide identity with OFV-Orc1 (LC222629) whereas subgroup II specific amplicon sequence (MZ645930) shared 98-99 % nucleotide identity with OFV-Orc2 (AB244417). Further confirmation was done by USDA-APHIS-PPQ-Plant Pathogen Confirmatory Diagnostics Laboratory utilizing optimized conventional RT-PCR protocols (Roy et al. 2020) and deep sequencing on a on a NextSeq550 Illumina platform. Assembled reads identified seven non-overlapping viral contigs. Five RNA1 and two RNA2 contigs covered more than 97% of the bipartite OFV genome with average coverage depth of 5297.61 and 5186.04, respectively. Contigs of RNA1 and RNA2 shared 98-99% nt identity to OFV-Orc2-RNA1 (AB244417) and OFV-Orc-RNA2 (AB244418 and LC222630). No other pathogen sequences were identified. This is the first time the genus Smilax has been identified as a natural host of OFV. Very recent findings of OFV-Orc in Florida in Liriope, Aspidistra, and Ophiopogon among the Asparagaceae family members (Fife et al; 2021) and now in the Smilacaceae suggest a broader host range of the virus than previously known; further research should be conducted to better characterize the potential risk of introduction into citrus in Florida.
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Affiliation(s)
- Kishore Dey
- Florida Department of Agriculture and Consumer Services, 70124, 1911 SW 34 street,, Gainesville, Gainesville, Florida, United States, 32608
- United States;
| | - Maria Velez-Climent
- Florida Department of Agriculture and Consumer Services, 70124, Gainesville, Florida, United States;
| | - Chellappan Padmanabhan
- USDA, Animal Plant Health Inspection Service; Plant Protection and Quarantine, Science and Technology, Plant Pathogen Confirmatory Diagnostics Laboratory, Laurel, Maryland, United States;
| | - Schyler Nunziata
- USDA, Animal Plant Health Inspection Service; Plant Protection and Quarantine, Science and Technology, Plant Pathogen Confirmatory Diagnostics Laboratory, National Plant Germplasm and Biotechnology Laboratory, Laurel, Maryland, United States;
| | - Yazmin Rivera
- USDA, Animal Plant Health Inspection Service; Plant Protection and Quarantine, Science and Technology, Plant Pathogen Confirmatory Diagnostics Laboratory, Laurel, Maryland, United States;
| | - John McVay
- Florida Department of Agriculture and Consumer Services, 70124, Plant Industry, 1911 Sw 34th St, Gainesville, Gainesville, Florida, United States, 32605;
| | - Avijit Roy
- USDA Agricultural Research Service, 17123, Molecular Plant Pathology Laboratory, Building 004, Room 117, BARC-West, 10300 Baltimore Avenue, Washington, District of Columbia, United States, 20250;
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Rieux A, Campos P, Duvermy A, Scussel S, Martin D, Gaudeul M, Lefeuvre P, Becker N, Lett JM. Contribution of historical herbarium small RNAs to the reconstruction of a cassava mosaic geminivirus evolutionary history. Sci Rep 2021; 11:21280. [PMID: 34711837 PMCID: PMC8553777 DOI: 10.1038/s41598-021-00518-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 10/13/2021] [Indexed: 12/30/2022] Open
Abstract
Emerging viral diseases of plants are recognised as a growing threat to global food security. However, little is known about the evolutionary processes and ecological factors underlying the emergence and success of viruses that have caused past epidemics. With technological advances in the field of ancient genomics, it is now possible to sequence historical genomes to provide a better understanding of viral plant disease emergence and pathogen evolutionary history. In this context, herbarium specimens represent a valuable source of dated and preserved material. We report here the first historical genome of a crop pathogen DNA virus, a 90-year-old African cassava mosaic virus (ACMV), reconstructed from small RNA sequences bearing hallmarks of small interfering RNAs. Relative to tip-calibrated dating inferences using only modern data, those performed with the historical genome yielded both molecular evolution rate estimates that were significantly lower, and lineage divergence times that were significantly older. Crucially, divergence times estimated without the historical genome appeared in discordance with both historical disease reports and the existence of the historical genome itself. In conclusion, our study reports an updated time-frame for the history and evolution of ACMV and illustrates how the study of crop viral diseases could benefit from natural history collections.
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Affiliation(s)
- Adrien Rieux
- CIRAD, UMR PVBMT, 97410, St Pierre, La Réunion, France.
| | - Paola Campos
- CIRAD, UMR PVBMT, 97410, St Pierre, La Réunion, France
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 Rue Cuvier, CP 50, 75005, Paris, France
| | | | - Sarah Scussel
- CIRAD, UMR PVBMT, 97410, St Pierre, La Réunion, France
| | - Darren Martin
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Observatory, Cape Town, South Africa
| | - Myriam Gaudeul
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 Rue Cuvier, CP 50, 75005, Paris, France
- Herbier national (P), Muséum national d'Histoire Naturelle, CP39, 57 Rue Cuvier, 75005, Paris, France
| | | | - Nathalie Becker
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 Rue Cuvier, CP 50, 75005, Paris, France
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6
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Otero-Colina G, Ramos-González PL, Chabi-Jesus C, Freitas-Astúa J, Tassi AD, Kitajima EW. First detection of orchid fleck virus in orchids in Mexico. Virusdisease 2021; 32:167-172. [PMID: 33969160 DOI: 10.1007/s13337-021-00676-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 02/23/2021] [Indexed: 10/21/2022] Open
Abstract
For the first time, an isolate of the dichorhavirus orchid fleck virus (OFV, family Rhabdoviridae) was found infecting an orchid plant in Mexico. The infected sample of Epidendrum veroscriptum was collected in a nursery in Lagunillas, municipality of Zihuateutla, Edo. Puebla. Mites gathered on this plant were analyzed by light and scanning electron microscopy, which consistently indicated the presence of adults of the species Brevipalpus californicus, the common vector of OFV. Viral identification was based on symptoms, cytopathology, and reverse transcriptase-PCR/sequencing of genome fragments of the RNA1 and 2 molecules. Since isolates of OFV causing citrus leprosis have been previously detected in the Mexican states of Chiapas, Querétaro, and Jalisco, we promote a pertinent discussion and thought-provoking questions regarding the epidemiology and putative evolution of OFV.
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Affiliation(s)
- Gabriel Otero-Colina
- Campus Montecillo, Colegio de Potsgraduados, 56320 Montecillo, Edo. México México
| | - Pedro Luis Ramos-González
- Laboratório de Biologia Molecular Aplicada, Instituto Biológico, Av. Conselheiro Rodrigues Alves 1252, São Paulo, SP 04014-902 Brazil
| | - Camila Chabi-Jesus
- Laboratório de Biologia Molecular Aplicada, Instituto Biológico, Av. Conselheiro Rodrigues Alves 1252, São Paulo, SP 04014-902 Brazil.,PPG Microbiologia Agrícola, ESALQ/USP, CP 9, Piracicaba, SP 13418-900 Brazil
| | - Juliana Freitas-Astúa
- Laboratório de Biologia Molecular Aplicada, Instituto Biológico, Av. Conselheiro Rodrigues Alves 1252, São Paulo, SP 04014-902 Brazil.,Embrapa Mandioca e Fruticultura, Cruz das Almas, BA 44380-000 Brazil
| | - Aline D Tassi
- Laboratório de Biologia Molecular Aplicada, Instituto Biológico, Av. Conselheiro Rodrigues Alves 1252, São Paulo, SP 04014-902 Brazil.,Departamento de Fitopatologia e Nematologia, ESALQ/USP, CP 9, Piracicaba, SP 13418-900 Brazil
| | - Elliot W Kitajima
- Departamento de Fitopatologia e Nematologia, ESALQ/USP, CP 9, Piracicaba, SP 13418-900 Brazil
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7
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Chabi-Jesus C, Ramos-González PL, Postclam-Barro M, Fontenele RS, Harakava R, Bassanezi RB, Moreira AS, Kitajima EW, Varsani A, Freitas-Astúa J. Molecular Epidemiology of Citrus Leprosis Virus C: A New Viral Lineage and Phylodynamic of the Main Viral Subpopulations in the Americas. Front Microbiol 2021; 12:641252. [PMID: 33995302 PMCID: PMC8116597 DOI: 10.3389/fmicb.2021.641252] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 04/06/2021] [Indexed: 11/13/2022] Open
Abstract
Despite the importance of viral strains/variants as agents of emerging diseases, genetic and evolutionary processes affecting their ecology are not fully understood. To get insight into this topic, we assessed the population and spatial dynamic parameters of citrus leprosis virus C (CiLV-C, genus Cilevirus, family Kitaviridae). CiLV-C is the etiological agent of citrus leprosis disease, a non-systemic infection considered the main viral disorder affecting citrus orchards in Brazil. Overall, we obtained 18 complete or near-complete viral genomes, 123 complete nucleotide sequences of the open reading frame (ORF) encoding the putative coat protein, and 204 partial nucleotide sequences of the ORF encoding the movement protein, from 430 infected Citrus spp. samples collected between 1932 and 2020. A thorough examination of the collected dataset suggested that the CiLV-C population consists of the major lineages CRD and SJP, unevenly distributed, plus a third one called ASU identified in this work, which is represented by a single isolate found in an herbarium sample collected in Asuncion, Paraguay, in 1937. Viruses from the three lineages share about 85% nucleotide sequence identity and show signs of inter-clade recombination events. Members of the lineage CRD were identified both in commercial and non-commercial citrus orchards. However, those of the lineages SJP were exclusively detected in samples collected in the citrus belt of São Paulo and Minas Gerais, the leading Brazilian citrus production region, after 2015. The most recent common ancestor of viruses of the three lineages dates back to, at least, ∼1500 years ago. Since citrus plants were introduced in the Americas by the Portuguese around the 1520s, the Bayesian phylodynamic analysis suggested that the ancestors of the main CiLV-C lineages likely originated in contact with native vegetation of South America. The intensive expansion of CRD and SJP lineages in Brazil started probably linked to the beginning of the local citrus industry. The high prevalence of CiLV-C in the citrus belt of Brazil likely ensues from the intensive connectivity between orchards, which represents a potential risk toward pathogen saturation across the region.
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Affiliation(s)
- Camila Chabi-Jesus
- Escola Superior de Agricultura "Luiz de Queiroz", University of São Paulo, São Paulo, Brazil.,Instituto Biológico/IB, São Paulo, Brazil
| | | | | | - Rafaela Salgado Fontenele
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, United States
| | | | | | - Alecio S Moreira
- Fundo de Defesa da Citricultura, Araraquara, Brazil.,Embrapa Mandioca e Fruticultura, Cruz das Almas, Brazil
| | | | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, United States.,Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Observatory, Cape Town, South Africa
| | - Juliana Freitas-Astúa
- Instituto Biológico/IB, São Paulo, Brazil.,Embrapa Mandioca e Fruticultura, Cruz das Almas, Brazil
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Olmedo Velarde A, Roy A, Padmanabhan C, Nunziata S, Nakhla MK, Melzer M. First report of orchid fleck virus associated with citrus leprosis symptoms in rough lemon (Citrus jambhiri) and mandarin (C. reticulata) the United States. PLANT DISEASE 2021; 105:2258. [PMID: 33656365 DOI: 10.1094/pdis-12-20-2736-pdn] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Citrus leprosis is an economically important disease of citrus in South and Central America. The disease can be caused by several non-systemic viruses belonging to the genera Cilevirus (family Kitaviridae) and Dichorhavirus (family Rhabdoviridae) (Roy et al. 2015; Freitas-Astúa et al. 2018). In February 2020, lesions consistent with citrus leprosis were observed on the leaves and stems of rough lemon (Citrus jambhiri) and mandarin (C. reticulata) trees in Hilo, Hawaii. Brevipalpus mites, vector of orchid fleck virus (OFV), were also present on these trees (Freitas-Astúa et al. 2018). To identify the virus associated with the symptoms, total RNA was isolated using a NucleoSpin RNA Plus kit (Macherey-Nagel) and underwent reverse transcription (RT)-PCR with two newly designed universal primers specific for dichorhaviruses (Dichora-R1-F1: 5`-CAYCACTGYGCBRTNGCWGATGA, Dichora-R1-R1: 5`-AGKATRTSWGCCATCCKGGCTATBAG). The expected ~350 bp amplicon was obtained and directly sequenced in both directions. Blastn and Blastx searches revealed that the primer-trimmed consensus sequence (MT232917) shared 99.3% nucleotide (nt) and 100% amino acid (aa) identity with an OFV isolate from Germany (AF321775). OFV has two orchid- (OFV-Orc1 and OFV-Orc2) and two citrus- (OFV-Cit1 and OFV-Cit2) infecting strains (Roy et al. 2020). However, an isolate of OFV-Orc1 has recently been associated with citrus leprosis in South Africa (Cook et al. 2019). To confirm the presence of OFV in Hawaiian citrus and identify the strain, symptomatic tissue was submitted to USDA-APHIS-PPQ-S&T where total RNA were extracted from the symptomatic tissue using RNeasy Plant Mini kit (Qiagen). The RNA samples were tested with OFV-Orc and OFV-Cit generic and specific primers in a conventional RT-PCR assay following optimized RT-PCR protocols (Roy et al. 2020). Two additional sets of generic primers (OFV-Orc-GPF: 5'-AGCGATAACGACCTTGATATGACACC, OFV-Orc-GPR: 5'-TGAGTGGTAGTCAATG CTCCATCAT and OFV-R2-GF1: 5'- CARTGTCAGGAGGATGCATGGAA, OFV-R2-GR: 5'- GACCTGCTTGATGTAATTGCTTCCTTC') were designed based on available OFV phospho (P) and large (L) polyprotein gene sequences in GenBank. These assays detected OFV-Orc2 in the symptomatic citrus samples, with the nucleocapsid (1353 bp), P (626 bp), and L (831 bp) gene sequences sharing 97 to 98% identity with published OFV-Orc2 sequences (AB244417 and AB516441). Ribo-depleted RNA (Ribo-Zero, Illumina) was prepared using a TruSeq Stranded Total RNA Library Prep kit (Illumina) and underwent high throughput sequencing (HTS) on a MiSeq platform (Illumina). The resulting 19.6 million 2x75bp reads were de novo assembled using SPAdes v. 3.10.0 (Bankevitch et al. 2012). In addition to sequences corresponding to citrus tristeza virus and citrus vein enation virus, two contigs of 6,412 nt (average depth 18,821; MW021482) and 5,986 nt (average depth 19,278; MW021483), were found to have ≥98% identity to RNA1 (AB244417) and RNA2 (AB244418) of OFV isolate So (Japan), respectively. This is the first report of OFV in Hawaii and the first time leprosis has been observed in the USA since it was eradicated from Florida in the 1960s, although that outbreak was attributed to infection by citrus leprosis virus-N0, a distant relative of OFV (Hartung et al. 2015). The recent detection of citrus leprosis associated with OFV infection in South Africa (Cook et al. 2019) and now Hawaii underscores the threat this pathogen poses to the global citrus industry.
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Affiliation(s)
- Alejandro Olmedo Velarde
- University of Hawaii System, 3939, Plant & Environmental Protection Sciences, 3190 Maile Way, St John 315, Honolulu, Hawaii, United States, 96822;
| | - Avijit Roy
- USDA APHIS PPQ, CPHST Beltsville Laboratory, Bldg 580, BARC-East, Powder Mill Road, Beltsville, Maryland, United States, 20705;
| | - Chellappan Padmanabhan
- PPQ, CPHST, National Plant Germplasm and Biotechnology Laboratory, Laurel, Maryland, United States;
| | - Schyler Nunziata
- PPQ, CPHST, National Plant Germplasm and Biotechnology Laboratory, Laurel, Maryland, United States;
| | - Mark K Nakhla
- PPQ, CPHST, National Plant Germplasm and Biotechnology Laboratory, BARC-East, Bldg-580, Powder Mill Rd, Beltsville, Maryland, United States, 20705;
| | - Michael Melzer
- University of Hawaii, Plant and Environmental Protection Sciences, 3190 Maile Way, St. John 310, Honolulu, Hawaii, United States, 96822;
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9
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Roy A, Stone AL, Otero-Colina G, Wei G, Brlansky RH, Ochoa R, Bauchan G, Schneider WL, Nakhla MK, Hartung JS. Reassortment of Genome Segments Creates Stable Lineages Among Strains of Orchid Fleck Virus Infecting Citrus in Mexico. PHYTOPATHOLOGY 2020; 110:106-120. [PMID: 31600117 DOI: 10.1094/phyto-07-19-0253-fi] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The genus Dichorhavirus contains viruses with bipartite, negative-sense, single-stranded RNA genomes that are transmitted by flat mites to hosts that include orchids, coffee, the genus Clerodendrum, and citrus. A dichorhavirus infecting citrus in Mexico is classified as a citrus strain of orchid fleck virus (OFV-Cit). We previously used RNA sequencing technologies on OFV-Cit samples from Mexico to develop an OFV-Cit-specific reverse transcription PCR (RT-PCR) assay. During assay validation, OFV-Cit-specific RT-PCR failed to produce an amplicon from some samples with clear symptoms of OFV-Cit. Characterization of this virus revealed that dichorhavirus-like particles were found in the nucleus. High-throughput sequencing of small RNAs from these citrus plants revealed a novel citrus strain of OFV, OFV-Cit2. Sequence comparisons with known orchid and citrus strains of OFV showed variation in the protein products encoded by genome segment 1 (RNA1). Strains of OFV clustered together based on host of origin, whether orchid or citrus, and were clearly separated from other dichorhaviruses described from infected citrus in Brazil. The variation in RNA1 between the original (now OFV-Cit1) and the new (OFV-Cit2) strain was not observed with genome segment 2 (RNA2), but instead, a common RNA2 molecule was shared among strains of OFV-Cit1 and -Cit2, a situation strikingly similar to OFV infecting orchids. We also collected mites at the affected groves, identified them as Brevipalpus californicus sensu stricto, and confirmed that they were infected by OFV-Cit1 or with both OFV-Cit1 and -Cit2. OFV-Cit1 and -Cit2 have coexisted at the same site in Toliman, Queretaro, Mexico since 2012. OFV strain-specific diagnostic tests were developed.
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Affiliation(s)
- Avijit Roy
- U.S. Department of Agriculture-APHIS PPQ S&T, Beltsville, MD 20705, U.S.A
| | - Andrew L Stone
- Foreign Disease Weed Science Research Unit, U.S. Department of Agriculture-Agriculture Research Service, Ft. Detrick, MD 21702, U.S.A
| | - Gabriel Otero-Colina
- Colegio de Postgraduados, Campus Montecillo, Texcoco, Edo. de Mex. CP56230, Mexico
| | - Gang Wei
- U.S. Department of Agriculture-APHIS PPQ S&T, Beltsville, MD 20705, U.S.A
| | | | - Ronald Ochoa
- U.S. Department of Agriculture-Agriculture Research Service, Beltsville, MD 20705, U.S.A
| | - Gary Bauchan
- U.S. Department of Agriculture-Agriculture Research Service, Beltsville, MD 20705, U.S.A
| | | | - Mark K Nakhla
- U.S. Department of Agriculture-APHIS PPQ S&T, Beltsville, MD 20705, U.S.A
| | - John S Hartung
- U.S. Department of Agriculture-Agriculture Research Service, Beltsville, MD 20705, U.S.A
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10
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Golyaev V, Candresse T, Rabenstein F, Pooggin MM. Plant virome reconstruction and antiviral RNAi characterization by deep sequencing of small RNAs from dried leaves. Sci Rep 2019; 9:19268. [PMID: 31848375 PMCID: PMC6917709 DOI: 10.1038/s41598-019-55547-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 10/15/2019] [Indexed: 12/23/2022] Open
Abstract
In plants, RNA interference (RNAi) generates small interfering (si)RNAs from entire genomes of viruses, satellites and viroids. Therefore, deep small (s)RNA sequencing is a universal approach for virome reconstruction and RNAi characterization. We tested this approach on dried barley leaves from field surveys. Illumina sequencing of sRNAs from 2 plant samples identified in both plants Hordeum vulgare endornavirus (HvEV) and barley yellow mosaic bymovirus (BaYMV) and, additionally in one plant, a novel strain of Japanese soil-borne wheat mosaic furovirus (JSBWMV). De novo and reference-based sRNA assembly yielded complete or near-complete genomic RNAs of these viruses. While plant sRNAs showed broad size distribution, viral sRNAs were predominantly 21 and 22 nucleotides long with 5′-terminal uridine or adenine, and were derived from both genomic strands. These bona fide siRNAs are presumably processed from double-stranded RNA precursors by Dicer-like (DCL) 4 and DCL2, respectively, and associated with Argonaute 1 and 2 proteins. For BaYMV (but not HvEV, or JSBWMV), 24-nucleotide sRNAs represented the third most abundant class, suggesting DCL3 contribution to anti-bymovirus defence. Thus, viral siRNAs are well preserved in dried leaf tissues and not contaminated by non-RNAi degradation products, enabling both complete virome reconstruction and inference of RNAi components mediating antiviral defense.
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Affiliation(s)
- Victor Golyaev
- BGPI, INRA Centre Occitanie, CIRAD, SupAgro, Université de Montpellier, Montpellier, 34984, France
| | - Thierry Candresse
- UMR 1332 Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, CS20032, Villenave d'Ornon cedex, 33882, France
| | - Frank Rabenstein
- Julius Kühn-Institut, Bundesforschungsinstitut für Kulturpflanzen, Erwin-Baur-Straße 27, Quedlinburg, 06484, Germany
| | - Mikhail M Pooggin
- BGPI, INRA Centre Occitanie, CIRAD, SupAgro, Université de Montpellier, Montpellier, 34984, France.
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11
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Fu S, Shao J, Roy A, Brlansky RH, Zhou C, Hartung JS. Transcriptomic analyses reveal physiological changes in sweet orange roots affected by citrus blight. BMC Genomics 2019; 20:969. [PMID: 31829190 PMCID: PMC6907255 DOI: 10.1186/s12864-019-6339-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 11/26/2019] [Indexed: 11/10/2022] Open
Abstract
Background Citrus blight is a very important progressive decline disease of commercial citrus. The etiology is unknown, although the disease can be transmitted by root grafts, suggesting a viral etiology. Diagnosis is made by demonstrating physical blockage of xylem cells that prevents the movement of water. This test was used to identify symptomatic trees from four commercial groves in Florida. Total RNA extracts of phloem-enriched scaffold root tissues were prepared from seven trees that failed to take up water and from one healthy tree. These RNA extracts were used for transcriptomic analyses using paired end RNA-Seq from an Illumina 2500 system. The expression of transcripts annotated as polyprotein of citrus endogenous pararetrovirus were estimated by both RT-qPCR and RNA-Seq. Results Transcripts from seven RNA-Seq libraries from trees affected by citrus blight were compared to a control tree. 129–148 million RNA fragments (two paired-end reads/fragment) were generated per library and were mapped to the sweet orange reference genome. In response to citrus blight stress, genes encoding aquaporins, proteins with water channel activity and several cellulose synthase genes were down-regulated, whereas genes involved in lignin and glucosinolate biosynthesis were up-regulated. Transcripts encoding proteins in pathways of carbohydrate metabolism, nucleotide synthesis, signaling, hormone metabolism, secondary metabolism, transport, and biotic stress pathways were overwhelmingly down regulated in all libraries. Conclusion Reduced water intake and xylem plugging were observed in the trees tested and the changes in their transcriptome were analyzed. Plants adapted to reduced water flow by regulating primary and secondary metabolism, nuclear transport and hormone associated pathways. The patterns of energy generation, transcription, translation and protein degradation were consistent with irreversible decline. The down regulation of cellulose synthase transcripts and up regulation of transcripts related to lignin production likely lead to an imbalance in the pathways leading to wood formation, and may lead to the blockage of the xylem vessels seen as the cardinal symptom of citrus blight. Transcripts of a pararetrovirus were elevated in the transcriptome of roots used in this study.
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Affiliation(s)
- Shimin Fu
- Citrus Research Institute, Southwest University, Chongqing, China.,United States Department of Agriculture-Agricultural Research Service, Molecular Plant Pathology Laboratory, Beltsville, MD, USA
| | - Jonathan Shao
- United States Department of Agriculture-Agricultural Research Service, Molecular Plant Pathology Laboratory, Beltsville, MD, USA
| | - Avijit Roy
- USDA-APHIS-PPQ-S&T, Beltsville, MD, 20705, USA
| | - Ronald H Brlansky
- Citrus Research and Education Center, University of Florida, Lake Alfred, FL, 33850, USA
| | - Changyong Zhou
- Citrus Research Institute, Southwest University, Chongqing, China.
| | - John S Hartung
- United States Department of Agriculture-Agricultural Research Service, Molecular Plant Pathology Laboratory, Beltsville, MD, USA.
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Pooggin MM. Small RNA-Omics for Plant Virus Identification, Virome Reconstruction, and Antiviral Defense Characterization. Front Microbiol 2018; 9:2779. [PMID: 30524398 PMCID: PMC6256188 DOI: 10.3389/fmicb.2018.02779] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 10/30/2018] [Indexed: 11/13/2022] Open
Abstract
RNA interference (RNAi)-based antiviral defense generates small interfering RNAs that represent the entire genome sequences of both RNA and DNA viruses as well as viroids and viral satellites. Therefore, deep sequencing and bioinformatics analysis of small RNA population (small RNA-ome) allows not only for universal virus detection and genome reconstruction but also for complete virome reconstruction in mixed infections. Viral infections (like other stress factors) can also perturb the RNAi and gene silencing pathways regulating endogenous gene expression and repressing transposons and host genome-integrated endogenous viral elements which can potentially be released from the genome and contribute to disease. This review describes the application of small RNA-omics for virus detection, virome reconstruction and antiviral defense characterization in cultivated and non-cultivated plants. Reviewing available evidence from a large and ever growing number of studies of naturally or experimentally infected hosts revealed that all families of land plant viruses, their satellites and viroids spawn characteristic small RNAs which can be assembled into contigs of sufficient length for virus, satellite or viroid identification and for exhaustive reconstruction of complex viromes. Moreover, the small RNA size, polarity and hotspot profiles reflect virome interactions with the plant RNAi machinery and allow to distinguish between silent endogenous viral elements and their replicating episomal counterparts. Models for the biogenesis and functions of small interfering RNAs derived from all types of RNA and DNA viruses, satellites and viroids as well as endogenous viral elements are presented and discussed.
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Affiliation(s)
- Mikhail M. Pooggin
- Institut National de la Recherche Agronomique, UMR BGPI, Montpellier, France
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Maliogka VI, Minafra A, Saldarelli P, Ruiz-García AB, Glasa M, Katis N, Olmos A. Recent Advances on Detection and Characterization of Fruit Tree Viruses Using High-Throughput Sequencing Technologies. Viruses 2018; 10:E436. [PMID: 30126105 PMCID: PMC6116224 DOI: 10.3390/v10080436] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 08/09/2018] [Accepted: 08/13/2018] [Indexed: 12/21/2022] Open
Abstract
Perennial crops, such as fruit trees, are infected by many viruses, which are transmitted through vegetative propagation and grafting of infected plant material. Some of these pathogens cause severe crop losses and often reduce the productive life of the orchards. Detection and characterization of these agents in fruit trees is challenging, however, during the last years, the wide application of high-throughput sequencing (HTS) technologies has significantly facilitated this task. In this review, we present recent advances in the discovery, detection, and characterization of fruit tree viruses and virus-like agents accomplished by HTS approaches. A high number of new viruses have been described in the last 5 years, some of them exhibiting novel genomic features that have led to the proposal of the creation of new genera, and the revision of the current virus taxonomy status. Interestingly, several of the newly identified viruses belong to virus genera previously unknown to infect fruit tree species (e.g., Fabavirus, Luteovirus) a fact that challenges our perspective of plant viruses in general. Finally, applied methodologies, including the use of different molecules as templates, as well as advantages and disadvantages and future directions of HTS in fruit tree virology are discussed.
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Affiliation(s)
- Varvara I Maliogka
- Laboratory of Plant Pathology, School of Agriculture, Faculty of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece.
| | - Angelantonio Minafra
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Via G. Amendola 122/D, 70126 Bari, Italy.
| | - Pasquale Saldarelli
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Via G. Amendola 122/D, 70126 Bari, Italy.
| | - Ana B Ruiz-García
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Ctra. Moncada-Náquera km 4.5, 46113 Moncada, Valencia, Spain.
| | - Miroslav Glasa
- Institute of Virology, Biomedical Research Centre, Slovak Academy of Sciences, Dúbravská cesta 9, 84505 Bratislava, Slovak Republic.
| | - Nikolaos Katis
- Laboratory of Plant Pathology, School of Agriculture, Faculty of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece.
| | - Antonio Olmos
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Ctra. Moncada-Náquera km 4.5, 46113 Moncada, Valencia, Spain.
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Freitas-Astúa J, Ramos-González PL, Arena GD, Tassi AD, Kitajima EW. Brevipalpus-transmitted viruses: parallelism beyond a common vector or convergent evolution of distantly related pathogens? Curr Opin Virol 2018; 33:66-73. [PMID: 30081359 DOI: 10.1016/j.coviro.2018.07.010] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2018] [Revised: 07/12/2018] [Accepted: 07/16/2018] [Indexed: 12/20/2022]
Abstract
Although diseases caused by Brevipalpus-transmitted viruses (BTV) became relevant for agriculture a century ago, their causal agents have been only recently characterized and classified in two new genera of plant-infecting viruses: Cilevirus and Dichorhavirus. In this review, we highlight both similarities and differences between these viruses emphasizing their current taxonomy and historical classification, phylogeny, genomic organization, gene expression, and the latest research developments on BTVs. Additionally, we stress particular features of interactions with their mite vectors and plant hosts that support, from an evolutionary perspective, the potential convergence of both viral groups.
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Affiliation(s)
- Juliana Freitas-Astúa
- Embrapa Cassava and Fruits, 44380-000 Cruz das Almas, BA, Brazil; Instituto Biológico, 04014-900 São Paulo, SP, Brazil.
| | | | - Gabriella Dias Arena
- Centro Apta Citros Sylvio Moreira, IAC, 13490-000 Cordeirópolis, SP, Brazil; Instituto de Biologia, Unicamp, 13083-862 Campinas, SP, Brazil
| | - Aline Daniele Tassi
- Departmento de Fitopatologia e Nematologia, ESALQ/USP, 13418-900 Piracicaba, SP, Brazil
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15
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Chabi-Jesus C, Ramos-González PL, Tassi AD, Guerra-Peraza O, Kitajima EW, Harakava R, Beserra JEA, Salaroli RB, Freitas-Astúa J. Identification and Characterization of Citrus Chlorotic Spot Virus, a New Dichorhavirus Associated with Citrus Leprosis-Like Symptoms. PLANT DISEASE 2018; 102:1588-1598. [PMID: 30673423 DOI: 10.1094/pdis-09-17-1425-re] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Local chlorotic spots resembling early lesions characteristic of citrus leprosis (CL) were observed in leaves of two sweet orange (Citrus sinensis L.) trees in Teresina, State of Piauí, Brazil, in early 2017. However, despite the similarities, these spots were generally larger than those of a typical CL and showed rare or no necrosis symptoms. In symptomatic tissues, transmission electron microscopy revealed the presence of viroplasms in the nuclei of the infected parenchymal cells and rod-shaped particles with an average size of approximately 40 × 100 nm, resembling those typically observed during infection by dichorhaviruses. A bipartite genome of the putative novel virus, tentatively named citrus chlorotic spot virus (CiCSV) (RNA1 = 6,518 nucleotides [nt] and RNA2 = 5,987 nt), revealed the highest nucleotide sequence identity values with the dichorhaviruses coffee ringspot virus strain Lavras (73.8%), citrus leprosis virus N strain Ibi1 (58.6%), and orchid fleck virus strain So (56.9%). In addition to citrus, CiCSV was also found in local chlorotic lesions on leaves of the ornamental plant beach hibiscus (Talipariti tiliaceum (L.) Fryxell). Morphological characterization of mites recovered from the infected plants revealed at least two different types of Brevipalpus. One of them corresponds to Brevipalpus yothersi. The other is slightly different from B. yothersi mites but comprises traits that possibly place it as another species. A mix of the two mite types collected on beach hibiscus successfully transmitted CiCSV to arabidopsis plants but additional work is required to verify whether both types of flat mite may act as viral vectors. The current study reveals a newly described dichorhavirus associated with a citrus disease in the northeastern region of Brazil.
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Affiliation(s)
- C Chabi-Jesus
- Instituto Biológico, São Paulo, SP, Brazil; and PPG Microbiologia Agrícola ESALQ/USP, Piracicaba, SP, Brazil
| | | | - A D Tassi
- LFN/ESALQ/USP, 13418-900 Piracicaba, SP, Brazil
| | - O Guerra-Peraza
- Instituto Biológico, São Paulo; and Citrus Research & Education Center, University of Florida
| | | | | | | | | | - J Freitas-Astúa
- Instituto Biológico, São Paulo; and Embrapa Mandioca e Fruticultura, Cruz das Almas, BA, Brazil
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16
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Complete Nucleotide Sequence of a Novel Hibiscus-Infecting Cilevirus from Florida and Its Relationship with Closely Associated Cileviruses. GENOME ANNOUNCEMENTS 2018; 6:6/4/e01521-17. [PMID: 29371356 PMCID: PMC5786682 DOI: 10.1128/genomea.01521-17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The complete nucleotide sequence of a recently discovered Florida (FL) isolate of hibiscus-infecting cilevirus (HiCV) was determined by Sanger sequencing. The movement and coat protein gene sequences of the HiCV-FL isolate are more divergent than other genes of the previously sequenced HiCV-HI (Hawaii) isolate.
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17
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Abstract
A group of related bacilliform, nuclear viruses with a bisegmented negative-sense RNA genome that are transmitted by Brevipalpus mites likely in a circulative-propagative manner were recently classified in the new genus Dichorhavirus, family Rhabdoviridae. These viruses cause localized lesions on leaves, stems, and fruits of economically significant horticultural and ornamental plant species. Among its members, orchid fleck virus, citrus leprosis virus N, and coffee ringspot virus are most prominent. This chapter summarizes the current knowledge about these viruses, available detection techniques, and their interactions with their plant hosts and mite vectors.
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18
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Jeger M, Bragard C, Caffier D, Dehnen-Schmutz K, Gilioli G, Gregoire JC, Jaques Miret JA, MacLeod A, Navajas Navarro M, Niere B, Parnell S, Potting R, Rafoss T, Rossi V, Urek G, Van Bruggen A, Van der Werf W, West J, Chatzivassiliou E, Winter S, Catara A, Duran-Vila N, Hollo G, Candresse T. Pest categorisation of Citrus leprosis viruses. EFSA J 2017; 15:e05110. [PMID: 32625390 PMCID: PMC7009949 DOI: 10.2903/j.efsa.2017.5110] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The EFSA Panel on Plant Health performed a pest categorisation of the Citrus leprosis viruses for the EU territory and identified five distinct viruses, Citrus leprosis virus C (CiLV‐C), Citrus leprosis virus C2 (CiLV‐C2), Hibiscus green spot virus 2 (HGSV‐2), the Citrus strain of Orchid fleck virus (OFV) and Citrus leprosis virus N sensu novo (CiLV‐N) as causing this severe disease, most significantly in sweet orange and mandarin. These viruses have in common that they do not cause systemic infections in their hosts and that they all are transmitted by Brevipalpus spp. mites (likely but not confirmed for HGSV‐2). Mites represent the most important means of virus spread, while plants for planting of Citrus are only considered of minor significance. These well characterised viruses occur in South and Central America. Leprosis is currently regulated in directive 2000/29 EC and, together with its associated viruses, has never been recorded in the EU. All five viruses have the potential to enter into, establish in and spread within the EU territory, with plants for planting of non‐regulated hosts, fruits of Citrus and hitch‐hiking of viruliferous mites identified as the most significant pathways. Given the severity of the leprosis disease, the introduction and spread of the various viruses would have negative consequences on the EU citrus industry, the magnitude of which is difficult to evaluate given the uncertainties affecting the Brevipalpus spp. vectors (identity, distribution, density, transmission specificity and efficiency). Overall, leprosis and its five associated viruses meet all the criteria evaluated by EFSA to qualify as Union quarantine pests, but do not fulfil those of being present in the EU or of plants for planting being the main spread mechanism to qualify as Union regulated non‐quarantine pests. The main uncertainties affecting this categorisation concern the Brevipalpus spp. mite vectors.
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Ramos-González PL, Chabi-Jesus C, Guerra-Peraza O, Tassi AD, Kitajima EW, Harakava R, Salaroli RB, Freitas-Astúa J. Citrus leprosis virus N: A New Dichorhavirus Causing Citrus Leprosis Disease. PHYTOPATHOLOGY 2017; 107:963-976. [PMID: 28398876 DOI: 10.1094/phyto-02-17-0042-r] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Citrus leprosis (CL) is a viral disease endemic to the Western Hemisphere that produces local necrotic and chlorotic lesions on leaves, branches, and fruit and causes serious yield reduction in citrus orchards. Samples of sweet orange (Citrus × sinensis) trees showing CL symptoms were collected during a survey in noncommercial citrus areas in the southeast region of Brazil in 2013 to 2016. Transmission electron microscopy analyses of foliar lesions confirmed the presence of rod-like viral particles commonly associated with CL in the nucleus and cytoplasm of infected cells. However, every attempt to identify these particles by reverse-transcription polymerase chain reaction tests failed, even though all described primers for the detection of known CL-causing cileviruses and dichorhaviruses were used. Next-generation sequencing of total RNA extracts from three symptomatic samples revealed the genome of distinct, although highly related (>92% nucleotide sequence identity), viruses whose genetic organization is similar to that of dichorhaviruses. The genome sequence of these viruses showed <62% nucleotide sequence identity with those of orchid fleck virus and coffee ringspot virus. Globally, the deduced amino acid sequences of the open reading frames they encode share 32.7 to 63.8% identity with the proteins of the dichorhavirids. Mites collected from both the naturally infected citrus trees and those used for the transmission of one of the characterized isolates to Arabidopsis plants were anatomically recognized as Brevipalpus phoenicis sensu stricto. Molecular and biological features indicate that the identified viruses belong to a new species of CL-associated dichorhavirus, which we propose to call Citrus leprosis N dichorhavirus. Our results, while emphasizing the increasing diversity of viruses causing CL disease, lead to a reevaluation of the nomenclature of those viruses assigned to the genus Dichorhavirus. In this regard, a comprehensive discussion is presented.
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Affiliation(s)
- Pedro Luis Ramos-González
- First, second, third, sixth, and eighth authors: Lab. Bioquímica Fitopatológica, Instituto Biológico, São Paulo 04014-002, Brazil; second, fourth, fifth, and seventh authors: Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, São Paulo 13418-900, Brazil; third author: Citrus Research & Education Center, University of Florida, Lake Alfred 33850; and eighth author: Embrapa Mandioca e Fruticultura, Cruz das Almas, Bahia 44380-000, Brazil
| | - Camila Chabi-Jesus
- First, second, third, sixth, and eighth authors: Lab. Bioquímica Fitopatológica, Instituto Biológico, São Paulo 04014-002, Brazil; second, fourth, fifth, and seventh authors: Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, São Paulo 13418-900, Brazil; third author: Citrus Research & Education Center, University of Florida, Lake Alfred 33850; and eighth author: Embrapa Mandioca e Fruticultura, Cruz das Almas, Bahia 44380-000, Brazil
| | - Orlene Guerra-Peraza
- First, second, third, sixth, and eighth authors: Lab. Bioquímica Fitopatológica, Instituto Biológico, São Paulo 04014-002, Brazil; second, fourth, fifth, and seventh authors: Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, São Paulo 13418-900, Brazil; third author: Citrus Research & Education Center, University of Florida, Lake Alfred 33850; and eighth author: Embrapa Mandioca e Fruticultura, Cruz das Almas, Bahia 44380-000, Brazil
| | - Aline Daniele Tassi
- First, second, third, sixth, and eighth authors: Lab. Bioquímica Fitopatológica, Instituto Biológico, São Paulo 04014-002, Brazil; second, fourth, fifth, and seventh authors: Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, São Paulo 13418-900, Brazil; third author: Citrus Research & Education Center, University of Florida, Lake Alfred 33850; and eighth author: Embrapa Mandioca e Fruticultura, Cruz das Almas, Bahia 44380-000, Brazil
| | - Elliot Watanabe Kitajima
- First, second, third, sixth, and eighth authors: Lab. Bioquímica Fitopatológica, Instituto Biológico, São Paulo 04014-002, Brazil; second, fourth, fifth, and seventh authors: Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, São Paulo 13418-900, Brazil; third author: Citrus Research & Education Center, University of Florida, Lake Alfred 33850; and eighth author: Embrapa Mandioca e Fruticultura, Cruz das Almas, Bahia 44380-000, Brazil
| | - Ricardo Harakava
- First, second, third, sixth, and eighth authors: Lab. Bioquímica Fitopatológica, Instituto Biológico, São Paulo 04014-002, Brazil; second, fourth, fifth, and seventh authors: Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, São Paulo 13418-900, Brazil; third author: Citrus Research & Education Center, University of Florida, Lake Alfred 33850; and eighth author: Embrapa Mandioca e Fruticultura, Cruz das Almas, Bahia 44380-000, Brazil
| | - Renato Barbosa Salaroli
- First, second, third, sixth, and eighth authors: Lab. Bioquímica Fitopatológica, Instituto Biológico, São Paulo 04014-002, Brazil; second, fourth, fifth, and seventh authors: Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, São Paulo 13418-900, Brazil; third author: Citrus Research & Education Center, University of Florida, Lake Alfred 33850; and eighth author: Embrapa Mandioca e Fruticultura, Cruz das Almas, Bahia 44380-000, Brazil
| | - Juliana Freitas-Astúa
- First, second, third, sixth, and eighth authors: Lab. Bioquímica Fitopatológica, Instituto Biológico, São Paulo 04014-002, Brazil; second, fourth, fifth, and seventh authors: Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, São Paulo 13418-900, Brazil; third author: Citrus Research & Education Center, University of Florida, Lake Alfred 33850; and eighth author: Embrapa Mandioca e Fruticultura, Cruz das Almas, Bahia 44380-000, Brazil
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Kondo H, Hirota K, Maruyama K, Andika IB, Suzuki N. A possible occurrence of genome reassortment among bipartite rhabdoviruses. Virology 2017; 508:18-25. [PMID: 28478311 DOI: 10.1016/j.virol.2017.04.027] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 04/23/2017] [Accepted: 04/25/2017] [Indexed: 12/18/2022]
Abstract
Orchid fleck virus (OFV) represents a rhabdovirus with a unique bipartite genome. OFV genetic diversity at the whole genome level has not been described. Using the partial genome sequence of RNA1, we have determined that several OFV isolates derived from orchids in Japan belong to two genetically distant subgroups: subgroup I, the members of which are distributed worldwide but previously not known in Asia, and subgroup II, which is commonly distributed in Japan. However, complete genome sequence analysis of a novel Japanese subgroup I isolate revealed that although its RNA1 sequence differs considerably from those of subgroup II isolates, its RNA2 sequence is almost identical to them. Based on phylogenetic and recombination analyses, the genome reassortment events were predicted to occur between OFV subgroups including other unseen strains. Our data show that genome reassortment contributes to the genetic diversities of the bipartite rhabdoviruses and its occurrence may be geographically constrained.
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Affiliation(s)
- Hideki Kondo
- Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki 710-0046, Japan.
| | - Keisuke Hirota
- Tokushima Agriculture, Forestry and Fisheries Technology Support Center, Tokushima, Tokushima Prefecture 779-3233, Japan
| | - Kazuyuki Maruyama
- Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki 710-0046, Japan
| | - Ida Bagus Andika
- Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki 710-0046, Japan
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki 710-0046, Japan
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Tassi AD, Garita-Salazar LC, Amorim L, Novelli VM, Freitas-Astúa J, Childers CC, Kitajima EW. Virus-vector relationship in the Citrus leprosis pathosystem. EXPERIMENTAL & APPLIED ACAROLOGY 2017; 71:227-241. [PMID: 28417249 PMCID: PMC5403852 DOI: 10.1007/s10493-017-0123-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 04/04/2017] [Indexed: 05/28/2023]
Abstract
Citrus leprosis has been one of the most destructive diseases of citrus in the Americas. In the last decade important progress has been achieved such as the complete genome sequencing of its main causal agent, Citrus leprosis virus C (CiLV-C), belonging to a new genus Cilevirus. It is transmitted by Brevipalpus yothersi Baker (Acari: Tenuipalpidae), and is characterized by the localized symptoms it induces on the leaves, fruits and stems. It occurs in the American continents from Mexico to Argentina. The virus was until recently considered restricted to Citrus spp. However, it was found naturally infecting other plants species as Swinglea glutinosa Merrill and Commelina benghalensis L., and has been experimentally transmitted by B. yothersi to a large number of plant species. Despite these advances little is known about the virus-vector relationship that is a key to understanding the epidemiology of the disease. Some components of the CiLV-C/B. yothersi relationship were determined using the common bean (Phaseolus vulgaris L. cv. 'IAC Una') as a test plant. They included: (a) the virus acquisition access period was 4 h; (b) the virus inoculation access period was 2 h; (c) the latent period between acquisition and inoculation was 7 h; (d) the period of retention of the virus by a single viruliferous mite was at least 12 days; (d) the percentage of viruliferous individuals from mite colonies on infected tissues ranged from 25 to 60%. The experiments confirmed previous data that all developmental stages of B. yothersi (larva, protonymph and deutonymph, adult female and male) were able to transmit CiLV-C and that transovarial transmission of the virus did not occur. CiLV-C can be acquired from lesions on leaves, fruits and stems by B. yothersi. Based on the distribution of lesions produced by single viruliferous B. yothersi on bean leaves, it is concluded that they tend to feed in restricted areas, usually near the veins. The short latent and transmission periods during the larval stage suggest that the CiLV-C/B. yothersi relationship is of the persistent circulative type.
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Affiliation(s)
- Aline Daniele Tassi
- Departamento de Fitopatologia e Nematologia, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, CP 9, Piracicaba, SP 13418-900 Brazil
| | - Laura Cristina Garita-Salazar
- Departamento de Fitopatologia e Nematologia, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, CP 9, Piracicaba, SP 13418-900 Brazil
| | - Lilian Amorim
- Departamento de Fitopatologia e Nematologia, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, CP 9, Piracicaba, SP 13418-900 Brazil
| | - Valdenice Moreira Novelli
- Instituto Agronômico de Campinas, Centro APTA Citros Sylvio Moreira, CP 4, Cordeirópolis, SP 13490-900 Brazil
| | - Juliana Freitas-Astúa
- Embrapa Mandioca e Fruticultura, Cruz das Almas, BA 44380-000 Brazil
- Instituto Biológico, São Paulo, SP 04014-900 Brazil
| | - Carl C. Childers
- Citrus Research and Education Center, IFAS, University of Florida, 700 Experiment Station Road, Lake Alfred, FL 33850 USA
| | - Elliot W. Kitajima
- Departamento de Fitopatologia e Nematologia, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, CP 9, Piracicaba, SP 13418-900 Brazil
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Dietzgen RG, Kondo H, Goodin MM, Kurath G, Vasilakis N. The family Rhabdoviridae: mono- and bipartite negative-sense RNA viruses with diverse genome organization and common evolutionary origins. Virus Res 2017; 227:158-170. [PMID: 27773769 PMCID: PMC5124403 DOI: 10.1016/j.virusres.2016.10.010] [Citation(s) in RCA: 147] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 10/18/2016] [Accepted: 10/18/2016] [Indexed: 12/24/2022]
Abstract
The family Rhabdoviridae consists of mostly enveloped, bullet-shaped or bacilliform viruses with a negative-sense, single-stranded RNA genome that infect vertebrates, invertebrates or plants. This ecological diversity is reflected by the diversity and complexity of their genomes. Five canonical structural protein genes are conserved in all rhabdoviruses, but may be overprinted, overlapped or interspersed with several novel and diverse accessory genes. This review gives an overview of the characteristics and diversity of rhabdoviruses, their taxonomic classification, replication mechanism, properties of classical rhabdoviruses such as rabies virus and rhabdoviruses with complex genomes, rhabdoviruses infecting aquatic species, and plant rhabdoviruses with both mono- and bipartite genomes.
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Affiliation(s)
- Ralf G Dietzgen
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Queensland 4072, Australia.
| | - Hideki Kondo
- Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046, Japan
| | - Michael M Goodin
- Department of Plant Pathology, University of Kentucky, Lexington, KY 40546, USA
| | - Gael Kurath
- U.S. Geological Survey, Western Fisheries Research Centre, Seattle, WA, USA
| | - Nikos Vasilakis
- Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, TX, 77555, USA
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Ramos-González PL, Chabi-Jesus C, Guerra-Peraza O, Breton MC, Arena GD, Nunes MA, Kitajima EW, Machado MA, Freitas-Astúa J. Phylogenetic and Molecular Variability Studies Reveal a New Genetic Clade of Citrus leprosis virus C. Viruses 2016; 8:E153. [PMID: 27275832 PMCID: PMC4926173 DOI: 10.3390/v8060153] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 05/10/2016] [Accepted: 05/24/2016] [Indexed: 01/02/2023] Open
Abstract
Citrus leprosis virus C (CiLV-C) causes a severe disease affecting citrus orchards in the Western hemisphere. This study reveals the molecular variability of the virus by analyzing four genomic regions (p29, p15, MP and RNA2-intergenic region) distributed over its two RNAs. Nucleotide diversity (π) values were relatively low but statistically different over the analyzed genes and subpopulations, indicating their distinct evolutionary history. Values of πp29 and πMP were higher than those of πp15 and πRNA2-IR, whereas πMP was increased due to novel discovered isolates phylogenetically clustered in a divergent clade that we called SJP. Isolate BR_SP_SJP_01 RNA1 and RNA2 sequences, clade SJP, showed an identity of 85.6% and 88.4%, respectively, with those corresponding to CiLV-C, the type member of the genus Cilevirus, and its RNA2 5'-proximal region was revealed as a minor donor in a putative inter-clade recombination event. In addition to citrus, BR_SP_SJP_01 naturally infects the weed Commelina benghalensis and is efficiently transmitted by Brevipalpus yothersi mites. Our data demonstrated that negative selection was the major force operating in the evaluated viral coding regions and defined amino acids putatively relevant for the biological function of cilevirus proteins. This work provides molecular tools and sets up a framework for further epidemiological studies.
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Affiliation(s)
- Pedro Luis Ramos-González
- Laboratório de Biotecnologia, Centro de Citricultura Sylvio Moreira, Instituto Agronômico de Campinas, Cordeirópolis, São Paulo 13490-970, Brazil.
- Departamento de Bioquímica Fitopatológica, Instituto Biológico, São Paulo 04014-002, Brazil.
| | - Camila Chabi-Jesus
- Laboratório de Biotecnologia, Centro de Citricultura Sylvio Moreira, Instituto Agronômico de Campinas, Cordeirópolis, São Paulo 13490-970, Brazil.
- Departamento de Bioquímica Fitopatológica, Instituto Biológico, São Paulo 04014-002, Brazil.
- Departamento de Microbiologia Agrícola, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, São Paulo 13418-900, Brazil.
| | - Orlene Guerra-Peraza
- Departamento de Bioquímica Fitopatológica, Instituto Biológico, São Paulo 04014-002, Brazil.
| | - Michèle Claire Breton
- Laboratório de Biotecnologia, Centro de Citricultura Sylvio Moreira, Instituto Agronômico de Campinas, Cordeirópolis, São Paulo 13490-970, Brazil.
| | - Gabriella Dias Arena
- Laboratório de Biotecnologia, Centro de Citricultura Sylvio Moreira, Instituto Agronômico de Campinas, Cordeirópolis, São Paulo 13490-970, Brazil.
- Instituto de Biologia, Universidade de Campinas, Campinas, São Paulo 13083-970, Brazil.
| | - Maria Andreia Nunes
- Laboratório de Biotecnologia, Centro de Citricultura Sylvio Moreira, Instituto Agronômico de Campinas, Cordeirópolis, São Paulo 13490-970, Brazil.
| | - Elliot Watanabe Kitajima
- Departamento de Fitopatologia e Nematologia, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, São Paulo 13418-900, Brazil.
| | - Marcos Antonio Machado
- Laboratório de Biotecnologia, Centro de Citricultura Sylvio Moreira, Instituto Agronômico de Campinas, Cordeirópolis, São Paulo 13490-970, Brazil.
| | - Juliana Freitas-Astúa
- Departamento de Bioquímica Fitopatológica, Instituto Biológico, São Paulo 04014-002, Brazil.
- Embrapa Cassava and Fruits, Cruz das Almas, Bahia 44380-000, Brazil.
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