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Rubio L, Arruabarrena A, Salvo M, Castells M, Bertalmío A, Hernández-Rodríguez L, Benítez-Galeano MJ, Maeso D, Colina R, Rivas F. Biological and molecular characterization of a resistance-breaking isolate of citrus tristeza virus from Uruguay and its effects on Poncirus trifoliata growth performance. Arch Virol 2023; 168:123. [PMID: 36988730 DOI: 10.1007/s00705-023-05749-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 02/11/2023] [Indexed: 03/30/2023]
Abstract
Resistance-breaking (RB) isolates of citrus tristeza virus (CTV) can replicate and move systemically in Poncirus trifoliata, a rootstock widely used for management of decline caused by CTV and other purposes. In Uruguay, severe CTV isolates are prevalent, and an RB isolate (designated as RB-UY1) was identified. In order to predict the implications of this genotype circulating in citrus crops grafted on trifoliate rootstocks, the aim of this work was to determine the biological and molecular characteristics of this isolate, the efficiency of its transmission by Toxoptera citricida, and its effects on plant growth performance of P. trifoliata. Our results show that RB-UY1 can be classified as a mild isolate, that it is phylogenetically associated with the RB1 group, and that it is efficiently transmitted by T. citrida. They also suggest that the RB-UY1 isolate should not affect the performance of citrus crops grafted on trifoliate rootstocks, although some growth parameters of P. trifoliata seedlings were affected four years after inoculation.
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Affiliation(s)
- Leticia Rubio
- Instituto Nacional de Investigación Agropecuaria (INIA), Estación Experimental INIA Salto Grande. Camino al Terrible, Salto, CP 50000, Uruguay.
| | - Ana Arruabarrena
- Instituto Nacional de Investigación Agropecuaria (INIA), Estación Experimental INIA Salto Grande. Camino al Terrible, Salto, CP 50000, Uruguay
| | - Matías Salvo
- Instituto Nacional de Investigación Agropecuaria (INIA), Estación Experimental INIA Salto Grande. Camino al Terrible, Salto, CP 50000, Uruguay
| | - Matías Castells
- Laboratorio de Virología Molecular, Centro Universitario Regional Litoral Norte (CENUR Litoral Norte), Universidad de la República, Rivera 1350, Salto, CP 50000, Uruguay
| | - Ana Bertalmío
- Instituto Nacional de Investigación Agropecuaria (INIA), Estación Experimental INIA Salto Grande. Camino al Terrible, Salto, CP 50000, Uruguay
| | - Lester Hernández-Rodríguez
- Instituto Nacional de Investigación Agropecuaria (INIA), Estación Experimental INIA Salto Grande. Camino al Terrible, Salto, CP 50000, Uruguay
| | - María J Benítez-Galeano
- Laboratorio de Virología Molecular, Centro Universitario Regional Litoral Norte (CENUR Litoral Norte), Universidad de la República, Rivera 1350, Salto, CP 50000, Uruguay
| | - Diego Maeso
- Instituto Nacional de Investigación Agropecuaria (INIA), Estación Experimental INIA Salto Grande. Camino al Terrible, Salto, CP 50000, Uruguay
| | - Rodney Colina
- Laboratorio de Virología Molecular, Centro Universitario Regional Litoral Norte (CENUR Litoral Norte), Universidad de la República, Rivera 1350, Salto, CP 50000, Uruguay
| | - Fernando Rivas
- Instituto Nacional de Investigación Agropecuaria (INIA), Estación Experimental INIA Salto Grande. Camino al Terrible, Salto, CP 50000, Uruguay
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Alves MN, Raiol-Junior LL, Girardi EA, Miranda M, Wulff NA, Carvalho EV, Lopes SA, Ferro JA, Ollitrault P, Peña L. Insight into resistance to ' Candidatus Liberibacter asiaticus,' associated with Huanglongbing, in Oceanian citrus genotypes. Front Plant Sci 2022; 13:1009350. [PMID: 36160987 PMCID: PMC9500433 DOI: 10.3389/fpls.2022.1009350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 08/22/2022] [Indexed: 06/16/2023]
Abstract
Huanglongbing (HLB), the most destructive citrus disease, is associated with unculturable, phloem-limited Candidatus Liberibacter species, mainly Ca. L. asiaticus (Las). Las is transmitted naturally by the insect Diaphorina citri. In a previous study, we determined that the Oceanian citrus relatives Eremocitrus glauca, Microcitrus warburgiana, Microcitrus papuana, and Microcitrus australis and three hybrids among them and Citrus were full-resistant to Las. After 2 years of evaluations, leaves of those seven genotypes remained Las-free even with their susceptible rootstock being infected. However, Las was detected in their stem bark above the scion-rootstock graft union. Aiming to gain an understanding of the full-resistance phenotype, new experiments were carried out with the challenge-inoculated Oceanian citrus genotypes through which we evaluated: (1) Las acquisition by D. citri fed onto them; (2) Las infection in sweet orange plants grafted with bark or budwood from them; (3) Las infection in sweet orange plants top-grafted onto them; (4) Las infection in new shoots from rooted plants of them; and (5) Las infection in new shoots of them after drastic back-pruning. Overall, results showed that insects that fed on plants from the Oceanian citrus genotypes, their canopies, new flushes, and leaves from rooted cuttings evaluated remained quantitative real-time polymerase chain reaction (qPCR)-negative. Moreover, their budwood pieces were unable to infect sweet orange through grafting. Furthermore, sweet orange control leaves resulted infected when insects fed onto them and graft-receptor susceptible plants. Genomic and morphological analysis of the Oceanian genotypes corroborated that E. glauca and M. warburgiana are pure species while our M. australis accession is an M. australis × M. inodora hybrid and M. papuana is probably a M. papuana × M. warburgiana hybrid. E. glauca × C. sinensis hybrid was found coming from a cross between E. glauca and mandarin or tangor. Eremocitrus × Microcitrus hybrid is a complex admixture of M. australasica, M. australis, and E. glauca while the last hybrid is an M. australasica × M. australis admixture. Confirmation of consistent full resistance in these genotypes with proper validation of their genomic parentages is essential to map properly genomic regions for breeding programs aimed to generate new Citrus-like cultivars yielding immunity to HLB.
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Affiliation(s)
- Mônica N. Alves
- Fundo de Defesa da Citricultura, Araraquara, Brazil
- Faculdade de Ciências Agrárias e Veterinárias (FCAV), Universidade Estadual Paulista (UNESP), Jaboticabal, Brazil
| | - Laudecir L. Raiol-Junior
- Fundo de Defesa da Citricultura, Araraquara, Brazil
- Empresa Brasileira de Pesquisa Agropecuária, Cruz das Almas, Brazil
| | - Eduardo A. Girardi
- Fundo de Defesa da Citricultura, Araraquara, Brazil
- Empresa Brasileira de Pesquisa Agropecuária, Cruz das Almas, Brazil
| | - Maéva Miranda
- CIRAD, UMR AGAP Institut, Montpellier, France
- AGAP Institut, Univ. Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | | | - Everton V. Carvalho
- Fundo de Defesa da Citricultura, Araraquara, Brazil
- Empresa Brasileira de Pesquisa Agropecuária, Cruz das Almas, Brazil
| | | | - Jesus A. Ferro
- Faculdade de Ciências Agrárias e Veterinárias (FCAV), Universidade Estadual Paulista (UNESP), Jaboticabal, Brazil
| | - Patrick Ollitrault
- CIRAD, UMR AGAP Institut, Montpellier, France
- AGAP Institut, Univ. Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Leandro Peña
- Fundo de Defesa da Citricultura, Araraquara, Brazil
- Instituto de Biologia Molecular y Celular de Plantas – Consejo Superior de Investigaciones Científicas, Universidad Politécnica de Valencia, Valencia, Spain
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Wallis CM, Gorman Z, Rattner R, Hajeri S, Yokomi R. Amino acid, sugar, phenolic, and terpenoid profiles are capable of distinguishing Citrus tristeza virus infection status in citrus cultivars: Grapefruit, lemon, mandarin, and sweet orange. PLoS One 2022; 17:e0268255. [PMID: 35536831 PMCID: PMC9089872 DOI: 10.1371/journal.pone.0268255] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 04/26/2022] [Indexed: 11/18/2022] Open
Abstract
Citrus tristeza virus (CTV) is the most severe viral disease for citrus production. Many strains of CTV have been characterized and their symptomology widely varies, ranging from asymptomatic or mild infections to severe symptomology that results in substantial yield loss or host death. The capacity of the different CTV strains to affect the biochemistry of different citrus species has remained largely unstudied, despite that associated metabolomic shifts would be relevant toward symptom development. Thus, amino acid, sugar, phenolic, and terpenoid levels were assessed in leaves of healthy and CTV-infected grapefruit, lemon, mandarin, and two different sweet orange cultivars. Both mild [VT-negative (VT-)] and severe [VT-positive (VT+)] CTV genotype strains were utilized. When looking at overall totals of these metabolite classes, only amino acid levels were significantly increased by infection of citrus with severe CTV strains, relative to mild CTV strains or healthy plants. No significant trends of CTV infection on summed amounts of all sugar, phenolic, or terpenoid compounds were observed. However, individual compound levels were affected by CTV infections. Subsequent canonical discriminant analysis (CDA) that utilized profiles of individual amino acids, terpenoids, or phenolics successfully distinguished leaf samples to specific citrus varieties and identified infection status with good accuracy. Collectively, this study reveals biochemical patterns associated with severity of CTV infections that can potentially be utilized to help identify in-field CTV infections of economic relevance.
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Affiliation(s)
- Christopher M. Wallis
- Crop Diseases, Pests and Genetics Research Unit, United States Department of Agriculture—Agricultural Research Service San Joaquin Valley Agricultural Sciences Center, Parlier, California, United States of America
| | - Zachary Gorman
- Crop Diseases, Pests and Genetics Research Unit, United States Department of Agriculture—Agricultural Research Service San Joaquin Valley Agricultural Sciences Center, Parlier, California, United States of America
| | - Rachel Rattner
- Crop Diseases, Pests and Genetics Research Unit, United States Department of Agriculture—Agricultural Research Service San Joaquin Valley Agricultural Sciences Center, Parlier, California, United States of America
| | - Subhas Hajeri
- Citrus Pest Detection Program, Central California Tristeza Eradication Agency, Tulare, California, United States of America
| | - Raymond Yokomi
- Crop Diseases, Pests and Genetics Research Unit, United States Department of Agriculture—Agricultural Research Service San Joaquin Valley Agricultural Sciences Center, Parlier, California, United States of America
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Ghosh DK, Kokane A, Kokane S, Mukherjee K, Tenzin J, Surwase D, Deshmukh D, Gubyad M, Biswas KK. A Comprehensive Analysis of Citrus Tristeza Variants of Bhutan and Across the World. Front Microbiol 2022; 13:797463. [PMID: 35464978 PMCID: PMC9024366 DOI: 10.3389/fmicb.2022.797463] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 01/19/2022] [Indexed: 11/29/2022] Open
Abstract
Mandarin orange is economically one of the most important fruit crops in Bhutan. However, in recent years, orange productivity has dropped due to severe infection of citrus tristeza virus (CTV) associated with the gradual decline of citrus orchards. Although the disease incidence has been reported, very limited information is available on genetic variability among the Bhutanese CTV variants. This study used reverse transcription PCR (RT-PCR) to detect CTV in collected field samples and recorded disease incidence up to 71.11% in Bhutan’s prominent citrus-growing regions. To elucidate the extent of genetic variabilities among the Bhutanese CTV variants, we targeted four independent genomic regions (5′ORF1a, p25, p23, and p18) and analyzed a total of 64 collected isolates. These genomic regions were amplified and sequenced for further comparative bioinformatics analysis. Comprehensive phylogenetic reconstructions of the GenBank deposited sequences, including the corresponding genomic locations from 53 whole-genome sequences, revealed unexpected and rich diversity among Bhutanese CTV variants. A resistant-breaking (RB) variant was also identified for the first time from the Asian subcontinent. Our analyses unambiguously identified five (T36, T3, T68, VT, and HA16-5) major, well-recognized CTV strains. Bhutanese CTV variants form two additional newly identified distinct clades with higher confidence, B1 and B2, named after Bhutan. The origin of each of these nine clades can be traced back to their root in the north-eastern region of India and Bhutan. Together, our study established a definitive framework for categorizing global CTV variants into their distinctive clades and provided novel insights into multiple genomic region-based genetic diversity assessments, including their pathogenicity status.
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Affiliation(s)
- Dilip Kumar Ghosh
- Plant Virology Laboratory, ICAR-Central Citrus Research Institute, Nagpur, India
- *Correspondence: Dilip Kumar Ghosh,
| | - Amol Kokane
- Plant Virology Laboratory, ICAR-Central Citrus Research Institute, Nagpur, India
| | - Sunil Kokane
- Plant Virology Laboratory, ICAR-Central Citrus Research Institute, Nagpur, India
| | - Krishanu Mukherjee
- Whitney Laboratory for Marine Biosciences, University of Florida, St. Augustine, FL, United States
| | - Jigme Tenzin
- National Citrus Program, Department of Agriculture, Royal Government of Bhutan, Thimpu, Bhutan
| | - Datta Surwase
- Plant Virology Laboratory, ICAR-Central Citrus Research Institute, Nagpur, India
| | - Dhanshree Deshmukh
- Plant Virology Laboratory, ICAR-Central Citrus Research Institute, Nagpur, India
| | - Mrugendra Gubyad
- Plant Virology Laboratory, ICAR-Central Citrus Research Institute, Nagpur, India
| | - Kajal Kumar Biswas
- Department of Plant Pathology, Indian Agricultural Research Institute, New Delhi, India
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Britt K, Gebben S, Levy A, Achor D, Sieburth P, Stevens K, Al Rwahnih M, Batuman O. Analysis of Citrus Tristeza Virus Incidences within Asian Citrus Psyllid (Diaphorina citri) Populations in Florida via High-Throughput Sequencing. Insects 2022; 13:275. [PMID: 35323573 PMCID: PMC8954720 DOI: 10.3390/insects13030275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 03/04/2022] [Accepted: 03/07/2022] [Indexed: 11/17/2022]
Abstract
The destructive citrus disease, Huanglongbing (HLB) or citrus greening, continues to devastate Florida’s citrus industry. A hemipteran insect, the Asian citrus psyllid (ACP), disperses Candidatus Liberibacter asiaticus, one of the putative bacterial pathogens of HLB. This study builds upon ongoing research utilizing high-throughput sequencing to analyze the virome of ACP populations collected from citrus groves throughout Florida. Following the widespread detection of sequences aligning to the genome of citrus tristeza virus (CTV) across consecutive years in the Florida ACP virome, we continued to detect a pervasive amount of CTV in Florida ACPs during subsequent years. Simultaneously, we also detected mixed infections of CTV strains in pooled ACPs from different Florida regions. Predating the HLB epidemic, CTV has been present in Florida for many years and our results confirm its widespread and diverse persistence in Florida citrus groves through a unique lens, the ACP. CTV presence in the ACP likely results from feeding on CTV-infected citrus trees in Florida citrus groves, which may help to understand an overlapping presence of CTV and HLB, both endemic citrus pathosystems in the state, and their role in future integrated pest management strategies.
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Pais da Cunha AT, Chiumenti M, Ladeira LC, Abou Kubaa R, Loconsole G, Pantaleo V, Minafra A. High throughput sequencing from Angolan citrus accessions discloses the presence of emerging CTV strains. Virol J 2021; 18:62. [PMID: 33757535 PMCID: PMC7988965 DOI: 10.1186/s12985-021-01535-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 03/12/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Citrus industry is worldwide dramatically affected by outbreaks of Citrus tristeza virus (CTV). Controls should be applied to nurseries, which could act as diversity hotspots for CTV. Early detection and characterization of dangerous or emerging strains of this virus greatly help to prevent outbreaks of disease. This is particularly relevant in those growing regions where no dedicated certification programs are currently in use. METHODS Double-stranded RNA extracted from Citrus spp. samples, collected in two locations in Angola, were pooled and submitted to a random-primed RNA-seq. This technique was performed to acquire a higher amount of data in the survey, before the amplification and sequencing of genes from single plants. To confirm the CTV infection in individual plants, as suggested by RNA-seq information from the pooled samples, the analysis was integrated with multiple molecular marker amplification (MMM) for the main known CTV strains (T30, T36, VT and T3). RESULTS From the analysis of HTS data, several assembled contigs were identified as CTV and classified according to their similarity to the established strains. By the MMM amplification, only five individual accessions out of the eleven pooled samples, resulted to be infected by CTV. Amplified coat protein genes from the five positive sources were cloned and sequenced and submitted to phylogenetic analysis, while a near-complete CTV genome was also reconstructed by the fusion of three overlapping contigs. CONCLUSION Phylogenetic analysis of the ORF1b and CP genes, retrieved by de novo assembly and RT-PCR, respectively, revealed the presence of a wide array of CTV strains in the surveyed citrus-growing spots in Angola. Importantly, molecular variants among those identified from HTS showed high similarity with known severe strains as well as to recently described and emerging strains in other citrus-growing regions, such as S1 (California) or New Clade (Uruguay).
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Affiliation(s)
- Aderito Tomàs Pais da Cunha
- Instituto Superior Politécnico do Kuanza Sul (ISPKS), Rua 12 de Novembro, Sumbe, Angola
- Centro Nacional de Investigação Científica (CNIC), 201 Ho Chi Min Avenue, CP 34, Luanda, Angola
| | - Michela Chiumenti
- Institute for Sustainable Plant Protection - Consiglio Nazionale delle Ricerche (CNR), Via Giovanni Amendola 165/A, Bari, Italy
| | | | - Raied Abou Kubaa
- Institute for Sustainable Plant Protection - Consiglio Nazionale delle Ricerche (CNR), Via Giovanni Amendola 165/A, Bari, Italy
| | - Giuliana Loconsole
- Institute for Sustainable Plant Protection - Consiglio Nazionale delle Ricerche (CNR), Via Giovanni Amendola 165/A, Bari, Italy
| | - Vitantonio Pantaleo
- Institute for Sustainable Plant Protection - Consiglio Nazionale delle Ricerche (CNR), Via Giovanni Amendola 165/A, Bari, Italy
| | - Angelantonio Minafra
- Institute for Sustainable Plant Protection - Consiglio Nazionale delle Ricerche (CNR), Via Giovanni Amendola 165/A, Bari, Italy.
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Park JW, da Graça JV, Sétamou M, Kunta M. Diversity of Citrus tristeza virus Strains in the Upper Gulf Coast Area of Texas. Plant Dis 2021; 105:592-598. [PMID: 32840435 DOI: 10.1094/pdis-02-20-0410-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Citrus tristeza virus (CTV) in Texas was first reported in the 1950s and has since been sporadically reported in the residential areas in the Upper Gulf Coast region. Because the major rootstock for commercial citriculture in South Texas is sour orange, which is susceptible to CTV decline, the spread of CTV into South Texas can pose a great threat to Texas citrus industry. Thirty-six CTV-positive samples, collected during surveys conducted in the Upper Gulf Coast area of Texas from 2013 to 2018, were first analyzed by strain-specific real-time PCR (RT-PCR) targeting various regions of CTV Open reading frame (Orf) 1a and then by amplicon sequencing derived from p25 and p20 region of CTV genome. Among 36 samples, 33 were successfully genotyped by strain-specific RT-PCR and by amplicon sequencing followed by phylogenetic analysis. Variability in the detection of CTV strains was observed over a 6-year period. In 2013, T3 and T30 were the only strains detected in the Upper Gulf Coast of Texas, but in further surveys until 2018, additional strains were detected, including T36, VT, and RB. Mixed infections were also detected in 14 samples comprising about 42% of CTV samples examined in the study. Although genotyping mixed infection samples by targeting Orf 1a and full-length p25, residing in the 5' and 3' region of the CTV genome, respectively, confirmed the presence of multiple strains in these samples, incongruent genotyping data were observed. These findings suggested that the current status of CTV strain diversity in Texas Upper Gulf Coast region might have been established by multiple introductions of CTV-infected plant materials for propagation and with a potential recombination in planta.
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Affiliation(s)
- Jong-Won Park
- Texas A&M University-Kingsville Citrus Center, Weslaco, TX 78599
| | - John V da Graça
- Texas A&M University-Kingsville Citrus Center, Weslaco, TX 78599
| | - Mamoudou Sétamou
- Texas A&M University-Kingsville Citrus Center, Weslaco, TX 78599
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Abstract
In California, citrus tristeza virus (CTV) is regulated by a State Interior Quarantine. In CTV abatement districts in central California, trees with CTV that react to MCA13 (MCA13-positive [MCA13+]), a strain-discriminating monoclonal antibody, are rogued to prevent virus spread. The Tulare County Pest Control District, however, does not participate in this abatement program except for a 1.6-km2 zone around the Lindcove Research and Extension Center, Exeter, CA. To quantify CTV spread under these two disparate management programs, CTV surveys were conducted in abatement plots with mandatory aphid control and nonabatement plots. Abatement plot surveys used hierarchical sampling of 25% of trees with samples pooled from four adjacent trees. Detection of MCA13+ CTV in a sample prompted resampling and testing of individual trees. From 2008 to 2018, incidence of CTV increased by an average of 3.9%, with only two MCA13+ samples detected. In contrast, in nonabatement plots, incidence of CTV increased by an average of 4.6% between 2015 and 2018. Increase in MCA13-negative (MCA-) isolates was 11 times greater than that of MCA13+ isolates, with the number of MCA13+ trees increasing by 19 trees between 2015 and 2018. MCA13- isolates were more randomly distributed, suggesting primary spread, whereas MCA13+ CTV isolates were more aggregated, suggesting some secondary spread. These results suggest that spread of MCA13+ isolates was limited by a combination of tree removal and aphid vector suppression. MCA13+ samples were VT isolates with some mixtures with T30 isolates. Despite the presence of VT isolates, all CTV-infected trees were asymptomatic.
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Affiliation(s)
- Raymond K Yokomi
- United States Department of Agriculture-Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, 9611 South Riverbend Avenue, Parlier, CA 93648-9757, U.S.A
| | - Mark S Sisterson
- United States Department of Agriculture-Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, 9611 South Riverbend Avenue, Parlier, CA 93648-9757, U.S.A
| | - Subhas Hajeri
- Citrus Pest Detection Program, Central California Tristeza Eradication Agency, 22847 Road 140, Tulare, CA 93274-9367, U.S.A
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Wu J, Zhang S, Atta S, Yang C, Zhou Y, Di Serio F, Zhou C, Cao M. Discovery and Survey of a New Mandarivirus Associated with Leaf Yellow Mottle Disease of Citrus in Pakistan. Plant Dis 2020; 104:1593-1600. [PMID: 32357118 DOI: 10.1094/pdis-08-19-1744-re] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
During biological indexing for viruses in citrus trees, in a collection of Symons sweet orange (SSO) (Citrus sinensis L. Osbeck) graft inoculated with bark tissues of citrus trees from the Punjab Province in Pakistan, several SSO trees exhibited leaf symptoms of vein yellowing and mottle. High-throughput sequencing by Illumina of RNA preparation depleted of ribosomal RNAs from one symptomatic tree, followed by BLAST analyses, allowed identification of a novel virus, tentatively named citrus yellow mottle-associated virus (CiYMaV). Genome features of CiYMaV are typical of members of the genus Mandarivirus (family Alphaflexiviridae). Virus particles with elongated flexuous shape and size resembling those of mandariviruses were observed by transmission electron microscopy. The proteins encoded by CiYMaV share high sequence identity, conserved motifs, and phylogenetic relationships with the corresponding proteins encoded by Indian citrus ringspot virus (ICRSV) and citrus yellow vein clearing virus (CYVCV), the two current members of the genus Mandarivirus. Although CYVCV is the virus most closely related to CiYMaV, the two viruses can be serologically and biologically discriminated from each other. A reverse-transcription PCR method designed to specifically detect CiYMaV revealed high prevalence (62%) of this virus in 120 citrus trees from the Punjab Province, Pakistan, where the novel virus was found mainly in mixed infection with CYVCV and citrus tristeza virus. However, a preliminary survey on samples from 200 citrus trees from the Yunnan Province, China failed to detect CiYMaV in this region, suggesting that the molecular, serological, and biological data provided here are timely and can help to prevent the spread of this virus in citrus-producing countries.
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Affiliation(s)
- Jiaxing Wu
- National Citrus Engineering and Technology Research Center, Citrus Research Institute, Southwest University, Beibei, Chongqing 400712, China
| | - Song Zhang
- National Citrus Engineering and Technology Research Center, Citrus Research Institute, Southwest University, Beibei, Chongqing 400712, China
| | - Sagheer Atta
- Faculty of Agricultural Sciences, Ghazi University, Dera Ghazi Khan 32200, Pakistan
| | - Caixia Yang
- Liaoning Key Laboratory of Urban Integrated Pest Management and Ecological Security, College of Life Science and Engineering Shenyang University, Shenyang 110044, China
| | - Yan Zhou
- National Citrus Engineering and Technology Research Center, Citrus Research Institute, Southwest University, Beibei, Chongqing 400712, China
| | - Francesco Di Serio
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Bari 70126, Italy
| | - Changyong Zhou
- National Citrus Engineering and Technology Research Center, Citrus Research Institute, Southwest University, Beibei, Chongqing 400712, China
| | - Mengji Cao
- National Citrus Engineering and Technology Research Center, Citrus Research Institute, Southwest University, Beibei, Chongqing 400712, China
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Saponari M, Giampetruzzi A, Selvaraj V, Maheshwari Y, Yokomi R. Identification and Characterization of Resistance-Breaking (RB) Isolates of Citrus tristeza virus. Methods Mol Biol 2020; 2015:105-126. [PMID: 31222699 DOI: 10.1007/978-1-4939-9558-5_8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Resistance-breaking (RB) strains constitute a clade of biological and genetically distinct isolates of Citrus tristeza virus (CTV) that replicate and move systemically in Poncirus trifoliata (trifoliate orange), resistant to other known strains of CTV. Molecular markers have been developed by comparative genome analysis to allow quick identification of potential RB isolates. Here, methods are described to identify and characterize RB strains by reverse transcription-polymerase chain reaction (RT-PCR), quantitative real-time RT-PCR (RT-qPCR), full-length genome sequencing, and biological indexing.
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Affiliation(s)
- Maria Saponari
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Bari, Italy.
| | - Annalisa Giampetruzzi
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Bari, Italy
| | | | - Yogita Maheshwari
- San Joaquin Valley Agricultural Sciences Center, USDA-ARS, Parlier, CA, USA
| | - Raymond Yokomi
- San Joaquin Valley Agricultural Sciences Center, USDA-ARS, Parlier, CA, USA
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Tan SH, Osman F, Bodaghi S, Dang T, Greer G, Huang A, Hammado S, Abu-Hajar S, Campos R, Vidalakis G. Full genome characterization of 12 citrus tatter leaf virus isolates for the development of a detection assay. PLoS One 2019; 14:e0223958. [PMID: 31622412 PMCID: PMC6797102 DOI: 10.1371/journal.pone.0223958] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 09/18/2019] [Indexed: 12/05/2022] Open
Abstract
Citrus tatter leaf virus (CTLV) threatens citrus production worldwide because it induces bud-union crease on the commercially important Citrange (Poncirus trifoliata × Citrus sinensis) rootstocks. However, little is known about its genomic diversity and how such diversity may influence virus detection. In this study, full-length genome sequences of 12 CTLV isolates from different geographical areas, intercepted and maintained for the past 60 years at the Citrus Clonal Protection Program (CCPP), University of California, Riverside, were characterized using next generation sequencing. Genome structure and sequence for all CTLV isolates were similar to Apple stem grooving virus (ASGV), the type species of Capillovirus genus of the Betaflexiviridae family. Phylogenetic analysis highlighted CTLV’s point of origin in Asia, the virus spillover to different plant species and the bottleneck event of its introduction in the United States of America (USA). A reverse transcription quantitative polymerase chain reaction assay was designed at the most conserved genome area between the coat protein and the 3’-untranslated region (UTR), as identified by the full genome analysis. The assay was validated with different parameters (e.g. specificity, sensitivity, transferability and robustness) using multiple CTLV isolates from various citrus growing regions and it was compared with other published assays. This study proposes that in the era of powerful affordable sequencing platforms the presented approach of systematic full-genome sequence analysis of multiple virus isolates, and not only a small genome area of a small number of isolates, becomes a guideline for the design and validation of molecular virus detection assays, especially for use in high value germplasm programs.
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Affiliation(s)
- Shih-hua Tan
- Department of Microbiology and Plant Pathology, University of California, Riverside, California, United States of America
| | - Fatima Osman
- Department of Plant Pathology, University of California, Davis, California, United States of America
| | - Sohrab Bodaghi
- Department of Microbiology and Plant Pathology, University of California, Riverside, California, United States of America
| | - Tyler Dang
- Department of Microbiology and Plant Pathology, University of California, Riverside, California, United States of America
| | - Greg Greer
- Department of Microbiology and Plant Pathology, University of California, Riverside, California, United States of America
| | - Amy Huang
- Department of Microbiology and Plant Pathology, University of California, Riverside, California, United States of America
| | - Sarah Hammado
- Department of Microbiology and Plant Pathology, University of California, Riverside, California, United States of America
| | - Shurooq Abu-Hajar
- Department of Microbiology and Plant Pathology, University of California, Riverside, California, United States of America
| | - Roya Campos
- Department of Microbiology and Plant Pathology, University of California, Riverside, California, United States of America
| | - Georgios Vidalakis
- Department of Microbiology and Plant Pathology, University of California, Riverside, California, United States of America
- * E-mail:
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Selvaraj V, Maheshwari Y, Hajeri S, Yokomi R. A rapid detection tool for VT isolates of Citrus tristeza virus by immunocapture-reverse transcriptase loop-mediated isothermal amplification assay. PLoS One 2019; 14:e0222170. [PMID: 31487325 PMCID: PMC6728045 DOI: 10.1371/journal.pone.0222170] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Accepted: 08/21/2019] [Indexed: 11/18/2022] Open
Abstract
Severe strains of Citrus tristeza virus (CTV) cause quick decline and stem pitting resulting in significant economic losses in citrus production. A immunocapture reverse-transcriptase loop-mediated amplification (IC-RT-LAMP) assay was developed in this study to detect the severe VT strains that are typically associated with severe CTV symptoms. The sensitivity of RT-LAMP assay was determined by ten-fold serial dilutions of CA-VT-AT39 RNA, in comparison to one-step RT-droplet digital (dd) PCR. RT-LAMP detected up to 0.002 ng RNA with an amplification time of 10:35 (min:sec.), equivalent to 11.3 copies as determined by one step RT-ddPCR. The RT-LAMP assay specifically detected CA-VT-AT39 RNA and did not cross react with other CTV genotypes tested (T36, T30, RB, S1 and T68). To facilitate rapid on-site detection, the RT-LAMP assay was improved by first capturing the CTV virions from citrus crude leaf sap using CTV-IgG (IC-RT-LAMP), thereby eliminating nucleic acid extraction steps. IC-RT-LAMP assay was optimized with two-fold dilutions of CTV-IgG ranging from 1:500 to 1:16,000. The IC-RT-LAMP assay detected the CA-VT-AT39 virions in all dilutions tested. The minimum amplification time was 6:45 (min:sec) with 1:500 and 1:1000 of CTV-IgG dilutions. The limit of detection of IC-RT-LAMP assay with crude leaf sap of CA-VT-AT39 was 1:320 with a maximum amplification time of 9:08 (min:sec). The IC-RT-LAMP assay was validated for VT genotype by comparing to IC-RT-qPCR using the CTV from 40 field tree samples. A 100% agreement was observed between tests, regardless of single or mixed infections of CTV VT with other genotypes. Therefore, the IC-RT-LAMP assay can serve as a useful tool in the management of potentially severe strains of CTV.
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Affiliation(s)
- Vijayanandraj Selvaraj
- USDA-ARS, San Joaquin Valley Agricultural Sciences Center, Parlier, CA, United States of America
| | - Yogita Maheshwari
- USDA-ARS, San Joaquin Valley Agricultural Sciences Center, Parlier, CA, United States of America
| | - Subhas Hajeri
- Citrus Pest Detection Program, Central California Tristeza Eradication Agency, Tulare, CA, United States of America
| | - Raymond Yokomi
- USDA-ARS, San Joaquin Valley Agricultural Sciences Center, Parlier, CA, United States of America
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13
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Ruiz-Ruiz S, Navarro B, Peña L, Navarro L, Moreno P, Di Serio F, Flores R. Citrus tristeza virus: Host RNA Silencing and Virus Counteraction. Methods Mol Biol 2019; 2015:195-207. [PMID: 31222705 DOI: 10.1007/978-1-4939-9558-5_14] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
To dissect the host RNA silencing response incited by citrus tristeza virus (CTV, genus Closterovirus), a (+) ssRNA of ~19300 nt, and the counter reaction deployed by the virus via its three RNA silencing suppressors (RSS), the small RNAs (sRNAs) of three virus-host combinations were deep sequenced. The subsequent analysis indicated that CTV sRNAs (1) constitute more than half of the total sRNAs in the susceptible Mexican lime and sweet orange, while only 3.5% in the restrictive sour orange; (2) are mostly of 21-22 nt, with those of (+) sense predominating slightly; and (3) derive from all the CTV genome, as evidenced by its entire recomposition from viral sRNA contigs but adopt an asymmetric pattern with a hotspot mapping at the 3'-terminal ~2500 nt. The citrus homologues of Arabidopsis Dicer-like (DCL) 4 and 2 most likely generate the 21 and 22 nt CTV sRNAs, respectively, by dicing the gRNA and the 3' co-terminal sgRNAs and, particularly, their double-stranded forms accumulating in infected cells. The plant sRNA profile, very similar and dominated by the 24 nt sRNAs in the three mock-inoculated controls, displayed a major reduction of the 24 nt sRNAs in Mexican lime and sweet orange, but not in sour orange. CTV infection also influences the levels of certain microRNAs.The high accumulation of CTV sRNAs in two of the citrus hosts examined suggests that it is not their synthesis, but their function, the target of the RSS encoded by CTV: p25 (intercellular), p23 (intracellular) and p20 (both). The two latter might block the loading of CTV sRNAs into the RNA silencing complex or interfere with it through alternative mechanisms. Of the three CTV RSS, p23 is the one that has been more thoroughly studied. It is a multifunctional RNA-binding protein with a putative Zn finger domain and basic motifs that (1) has no homologues in other closteroviruses, (2) accumulates in the nucleolus and plasmodesmata, (3) regulates the asymmetric balance of CTV (+) and (-) RNA strands, and (4) induces CTV syndromes and stimulates systemic infection in certain citrus species when expressed as a transgene ectopically or in phloem-associated cells.
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Affiliation(s)
- Susana Ruiz-Ruiz
- Instituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia-Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | - Beatriz Navarro
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Bari, Italy
| | - Leandro Peña
- Instituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia-Consejo Superior de Investigaciones Científicas, Valencia, Spain.,Instituto Valenciano de Investigaciones Agrarias, Moncada, Spain
| | - Luis Navarro
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Valencia, Spain
| | - Pedro Moreno
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Valencia, Spain
| | - Francesco Di Serio
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Bari, Italy
| | - Ricardo Flores
- Instituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia-Consejo Superior de Investigaciones Científicas, Valencia, Spain.
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Abstract
High-throughput sequencing (HTS) is a powerful tool employed by plant virologists for the detection of viruses, the characterization of virus genomes and the study of host-pathogen interactions. Virus detection has been an important application of this technology, which has resulted in the discovery of novel viruses or viral strains as well as for the detection of known viruses in a plant sample. Here we describe the entire process that needs to be considered for the genome analysis of Citrus tristeza virus (CTV) by HTS, including the experimental design, sample preparation, nucleic acid purification, HTS library construction, and bioinformatic analysis.
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Affiliation(s)
| | - Rachelle Bester
- Department of Genetics, Stellenbosch University, Matieland, South Africa
- Agricultural Research Council, Infruitec-Nietvoorbij: Institute for Deciduous Fruit, Vines and Wine, Stellenbosch, South Africa
| | - Antonio Olmos
- Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, Valencia, Spain.
| | - Hans Jacob Maree
- Department of Genetics, Stellenbosch University, Matieland, South Africa
- Citrus Research International, Nelspruit, Mpumalanga, South Africa
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Chen AYS, Watanabe S, Yokomi R, Ng JCK. Nucleotide heterogeneity at the terminal ends of the genomes of two California Citrus tristeza virus strains and their complete genome sequence analysis. Virol J 2018; 15:141. [PMID: 30219073 PMCID: PMC6139129 DOI: 10.1186/s12985-018-1041-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 08/13/2018] [Indexed: 11/10/2022] Open
Abstract
Background The non-translated regions at the genome ends of RNA viruses serve diverse functions and can exhibit various levels of nucleotide (nt) heterogeneity. However, the extent of nt heterogeneity at the extreme termini of Citrus tristeza virus (CTV) genomes has not been comprehensively documented. This study aimed to characterize two widely prevalent CTV genotypes, T36-CA and T30-CA, from California that have not been sequenced or analyzed substantially. The information obtained will be used in our ongoing effort to construct the infectious complementary (c) DNA clones of these viruses. Methods The terminal nts of the viral genomes were identified by sequencing cDNA clones of the plus- and/or minus-strand of the viral double-stranded (ds) RNAs generated using 5′ and 3′ rapid amplification of cDNA ends. Cloned cDNAs corresponding to the complete genome sequences of both viruses were generated using reverse transcription-polymerase chain reactions, sequenced, and subjected to phylogenetic analysis. Results Among the predominant terminal nts identified, some were identical to the consensus sequences in GenBank, while others were different or unique. Remarkably, one of the predominant 5′ nt variants of T36-CA contained the consensus nts “AATTTCAAA” in which a highly conserved cytidylate, seen in all other full-length T36 sequences, was absent. As expected, but never systematically verified before, unique variants with additional nt (s) incorporated upstream of the 5′ terminal consensus nts of T36-CA and T30-CA were also identified. In contrast to the extreme 5′ terminal nts, those at the extreme 3′ termini of T36-CA and T30-CA were more conserved compared to the reference sequences, although nt variants were also found. Notably, an additional thymidylate at the extreme 3′ end was identified in many T36-CA sequences. Finally, based on pairwise comparisons and phylogenetic analysis with multiple reference sequences, the complete sequences of both viruses were found to be highly conserved with those of the respective genotypes. Conclusions The extreme terminal nts in the T36-CA and T30-CA genomes were identified, revealing new insights on the heterogeneity of these CTV genomic regions. T36-CA and T30-CA were the first and the second genotypes, respectively, of CTV originating from California to be completely sequenced and analyzed. Electronic supplementary material The online version of this article (10.1186/s12985-018-1041-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Angel Y S Chen
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, 92521, USA
| | - Shizu Watanabe
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, 92521, USA
| | - Raymond Yokomi
- United States Department of Agriculture, Agricultural Research Service, Parlier, CA, 93648, USA
| | - James C K Ng
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, 92521, USA. .,Center for Infectious Diseases and Vector Research, University of California, Riverside, CA, 92521, USA.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Yokomi R, Selvaraj V, Maheshwari Y, Chiumenti M, Saponari M, Giampetruzzi A, Weng Z, Xiong Z, Hajeri S. Molecular and biological characterization of a novel mild strain of citrus tristeza virus in California. Arch Virol 2018; 163:1795-1804. [PMID: 29550931 DOI: 10.1007/s00705-018-3799-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 02/28/2018] [Indexed: 10/17/2022]
Abstract
Strain differentiating marker profiles of citrus tristeza virus (CTV) isolates from California have shown the presence of multiple genotypes. To better define the genetic diversity involved, full-length genome sequences from four California CTV isolates were determined by small-interfering RNA sequencing. Phylogenetic analysis and nucleotide sequence comparisons differentiated these isolates into the genotypes VT (CA-VT-AT39), T30 (CA-T30-AT4), and a new strain called S1 (CA-S1-L and CA-S1-L65). S1 isolates had three common recombination events within portions of genes from VT, T36 and RB strains and were transmissible by Aphis gossypii. Virus indexing showed that CA-VT-AT39 could be classified as a severe strain, whereas CA-T30-AT4, CA-S1-L and CA-S1-L65 were mild. CA-VT-AT39, CA-S1-L, and CA-S1-L65 reacted with monoclonal antibody MCA13, whereas CA-T30-AT4 did not. RT-PCR and RT-qPCR detection assays for the S1 strain were developed and used to screen MCA13-reactive isolates in a CTV collection from central California collected from 1968 to 2011. Forty-two isolates were found to contain the S1 strain, alone or in combinations with other genotypes. BLAST and phylogenetic analysis of the S1 p25 gene region with other extant CTV sequences from the NCBI database suggested that putative S1-like isolates might occur elsewhere (e.g., China, South Korea, Turkey, Bosnia and Croatia). This information is important for CTV evolution, detection of specific strains, and cross-protection.
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Affiliation(s)
- Raymond Yokomi
- United States Department of Agriculture-Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, 9611 South Riverbend Avenue, Parlier, CA, 93648-9757, USA.
| | - Vijayanandraj Selvaraj
- United States Department of Agriculture-Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, 9611 South Riverbend Avenue, Parlier, CA, 93648-9757, USA
| | - Yogita Maheshwari
- United States Department of Agriculture-Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, 9611 South Riverbend Avenue, Parlier, CA, 93648-9757, USA
| | - Michela Chiumenti
- Institute for Sustainable Plant Protection, Italian National Research Council, Sezione di Bari, Via Amendola 122/D, 70126, Bari, Italy
| | - Maria Saponari
- Institute for Sustainable Plant Protection, Italian National Research Council, Sezione di Bari, Via Amendola 122/D, 70126, Bari, Italy
| | - Annalisa Giampetruzzi
- Department of Soil Plant and Food Science, University of Bari Aldo Moro, Via Amendola 165/A, 70126, Bari, Italy
| | - Ziming Weng
- School of Plant Sciences and BIO5 Institute, University of Arizona, Tucson, AZ, 85721-7186, USA
| | - Zhongguo Xiong
- School of Plant Sciences and BIO5 Institute, University of Arizona, Tucson, AZ, 85721-7186, USA
| | - Subhas Hajeri
- Citrus Pest Detection Program, Central California Tristeza Eradication Agency, 22847 Road 140, Tulare, CA, 93274-9367, USA
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