1
|
Adegbola RO, Ponvert ND, Brown JK. Genetic Variability Among U.S.-Sentinel Cotton Plot Cotton Leafroll Dwarf Virus and Globally Available Reference Isolates Based on ORF0 Diversity. PLANT DISEASE 2024; 108:1799-1811. [PMID: 38277653 DOI: 10.1094/pdis-02-23-0243-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2024]
Abstract
The aphid-transmitted polerovirus, cotton leafroll dwarf virus (CLRDV), first characterized from symptomatic cotton plants in South America, has been identified in commercial cotton plantings in the United States. Here, the CLRDV intraspecific diversity was investigated by comparative sequence analysis of the most divergent CLRDV coding region, ORF0/P0. Bayesian analysis of ORF0 sequences for U.S. and reference populations resolved three well-supported sister clades comprising one U.S. and two South American lineages. Principal component analysis (PCA) identified seven statistically supported intraspecific populations. The Bayesian phylogeny and PCA dendrogram-inferred relationships were congruent. Population analysis of ORF0 sequences indicated most lineages have evolved under negative selection, albeit certain sites/isolates evolved under positive selection. Both U.S. and South American isolates exhibited extensive ORF0 diversity. At least two U.S. invasion foci were associated with their founder populations in Alabama-Georgia and eastern Texas. The Alabama-Georgia founder is implicated as the source of recent widespread expansion and establishment of secondary disease foci throughout the southeastern-central United States. Based on the geographically restricted distribution, spread of another extant Texas population appeared impeded by a population bottleneck. Extant CLRDV isolates represent several putative introductions potentially associated with catastrophic weather events dispersing viruliferous cotton aphids of unknown origin(s).
Collapse
Affiliation(s)
| | | | - Judith K Brown
- School of Plant Sciences, University of Arizona, Tucson, AZ 85721
| |
Collapse
|
2
|
Parkash V, Snider JL, Pilon C, Bag S, Jespersen D, Virk G, Dhillon KK. Differential sensitivities of photosynthetic component processes govern oxidative stress levels and net assimilation rates in virus-infected cotton. PHOTOSYNTHESIS RESEARCH 2023; 158:41-56. [PMID: 37470938 DOI: 10.1007/s11120-023-01038-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 07/03/2023] [Indexed: 07/21/2023]
Abstract
Cotton (Gossypium hirsutum L.) leafroll dwarf virus disease (CLRDD) is a yield-limiting threat to cotton production and can substantially limit net photosynthetic rates (AN). Previous research showed that AN was more sensitive to CLRDD-induced reductions in stomatal conductance than electron transport rate (ETR) through photosystem II (PSII). This observation coupled with leaf reddening symptomology led to the hypothesis that differential sensitivities of photosynthetic component processes to CLRDD would contribute to declines in AN and increases in oxidative stress, stimulating anthocyanin production. Thus, an experiment was conducted to define the relative sensitivity of photosynthetic component processes to CLRDD and to quantify oxidative stress and anthocyanin production in field-grown cotton. Among diffusional limitations to AN, reductions in mesophyll conductance and CO2 concentration in the chloroplast were the greatest constraints to AN under CLRDD. Multiple metabolic processes were also adversely impacted by CLRDD. ETR, RuBP regeneration, and carboxylation were important metabolic (non-diffusional) limitations to AN in symptomatic plants. Photorespiration and dark respiration were less sensitive than photosynthetic processes, contributing to declines in AN in symptomatic plants. Among thylakoid processes, reduction of PSI end electron acceptors was the most sensitive to CLRDD. Oxidative stress indicators (H2O2 production and membrane peroxidation) and anthocyanin contents were substantially higher in symptomatic plants, concomitant with reductions in carotenoid content and no change in energy dissipation by PSII. We conclude that differential sensitivities of photosynthetic processes to CLRDD and limited potential for energy dissipation at PSII increases oxidative stress, stimulating anthocyanin production as an antioxidative mechanism.
Collapse
Affiliation(s)
- Ved Parkash
- Department of Crop and Soil Sciences, University of Georgia, Tifton, GA, 31794, USA.
| | - John L Snider
- Department of Crop and Soil Sciences, University of Georgia, Tifton, GA, 31794, USA
| | - Cristiane Pilon
- Department of Crop and Soil Sciences, University of Georgia, Tifton, GA, 31794, USA
| | - Sudeep Bag
- Department of Plant Pathology, University of Georgia, Tifton, GA, 31794, USA
| | - David Jespersen
- Department of Crop and Soil Sciences, University of Georgia, Griffin, GA, 30223, USA
| | - Gurpreet Virk
- Department of Crop and Soil Sciences, University of Georgia, Tifton, GA, 31794, USA
| | - Kamalpreet Kaur Dhillon
- Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Tifton, GA, 31794, USA
| |
Collapse
|
3
|
Mahas JW, Mahas JB, Ray C, Kesheimer A, Steury TD, Conzemius SR, Crow W, Gore J, Greene JK, Kennedy GG, Kerns D, Malone S, Paula-Moraes S, Roberts P, Stewart SD, Taylor S, Toews M, Jacobson AL. The Spatiotemporal Distribution, Abundance, and Seasonal Dynamics of Cotton-Infesting Aphids in the Southern U.S. INSECTS 2023; 14:639. [PMID: 37504645 PMCID: PMC10380445 DOI: 10.3390/insects14070639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 07/04/2023] [Accepted: 07/13/2023] [Indexed: 07/29/2023]
Abstract
Cotton leafroll dwarf virus (CLRDV) is an emerging aphid-borne pathogen infecting cotton, Gossypium hirsutum L., in the southern United States (U.S.). The cotton aphid, Aphis gossypii Glover, infests cotton annually and is the only known vector to transmit CLRDV to cotton. Seven other species have been reported to feed on, but not often infest, cotton: Protaphis middletonii Thomas, Aphis craccivora Koch, Aphis fabae Scopoli, Macrosiphum euphorbiae Thomas, Myzus persicae Sulzer, Rhopalosiphum rufiabdominale Sasaki, and Smynthurodes betae Westwood. These seven have not been studied in cotton, but due to their potential epidemiological importance, an understanding of the intra- and inter-annual variations of these species is needed. In 2020 and 2021, aphids were monitored from North Carolina to Texas using pan traps around cotton fields. All of the species known to infest cotton, excluding A. fabae, were detected in this study. Protaphis middletonii and A. gossypii were the most abundant species identified. The five other species of aphids captured were consistently low throughout the study and, with the exception of R. rufiabdominale, were not detected at all locations. The abundance, distribution, and seasonal dynamics of cotton-infesting aphids across the southern U.S. are discussed.
Collapse
Affiliation(s)
- John W Mahas
- Department of Entomology and Plant Pathology, Auburn University, 301 Funchess Hall, Auburn, AL 36849, USA
| | - Jessica B Mahas
- Department of Entomology and Plant Pathology, Auburn University, 301 Funchess Hall, Auburn, AL 36849, USA
| | - Charles Ray
- Department of Entomology and Plant Pathology, Auburn University, 301 Funchess Hall, Auburn, AL 36849, USA
| | - Adam Kesheimer
- Department of Entomology and Plant Pathology, Auburn University, 301 Funchess Hall, Auburn, AL 36849, USA
| | - Todd D Steury
- College of Forestry, Wildlife and Environment, Auburn University, 602 Duncan Drive, Auburn, AL 36849, USA
| | - Sophia R Conzemius
- Edisto Research and Education Center, Department of Plant and Environmental Sciences, Clemson University, Blackville, SC 29817, USA
| | - Whitney Crow
- Delta Research and Extension Center, Mississippi State University, Stoneville, MS 39762, USA
| | - Jeffrey Gore
- Delta Research and Extension Center, Mississippi State University, Stoneville, MS 39762, USA
| | - Jeremy K Greene
- Edisto Research and Education Center, Department of Plant and Environmental Sciences, Clemson University, Blackville, SC 29817, USA
| | - George G Kennedy
- Department of Entomology and Plant Pathology, North Carolina State University, 3210 Ligon St., Raleigh, NC 27695, USA
| | - David Kerns
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA
| | - Sean Malone
- Virginia Tech, Tidewater Agricultural Research and Extension Center, Suffolk, VA 23437, USA
| | - Silvana Paula-Moraes
- West Florida Research and Education Center, Department of Entomology and Nematology, University of Florida, Jay, FL 32565, USA
| | - Phillip Roberts
- Department of Entomology, University of Georgia, 2360 Rainwater Rd., Tifton, GA 31793, USA
| | - Scott D Stewart
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996, USA
| | - Sally Taylor
- Virginia Tech, Tidewater Agricultural Research and Extension Center, Suffolk, VA 23437, USA
| | - Michael Toews
- Department of Entomology, University of Georgia, 2360 Rainwater Rd., Tifton, GA 31793, USA
| | - Alana L Jacobson
- Department of Entomology and Plant Pathology, Auburn University, 301 Funchess Hall, Auburn, AL 36849, USA
| |
Collapse
|
4
|
Edula SR, Bag S, Milner H, Kumar M, Suassuna ND, Chee PW, Kemerait RC, Hand LC, Snider JL, Srinivasan R, Roberts PM. Cotton leafroll dwarf disease: An enigmatic viral disease in cotton. MOLECULAR PLANT PATHOLOGY 2023; 24:513-526. [PMID: 37038256 PMCID: PMC10189767 DOI: 10.1111/mpp.13335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 03/18/2023] [Accepted: 03/21/2023] [Indexed: 05/18/2023]
Abstract
TAXONOMY Cotton leafroll dwarf virus (CLRDV) is a member of the genus Polerovirus, family Solemoviridae. Geographical Distribution: CLRDV is present in most cotton-producing regions worldwide, prominently in North and South America. PHYSICAL PROPERTIES The virion is a nonenveloped icosahedron with T = 3 icosahedral lattice symmetry that has a diameter of 26-34 nm and comprises 180 molecules of the capsid protein. The CsCl buoyant density of the virion is 1.39-1.42 g/cm3 and S20w is 115-127S. Genome: CLRDV shares genomic features with other poleroviruses; its genome consists of monopartite, single-stranded, positive-sense RNA, is approximately 5.7-5.8 kb in length, and is composed of seven open reading frames (ORFs) with an intergenic region between ORF2 and ORF3a. TRANSMISSION CLRDV is transmitted efficiently by the cotton aphid (Aphis gossypii Glover) in a circulative and nonpropagative manner. Host: CLRDV has a limited host range. Cotton is the primary host, and it has also been detected in different weeds in and around commercial cotton fields in Georgia, USA. SYMPTOMS Cotton plants infected early in the growth stage exhibit reddening or bronzing of foliage, maroon stems and petioles, and drooping. Plants infected in later growth stages exhibit intense green foliage with leaf rugosity, moderate to severe stunting, shortened internodes, and increased boll shedding/abortion, resulting in poor boll retention. These symptoms are variable and are probably influenced by the time of infection, plant growth stage, varieties, soil health, and geographical location. CLRDV is also often detected in symptomless plants. CONTROL Vector management with the application of chemical insecticides is ineffective. Some host plant varieties grown in South America are resistant, but all varieties grown in the United States are susceptible. Integrated disease management strategies, including weed management and removal of volunteer stalks, could reduce the abundance of virus inoculum in the field.
Collapse
Affiliation(s)
| | - Sudeep Bag
- Department of Plant PathologyUniversity of GeorgiaTiftonGeorgiaUSA
| | - Hayley Milner
- Department of Plant PathologyUniversity of GeorgiaTiftonGeorgiaUSA
| | - Manish Kumar
- Department of Plant PathologyUniversity of GeorgiaTiftonGeorgiaUSA
| | | | - Peng W. Chee
- Institute of Plant, Breeding, Genetics, and GenomicsUniversity of GeorgiaTiftonGeorgiaUSA
| | | | - Lavesta C. Hand
- Department of Crop and Soil SciencesUniversity of GeorgiaTiftonGeorgiaUSA
| | - John L. Snider
- Department of Crop and Soil SciencesUniversity of GeorgiaTiftonGeorgiaUSA
| | | | | |
Collapse
|
5
|
Heilsnis B, Mahas JB, Conner K, Pandey S, Clark W, Koebernick J, Srinivasan R, Martin K, Jacobson AL. Characterizing the vector competence of Aphis gossypii, Myzus persicae and Aphis craccivora (Hemiptera: Aphididae) to transmit cotton leafroll dwarf virus to cotton in the United States. JOURNAL OF ECONOMIC ENTOMOLOGY 2023:7160744. [PMID: 37171119 DOI: 10.1093/jee/toad080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 04/05/2023] [Accepted: 04/24/2023] [Indexed: 05/13/2023]
Abstract
Cotton leafroll dwarf virus (CLRDV) is a yield-limiting, aphid-transmitted virus that was identified in cotton, Gossypium hirsutum L., in the United States of America in 2017. CLRDV is currently classified in the genus Polerovirus, family Solemoviridae. Although 8 species of aphids (Hemiptera: Aphididae) are reported to infest cotton, Aphis gossypii Glover is the only known vector of CLRDV to this crop. Aphis gossypii transmits CLRDV in a persistent and nonpropagative manner, but acquisition and retention times have only been partially characterized in Brazil. The main objectives of this study were to characterize the acquisition access period, the inoculation access period, and retention times for a U.S. strain of CLRDV and A. gossypii population. A sub-objective was to test the vector competence of Myzus persicae Sulzer and Aphis craccivora Koch. In our study, A. gossypii apterous and alate morphs were able to acquire CLRDV in 30 min and 24 h, inoculate CLRDV in 45 and 15 min, and retain CLRDV for 15 and 23 days, respectively. Neither M. persicae nor A. craccivora acquired or transmitted CLRDV to cotton.
Collapse
Affiliation(s)
- Brianna Heilsnis
- Department of Crop, Soil, and Environmental Sciences, 201 Funchess Hall, Auburn University, Auburn, AL 36849, USA
| | - Jessica B Mahas
- Department of Entomology & Plant Pathology, 301 Funchess Hall, Auburn University, Auburn, AL 36849, USA
| | - Kassie Conner
- Alabama Cooperative Extension System, 961 S. Donahue Dr., Auburn University, Auburn, AL 36849, USA
| | - Sudeep Pandey
- Department of Entomology, University of Georgia, 1109 Experiment Street, Griffin, GA 30223, USA
| | - Wilson Clark
- Department of Entomology & Plant Pathology, 301 Funchess Hall, Auburn University, Auburn, AL 36849, USA
| | - Jenny Koebernick
- Department of Crop, Soil, and Environmental Sciences, 201 Funchess Hall, Auburn University, Auburn, AL 36849, USA
| | | | - Kathleen Martin
- Department of Entomology & Plant Pathology, 301 Funchess Hall, Auburn University, Auburn, AL 36849, USA
| | - Alana L Jacobson
- Department of Entomology & Plant Pathology, 301 Funchess Hall, Auburn University, Auburn, AL 36849, USA
| |
Collapse
|
6
|
Molecular Detection of Southern Tomato Amalgavirus Prevalent in Tomatoes and Its Genomic Characterization with Global Evolutionary Dynamics. Viruses 2022; 14:v14112481. [PMID: 36366579 PMCID: PMC9693158 DOI: 10.3390/v14112481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 11/04/2022] [Accepted: 11/04/2022] [Indexed: 11/11/2022] Open
Abstract
Southern tomato amalgavirus (STV) is a cryptic pathogen that is abundant in tomato production fields and intensifies the resurgence of tomato yellow stunt disease (ToYSD), together with other phytoviruses. Here, we mapped the geographical and genomic diversity, phylogenetics, and evolutionary dynamics of STV. We found that STV prevailed across China and Pakistan, with a maximum average rate of infection of 43.19% in Beijing, China, and 40.08% in Punjab, Pakistan. Subsequently, we amplified, cloned, and annotated the complete genome sequences of STV isolates from Solanum lycopersicum L. in China (OP548653 and OP548652) and Pakistan (MT066231) using Sanger and next-generation sequencing (NGS). These STV isolates displayed close evolutionary relationships with others from Asia, America, and Europe. Whole-genome-based molecular diversity analysis showed that STV populations had 33 haplotypes with a gene diversity (Hd) of 0.977 and a nucleotide diversity (π) of 0.00404. The genetic variability of RNA-dependent RNA-polymerase (RdRp) was higher than that of the putative coat protein (CP) p42. Further analysis revealed that STV isolates were likely to be recombinant but with a lower-to-moderate level of confidence. With a variable distribution pattern of positively and negatively selected sites, negative selection pressure predominantly acted on p42 and RdRp. These findings elaborated on the molecular variability and evolutionary trends among STV populations across major tomato-producing regions of the world.
Collapse
|
7
|
Determinants of Virus Variation, Evolution, and Host Adaptation. Pathogens 2022; 11:pathogens11091039. [PMID: 36145471 PMCID: PMC9501407 DOI: 10.3390/pathogens11091039] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 09/06/2022] [Accepted: 09/09/2022] [Indexed: 11/17/2022] Open
Abstract
Virus evolution is the change in the genetic structure of a viral population over time and results in the emergence of new viral variants, strains, and species with novel biological properties, including adaptation to new hosts. There are host, vector, environmental, and viral factors that contribute to virus evolution. To achieve or fine tune compatibility and successfully establish infection, viruses adapt to a particular host species or to a group of species. However, some viruses are better able to adapt to diverse hosts, vectors, and environments. Viruses generate genetic diversity through mutation, reassortment, and recombination. Plant viruses are exposed to genetic drift and selection pressures by host and vector factors, and random variants or those with a competitive advantage are fixed in the population and mediate the emergence of new viral strains or species with novel biological properties. This process creates a footprint in the virus genome evident as the preferential accumulation of substitutions, insertions, or deletions in areas of the genome that function as determinants of host adaptation. Here, with respect to plant viruses, we review the current understanding of the sources of variation, the effect of selection, and its role in virus evolution and host adaptation.
Collapse
|
8
|
Hoffmann LV, Branquinho AA, Barroso PAV, Vaslin MFS. Antibodies for the Coat Protein of Cotton Leafroll Dwarf Virus Detect Commelina sp. as an Intermediary Host for Cotton Blue Disease. FRONTIERS IN PLANT SCIENCE 2022; 13:814119. [PMID: 35909775 PMCID: PMC9328755 DOI: 10.3389/fpls.2022.814119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 06/09/2022] [Indexed: 05/29/2023]
Abstract
The cotton blue disease, caused by the cotton leafroll dwarf virus (CLRDV), leads to dwarfism, leaf rolling, and production loss in susceptible cotton varieties. To develop an enzyme-linked immunosorbent assay (ELISA) test to detect the virus in cotton and weeds, peptides based on the coat protein were used to produce polyclonal (α-GQE, α-PRN, and α-INK) and monoclonal (α-GQE, α-PRN, and α-NKF) antibodies. All six were tested as capture antibodies, and polyclonal α-GQE and the monocle onal α-NKF were labeled with the enzyme alkaline phosphatase and used as detection antibodies for a double antibody sandwich (DAS) ELISA method, in which p-nitrophenyl phosphate was added and measured by absorbance at 405 nm. The DAS-ELISA sandwich was efficient in discriminating between healthy and diseased plant extracts. The ELISA methodology detected the virus in the weeds Commelina sp., which was confirmed by RT-PCR. The monoclonal antibodies may be used to develop other diagnostic procedures.
Collapse
Affiliation(s)
| | | | | | - Maite F. S. Vaslin
- Virology Department, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| |
Collapse
|
9
|
Tarazi R, Vaslin MFS. The Viral Threat in Cotton: How New and Emerging Technologies Accelerate Virus Identification and Virus Resistance Breeding. FRONTIERS IN PLANT SCIENCE 2022; 13:851939. [PMID: 35449884 PMCID: PMC9016188 DOI: 10.3389/fpls.2022.851939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 03/07/2022] [Indexed: 05/12/2023]
Abstract
Cotton (Gossypium spp. L., Malvaceae) is the world's largest source of natural fibers. Virus outbreaks are fast and economically devasting regarding cotton. Identifying new viruses is challenging as virus symptoms usually mimic nutrient deficiency, insect damage, and auxin herbicide injury. Traditional viral identification methods are costly and time-consuming. Developing new resistant cotton lines to face viral threats has been slow until the recent use of molecular virology, genomics, new breeding techniques (NBT), remote sensing, and artificial intelligence (AI). This perspective article demonstrates rapid, sensitive, and cheap technologies to identify viral diseases and propose their use for virus resistance breeding.
Collapse
Affiliation(s)
- Roberto Tarazi
- Plant Molecular Virology Laboratory, Department of Virology, Microbiology Institute, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
- Programa de Pós-graduação em Biotecnologia e Bioprocessos da UFRJ, Rio de Janeiro, Brazil
| | - Maite F. S. Vaslin
- Plant Molecular Virology Laboratory, Department of Virology, Microbiology Institute, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
- Programa de Pós-graduação em Biotecnologia e Bioprocessos da UFRJ, Rio de Janeiro, Brazil
| |
Collapse
|
10
|
Umar M, Farooq T, Tegg RS, Thangavel T, Wilson CR. Genomic Characterisation of an Isolate of Brassica Yellows Virus Associated with Brassica Weed in Tasmania. PLANTS (BASEL, SWITZERLAND) 2022; 11:884. [PMID: 35406863 PMCID: PMC9003488 DOI: 10.3390/plants11070884] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/21/2022] [Accepted: 03/22/2022] [Indexed: 06/14/2023]
Abstract
Brassica yellows virus (BrYV), a tentative species in the genus Polerovirus, of the Solemoviridae family, is a phloem-restricted and aphid-transmitted virus with at least three genotypes (A, B, and C). It has been found across mainland China, South Korea, and Japan. BrYV was previously undescribed in Tasmania, and its genetic variability in the state remains unknown. Here, we describe a near-complete genome sequence of BrYV (genotype A) isolated from Raphanus raphanistrum in Tasmania using next-generation sequencing and sanger sequencing of RT-PCR products. BrYV-Tas (GenBank Accession no. OM469309) possesses a genome of 5516 nucleotides (nt) and shares higher sequence identity (about 90%) with other BrYV isolates. Phylogenetic analyses showed variability in the clustering patterns of the individual genes of BrYV-Tas. Recombination analysis revealed beginning and ending breakpoints at nucleotide positions 1922 to 5234 nt, with the BrYV isolate LC428359 and BrYV isolate KY310572 identified as major and minor parents, respectively. Results of the evolutionary analysis showed that the majority of the codons for each gene are evolving under purifying selection, though a few codons were also detected to have positive selection pressure. Taken together, our findings will facilitate an understanding of the evolutionary dynamics and genetic diversity of BrYV.
Collapse
Affiliation(s)
- Muhammad Umar
- New Town Research Laboratories, Tasmanian Institute of Agriculture, University of Tasmania, 13 St. Johns Avenue, New Town, TAS 7008, Australia; (M.U.); (R.S.T.); (T.T.)
| | - Tahir Farooq
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China;
| | - Robert S. Tegg
- New Town Research Laboratories, Tasmanian Institute of Agriculture, University of Tasmania, 13 St. Johns Avenue, New Town, TAS 7008, Australia; (M.U.); (R.S.T.); (T.T.)
| | - Tamilarasan Thangavel
- New Town Research Laboratories, Tasmanian Institute of Agriculture, University of Tasmania, 13 St. Johns Avenue, New Town, TAS 7008, Australia; (M.U.); (R.S.T.); (T.T.)
- Department of Agriculture and Fisheries (Queensland), Bundaberg Research Facility, 49 Ashfield Road, Bundaberg, QLD 4670, Australia
| | - Calum R. Wilson
- New Town Research Laboratories, Tasmanian Institute of Agriculture, University of Tasmania, 13 St. Johns Avenue, New Town, TAS 7008, Australia; (M.U.); (R.S.T.); (T.T.)
| |
Collapse
|
11
|
Fránová J, Lenz O, Přibylová J, Čmejla R, Valentová L, Koloniuk I. High Incidence of Strawberry Polerovirus 1 in the Czech Republic and Its Vectors, Genetic Variability and Recombination. Viruses 2021; 13:2487. [PMID: 34960756 PMCID: PMC8706236 DOI: 10.3390/v13122487] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Revised: 12/06/2021] [Accepted: 12/08/2021] [Indexed: 12/11/2022] Open
Abstract
In total, 332 strawberry plants from 33 different locations in the Czech Republic with or without disease symptoms were screened by RT-PCR for the presence of strawberry polerovirus 1 (SPV1) and five other viruses: strawberry mottle virus, strawberry crinkle virus, strawberry mild yellow edge virus, strawberry vein banding virus, and strawberry virus 1. SPV1 was detected in 115 tested strawberry plants (35%), including 89 mixed infections. No correlation between symptoms and the detected viruses was found. To identify potential invertebrate SPV1 vectors, strawberry-associated invertebrate species were screened by RT-PCR, and the virus was found in the aphids Aphis forbesi, A. gossypii, A. ruborum, A.sanquisorbae, Aulacorthum solani, Chaetosiphon fragaefolii, Myzus ascalonicus, and several other non-aphid invertebrate species. SPV1 was also detected in aphid honeydew. Subsequent tests of C. fragaefolii and A.gossypii virus transmission ability showed that at least 4 h of acquisition time were needed to acquire the virus. However, 1 day was sufficient for inoculation using C. fragaefolii. In conclusion, being aphid-transmitted like other tested viruses SPV1 was nevertheless the most frequently detected agent. Czech SPV1 isolates belonged to at least two phylogenetic clusters. The sequence analysis also indicated that recombination events influence evolution of SPV1 genomes.
Collapse
Affiliation(s)
- Jana Fránová
- Department of Plant Virology, Institute of Plant Molecular Biology, Biology Centre, Czech Academy of Sciences, 370 05 České Budějovice, Czech Republic; (O.L.); (J.P.)
| | - Ondřej Lenz
- Department of Plant Virology, Institute of Plant Molecular Biology, Biology Centre, Czech Academy of Sciences, 370 05 České Budějovice, Czech Republic; (O.L.); (J.P.)
| | - Jaroslava Přibylová
- Department of Plant Virology, Institute of Plant Molecular Biology, Biology Centre, Czech Academy of Sciences, 370 05 České Budějovice, Czech Republic; (O.L.); (J.P.)
| | - Radek Čmejla
- Laboratory for Molecular Biology, Research and Breeding Institute of Pomology Holovousy Ltd., Holovousy 129, 508 01 Hořice, Czech Republic; (R.Č.); (L.V.)
| | - Lucie Valentová
- Laboratory for Molecular Biology, Research and Breeding Institute of Pomology Holovousy Ltd., Holovousy 129, 508 01 Hořice, Czech Republic; (R.Č.); (L.V.)
| | - Igor Koloniuk
- Department of Plant Virology, Institute of Plant Molecular Biology, Biology Centre, Czech Academy of Sciences, 370 05 České Budějovice, Czech Republic; (O.L.); (J.P.)
| |
Collapse
|
12
|
Cotton Leafroll Dwarf Virus US Genomes Comprise Divergent Subpopulations and Harbor Extensive Variability. Viruses 2021; 13:v13112230. [PMID: 34835036 PMCID: PMC8618375 DOI: 10.3390/v13112230] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 10/29/2021] [Accepted: 11/02/2021] [Indexed: 11/21/2022] Open
Abstract
Cotton leafroll dwarf virus (CLRDV) was first reported in the United States (US) in 2017 from cotton plants in Alabama (AL) and has become widespread in cotton-growing states of the southern US. To investigate the genomic variability among CLRDV isolates in the US, complete genomes of the virus were obtained from infected cotton plants displaying mild to severe symptoms from AL, Florida, and Texas. Eight CLRDV genomes were determined, ranging in size from 5865 to 5867 bp, and shared highest nucleotide identity with other CLRDV isolates in the US, at 95.9–98.7%. Open reading frame (ORF) 0, encoding the P0 silencing suppressor, was the most variable gene, sharing 88.5–99.6% and 81.2–89.3% amino acid similarity with CLRDV isolates reported in cotton growing states in the US and in Argentina and Brazil in South America, respectively. Based on Bayesian analysis, the complete CLRDV genomes from cotton in the US formed a monophyletic group comprising three relatively divergent sister clades, whereas CLRDV genotypes from South America clustered as closely related sister-groups, separate from US isolates, patterns reminiscent of phylogeographical structuring. The CLRDV isolates exhibited a complex pattern of recombination, with most breakpoints evident in ORFs 2 and 3, and ORF5. Despite extensive nucleotide diversity among all available CLRDV genomes, purifying selection (dN/dS < 1) was implicated as the primary selective force acting on viral protein evolution.
Collapse
|
13
|
Davis RI, Jones LM, Pease B, Perkins SL, Vala HR, Kokoa P, Apa M, Dale CJ. Plant Virus and Virus-like Disease Threats to Australia's North Targeted by the Northern Australia Quarantine Strategy. PLANTS 2021; 10:plants10102175. [PMID: 34685987 PMCID: PMC8537380 DOI: 10.3390/plants10102175] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 10/06/2021] [Accepted: 10/11/2021] [Indexed: 11/18/2022]
Abstract
The Northern Australia Quarantine Strategy (NAQS) is a biosecurity initiative operated by the Australian federal government’s Department of Agriculture, Water and the Environment (DAWE). It is unique worldwide because it deals specifically with the potential arrival via unregulated pathways of exotic threats from overseas in a vast and sparsely populated region. It aims to protect the nation’s animal- and plant-based production industries, as well as the environment, from incursions of organisms from countries that lie immediately to the north. These are diseases, pests, and weeds present in these countries that are currently either absent from, or under active containment in, Australia and may arrive by natural or human-assisted means. This review article focuses on the plant viruses and virus-like diseases that are most highly targeted by the NAQS program. It presents eight pathogen species/group entries in the NAQS A list of target pathogens, providing an overview of the historical and current situation, and collates some new data obtained from surveillance activities conducted in northern Australia and collaborative work overseas.
Collapse
Affiliation(s)
- Richard I. Davis
- Northern Australia Quarantine Strategy, Department of Agriculture Water and Environment, GPO Box 858, Canberra, ACT 2601, Australia; (L.M.J.); (B.P.); (S.L.P.); (H.R.V.)
- Correspondence:
| | - Lynne M. Jones
- Northern Australia Quarantine Strategy, Department of Agriculture Water and Environment, GPO Box 858, Canberra, ACT 2601, Australia; (L.M.J.); (B.P.); (S.L.P.); (H.R.V.)
| | - Bradley Pease
- Northern Australia Quarantine Strategy, Department of Agriculture Water and Environment, GPO Box 858, Canberra, ACT 2601, Australia; (L.M.J.); (B.P.); (S.L.P.); (H.R.V.)
| | - Sandy L. Perkins
- Northern Australia Quarantine Strategy, Department of Agriculture Water and Environment, GPO Box 858, Canberra, ACT 2601, Australia; (L.M.J.); (B.P.); (S.L.P.); (H.R.V.)
| | - Harshitsinh R. Vala
- Northern Australia Quarantine Strategy, Department of Agriculture Water and Environment, GPO Box 858, Canberra, ACT 2601, Australia; (L.M.J.); (B.P.); (S.L.P.); (H.R.V.)
| | - Pere Kokoa
- National Agriculture Quarantine and Inspection Authority (NAQIA), P.O. Box 741, Port Moresby 121, Papua New Guinea; (P.K.); (M.A.)
| | - Marilyn Apa
- National Agriculture Quarantine and Inspection Authority (NAQIA), P.O. Box 741, Port Moresby 121, Papua New Guinea; (P.K.); (M.A.)
| | - Christopher J. Dale
- International Plant Health Surveillance Program, Department of Agriculture Water and Environment, GPO Box 858, Canberra, ACT 2601, Australia;
| |
Collapse
|
14
|
Parkash V, Sharma DB, Snider J, Bag S, Roberts P, Tabassum A, West D, Khanal S, Suassuna N, Chee P. Effect of Cotton Leafroll Dwarf Virus on Physiological Processes and Yield of Individual Cotton Plants. FRONTIERS IN PLANT SCIENCE 2021; 12:734386. [PMID: 34659302 PMCID: PMC8519356 DOI: 10.3389/fpls.2021.734386] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 08/26/2021] [Indexed: 05/26/2023]
Abstract
Cotton leafroll dwarf disease (CLRDD) caused by cotton leafroll dwarf virus (CLRDV) is an emerging threat to cotton production in the United States. The disease was first reported in Alabama in 2017 and subsequently has been reported in 10 other cotton producing states in the United States, including Georgia. A field study was conducted at field sites near Tifton, Georgia in 2019 and 2020 to evaluate leaf gas exchange, chlorophyll fluorescence, and leaf temperature responses for a symptomatic cultivar (diseased plants observed at regular frequency) at multiple stages of disease progression and for asymptomatic cultivars (0% disease incidence observed). Disease-induced reductions in net photosynthetic rate (A n, decreased by 63-101%), stomatal conductance (g s, decreased by 65-99%), and efficiency of the thylakoid reactions (32-92% decline in primary photochemistry) were observed, whereas leaf temperature significantly increased by 0.5-3.8°C at advanced stages of the disease. Net photosynthesis was substantially more sensitive to disease-induced declines in g s than the thylakoid reactions. Symptomatic plants with more advanced disease stages remained stunted throughout the growing season, and yield was reduced by 99% by CLRDD due to reductions in boll number per plant and declines in boll mass resulting from fewer seeds per boll. Asymptomatic cultivars exhibited more conservative gas exchange responses than apparently healthy plants of the symptomatic cultivar but were less productive. Overall, it is concluded that CLRDV limits stomatal conductance and photosynthetic activity of individual leaves, causing substantial declines in productivity for individual plants. Future studies should evaluate the physiological contributors to genotypic variation in disease tolerance under controlled conditions.
Collapse
Affiliation(s)
- Ved Parkash
- Department of Crop and Soil Sciences, University of Georgia, Tifton, GA, United States
| | - Divya Bhanu Sharma
- Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Tifton, GA, United States
| | - John Snider
- Department of Crop and Soil Sciences, University of Georgia, Tifton, GA, United States
| | - Sudeep Bag
- Department of Plant Pathology, University of Georgia, Tifton, GA, United States
| | - Phillip Roberts
- Department of Entomology, University of Georgia, Tifton, GA, United States
| | - Afsha Tabassum
- Department of Plant Pathology, University of Georgia, Tifton, GA, United States
| | - Dalton West
- Department of Crop and Soil Sciences, University of Georgia, Tifton, GA, United States
| | - Sameer Khanal
- Department of Crop and Soil Sciences, University of Georgia, Tifton, GA, United States
- Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Tifton, GA, United States
| | - Nelson Suassuna
- Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Tifton, GA, United States
| | - Peng Chee
- Department of Crop and Soil Sciences, University of Georgia, Tifton, GA, United States
- Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Tifton, GA, United States
| |
Collapse
|
15
|
Tabassum A, Bag S, Suassuna ND, Conner KN, Chee P, Kemerait RC, Roberts P. Genome analysis of cotton leafroll dwarf virus reveals variability in the silencing suppressor protein, genotypes and genomic recombinants in the USA. PLoS One 2021; 16:e0252523. [PMID: 34232966 PMCID: PMC8262794 DOI: 10.1371/journal.pone.0252523] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 05/17/2021] [Indexed: 11/18/2022] Open
Abstract
Cotton leafroll dwarf virus (CLRDV) is an emerging virus in cotton production in Georgia and several other Southeastern states in the USA. To better understand the genetic diversity of the virus population, the near complete genome sequences of six isolates from Georgia and one from Alabama were determined. The isolates sequenced were 5,866 nucleotides with seven open reading frames (ORFs). The isolates from Georgia were >94% identical with other isolates from the USA and South America. In the silencing suppressor protein (P0), at amino acid position 72, the isolates from Georgia and Alabama had a valine (V), similar to resistant-breaking 'atypical' genotypes in South America, while the Texas isolate had isoleucine (I), similar to the more aggressive 'typical' genotypes of CLRDV. At position 120, arginine (R) is unique to Georgia and China isolates, but absent in Alabama, Texas and South American isolates. Ten potential recombinant events were detected in the isolates sequenced. An increased understanding of CLRDV population structure and genetic diversity will help develop management strategies for CLRDV in the USA cotton belt.
Collapse
Affiliation(s)
- Afsha Tabassum
- Department of Plant Pathology, University of Georgia, Tifton, Georgia, United States of America
| | - Sudeep Bag
- Department of Plant Pathology, University of Georgia, Tifton, Georgia, United States of America
| | | | - Kassie N. Conner
- Alabama Cooperative Extension System, Auburn University, Auburn, Alabama, United States of America
| | - Peng Chee
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Tifton, Georgia, United States of America
| | - Robert C. Kemerait
- Department of Plant Pathology, University of Georgia, Tifton, Georgia, United States of America
| | - Phillip Roberts
- Department of Entomology, University of Georgia, Tifton, Georgia, United States of America
| |
Collapse
|
16
|
Wang Q, Xu FZ, An LL, Xiang HY, Zhang WH, Liu GS, Liu HB. Molecular characterization of a new recombinant brassica yellows virus infecting tobacco in China. Virus Genes 2019; 55:253-256. [PMID: 30697673 DOI: 10.1007/s11262-019-01636-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 01/07/2019] [Indexed: 10/27/2022]
Abstract
Brassica yellows virus (BrYV), prevalently distributed throughout mainland China and South Korea while triggering serious diseases in cruciferous crops, is proposed to be a new species in the genus Polerovirus within the family Luteoviridae. There are three distinct genotypes (BrYV-A, BrYV-B and BrYV-C) reported in cabbage and radish. Here, we describe a new BrYV isolate infecting tobacco plants in the field, which was named BrYV-NtabQJ. The complete genome sequence of BrYV-NtabQJ is 5741 nt in length, and 89% of the sequence shares higher sequence identities (about 90%) with different BrYV isolates. However, it possesses a quite divergent region within ORF5, which is more close to Beet western yellows virus (BWYV), Beet mild yellowing virus (BMYV) and Beet chlorosis virus (BChV). A significant recombination event was then detected among BrYV-NtabQJ, BrYV-B Beijng isolate (BrYV-BBJ) and BWYV Leonurus sibiricus isolate (BWYV-LS). It is proposed that BrYV-NtabQJ might be an interspecific recombinant between BrYV-BBJ and BWYV-LS, and the recombination might result in the successful aphid transmission of BrYV from cruciferous crops to tobacco. And it also poses new challenges for BrYV diagnosis and the vegetable production.
Collapse
Affiliation(s)
- Qian Wang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, People's Republic of China
| | - Fang-Zheng Xu
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, People's Republic of China
| | - Lu-Lu An
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, People's Republic of China
| | - Hai-Ying Xiang
- Yunnan Academy of Tobacco Science, Kunming, 650106, People's Republic of China
| | - Wei-Hua Zhang
- Vegetable and Flower Research Institute of Shandong Academy of Agricultural Sciences, Ji'nan, 250100, People's Republic of China
| | - Guan-Shan Liu
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, People's Republic of China.
| | - Hao-Bao Liu
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, People's Republic of China.
| |
Collapse
|
17
|
Agrofoglio YC, Delfosse VC, Casse MF, Hopp HE, Kresic IB, Distéfano AJ. Identification of a New Cotton Disease Caused by an Atypical Cotton Leafroll Dwarf Virus in Argentina. PHYTOPATHOLOGY 2017; 107:369-376. [PMID: 28035870 DOI: 10.1094/phyto-09-16-0349-r] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
An outbreak of a new disease occurred in cotton (Gossypium hirsutum) fields in northwest Argentina starting in the 2009-10 growing season and is still spreading steadily. The characteristic symptoms of the disease included slight leaf rolling and a bushy phenotype in the upper part of the plant. In this study, we determined the complete nucleotide sequences of two independent virus genomes isolated from cotton blue disease (CBD)-resistant and -susceptible cotton varieties. This virus genome comprised 5,866 nucleotides with an organization similar to that of the genus Polerovirus and was closely related to cotton leafroll dwarf virus, with protein identity ranging from 88 to 98%. The virus was subsequently transmitted to a CBD-resistant cotton variety using Aphis gossypii and symptoms were successfully reproduced. To study the persistence of the virus, we analyzed symptomatic plants from CBD-resistant varieties from different cotton-growing fields between 2013 and 2015 and showed the presence of the same virus strain. In addition, a constructed full-length infectious cDNA clone from the virus caused disease symptoms in systemic leaves of CBD-resistant cotton plants. Altogether, the new leafroll disease in CBD-resistant cotton plants is caused by an atypical cotton leafroll dwarf virus.
Collapse
Affiliation(s)
- Yamila C Agrofoglio
- First author: INTA-CICVyA, CONICET, Instituto de Biotecnología, 1686 Buenos Aires; second author: INTA-CICVyA, CONICET, Instituto de Biotecnología and School of Science and Technology, UNSAM, 1653 Buenos Aires; third and fifth authors: EEA Sáenz Peña, INTA, 3700 Chaco, Argentina; and fourth and sixth authors: INTA-CICVyA, Instituto de Biotecnología and DFBMC, FCEyN, UBA, 1428 Buenos Aires
| | - Verónica C Delfosse
- First author: INTA-CICVyA, CONICET, Instituto de Biotecnología, 1686 Buenos Aires; second author: INTA-CICVyA, CONICET, Instituto de Biotecnología and School of Science and Technology, UNSAM, 1653 Buenos Aires; third and fifth authors: EEA Sáenz Peña, INTA, 3700 Chaco, Argentina; and fourth and sixth authors: INTA-CICVyA, Instituto de Biotecnología and DFBMC, FCEyN, UBA, 1428 Buenos Aires
| | - María F Casse
- First author: INTA-CICVyA, CONICET, Instituto de Biotecnología, 1686 Buenos Aires; second author: INTA-CICVyA, CONICET, Instituto de Biotecnología and School of Science and Technology, UNSAM, 1653 Buenos Aires; third and fifth authors: EEA Sáenz Peña, INTA, 3700 Chaco, Argentina; and fourth and sixth authors: INTA-CICVyA, Instituto de Biotecnología and DFBMC, FCEyN, UBA, 1428 Buenos Aires
| | - Horacio E Hopp
- First author: INTA-CICVyA, CONICET, Instituto de Biotecnología, 1686 Buenos Aires; second author: INTA-CICVyA, CONICET, Instituto de Biotecnología and School of Science and Technology, UNSAM, 1653 Buenos Aires; third and fifth authors: EEA Sáenz Peña, INTA, 3700 Chaco, Argentina; and fourth and sixth authors: INTA-CICVyA, Instituto de Biotecnología and DFBMC, FCEyN, UBA, 1428 Buenos Aires
| | - Iván Bonacic Kresic
- First author: INTA-CICVyA, CONICET, Instituto de Biotecnología, 1686 Buenos Aires; second author: INTA-CICVyA, CONICET, Instituto de Biotecnología and School of Science and Technology, UNSAM, 1653 Buenos Aires; third and fifth authors: EEA Sáenz Peña, INTA, 3700 Chaco, Argentina; and fourth and sixth authors: INTA-CICVyA, Instituto de Biotecnología and DFBMC, FCEyN, UBA, 1428 Buenos Aires
| | - Ana J Distéfano
- First author: INTA-CICVyA, CONICET, Instituto de Biotecnología, 1686 Buenos Aires; second author: INTA-CICVyA, CONICET, Instituto de Biotecnología and School of Science and Technology, UNSAM, 1653 Buenos Aires; third and fifth authors: EEA Sáenz Peña, INTA, 3700 Chaco, Argentina; and fourth and sixth authors: INTA-CICVyA, Instituto de Biotecnología and DFBMC, FCEyN, UBA, 1428 Buenos Aires
| |
Collapse
|
18
|
Mukherjee AK, Mukherjee PK, Kranthi S. Genetic Similarity between Cotton Leafroll Dwarf Virus and Chickpea Stunt Disease Associated Virus in India. THE PLANT PATHOLOGY JOURNAL 2016; 32:580-583. [PMID: 27904466 PMCID: PMC5117868 DOI: 10.5423/ppj.nt.09.2015.0197] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2015] [Revised: 04/27/2016] [Accepted: 07/22/2016] [Indexed: 05/26/2023]
Abstract
The cotton leafroll dwarf virus (CLRDV) is one of the most devastating pathogens of cotton. This malady, known as cotton blue disease, is widespread in South America where it causes huge crop losses. Recently the disease has been reported from India. We noticed occurrence of cotton blue disease and chickpea stunt disease in adjoining cotton and chickpea fields and got interested in knowing if these two viral diseases have some association. By genetic studies, we have shown here that CLRDV is very close to chickpea stunt disease associated virus (CpSDaV). We were successful in transmitting the CLRDV from cotton to chickpea. Our studies indicate that CpSDaV and CLRDV in India are possibly two different strains of the same virus. These findings would be helpful in managing these serious diseases by altering the cropping patterns.
Collapse
Affiliation(s)
- Arup Kumar Mukherjee
- Division of Crop Protection, Central Institute for Cotton Research, Nagpur 440010,
India
- Division of Crop Protection, Central Rice Research Institute, Cuttack 753006,
India
| | - Prasun Kumar Mukherjee
- Division of Crop Protection, Central Institute for Cotton Research, Nagpur 440010,
India
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai 400085,
India
| | - Sandhya Kranthi
- Division of Crop Protection, Central Institute for Cotton Research, Nagpur 440010,
India
| |
Collapse
|
19
|
Complete genome sequence of a Chinese isolate of pepper vein yellows virus and evolutionary analysis based on the CP, MP and RdRp coding regions. Arch Virol 2015; 161:677-83. [PMID: 26620586 DOI: 10.1007/s00705-015-2691-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 11/15/2015] [Indexed: 02/04/2023]
Abstract
The genome sequence of pepper vein yellows virus (PeVYV) (PeVYV-HN, accession number KP326573), isolated from pepper plants (Capsicum annuum L.) grown at the Hunan Vegetables Institute (Changsha, Hunan, China), was determined by deep sequencing of small RNAs. The PeVYV-HN genome consists of 6244 nucleotides, contains six open reading frames (ORFs), and is similar to that of an isolate (AB594828) from Japan. Its genomic organization is similar to that of members of the genus Polerovirus. Sequence analysis revealed that PeVYV-HN shared 92% sequence identity with the Japanese PeVYV genome at both the nucleotide and amino acid levels. Evolutionary analysis based on the coat protein (CP), movement protein (MP), and RNA-dependent RNA polymerase (RdRP) showed that PeVYV could be divided into two major lineages corresponding to their geographical origins. The Asian isolates have a higher population expansion frequency than the African isolates. Negative selection and genetic drift (founder effect) were found to be the potential drivers of the molecular evolution of PeVYV. Moreover, recombination was not the distinct cause of PeVYV evolution. This is the first report of a complete genomic sequence of PeVYV in China.
Collapse
|
20
|
Phylogenetic relationships and the occurrence of interspecific recombination between beet chlorosis virus (BChV) and Beet mild yellowing virus (BMYV). Arch Virol 2014; 160:429-33. [DOI: 10.1007/s00705-014-2245-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Accepted: 09/24/2014] [Indexed: 10/24/2022]
|
21
|
de Andrade RRS, Vaslin MFS. SearchSmallRNA: a graphical interface tool for the assemblage of viral genomes using small RNA libraries data. Virol J 2014; 11:45. [PMID: 24607237 PMCID: PMC4007622 DOI: 10.1186/1743-422x-11-45] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Accepted: 02/19/2014] [Indexed: 01/19/2023] Open
Abstract
Background Next-generation parallel sequencing (NGS) allows the identification of viral pathogens by sequencing the small RNAs of infected hosts. Thus, viral genomes may be assembled from host immune response products without prior virus enrichment, amplification or purification. However, mapping of the vast information obtained presents a bioinformatics challenge. Methods In order to by pass the need of line command and basic bioinformatics knowledge, we develop a mapping software with a graphical interface to the assemblage of viral genomes from small RNA dataset obtained by NGS. SearchSmallRNA was developed in JAVA language version 7 using NetBeans IDE 7.1 software. The program also allows the analysis of the viral small interfering RNAs (vsRNAs) profile; providing an overview of the size distribution and other features of the vsRNAs produced in infected cells. Results The program performs comparisons between each read sequenced present in a library and a chosen reference genome. Reads showing Hamming distances smaller or equal to an allowed mismatched will be selected as positives and used to the assemblage of a long nucleotide genome sequence. In order to validate the software, distinct analysis using NGS dataset obtained from HIV and two plant viruses were used to reconstruct viral whole genomes. Conclusions SearchSmallRNA program was able to reconstructed viral genomes using NGS of small RNA dataset with high degree of reliability so it will be a valuable tool for viruses sequencing and discovery. It is accessible and free to all research communities and has the advantage to have an easy-to-use graphical interface. Availability and implementation SearchSmallRNA was written in Java and is freely available at http://www.microbiologia.ufrj.br/ssrna/.
Collapse
Affiliation(s)
| | - Maite F S Vaslin
- Departamento de Virologia, Instituto de Microbiologia, Universidade Federal do Rio de Janeiro (UFRJ), 21941-590 Rio de Janeiro, RJ, Brasil.
| |
Collapse
|
22
|
Kassem MA, Juarez M, Gómez P, Mengual CM, Sempere RN, Plaza M, Elena SF, Moreno A, Fereres A, Aranda MA. Genetic diversity and potential vectors and reservoirs of Cucurbit aphid-borne yellows virus in southeastern Spain. PHYTOPATHOLOGY 2013; 103:1188-1197. [PMID: 23802870 DOI: 10.1094/phyto-11-12-0280-r] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The genetic variability of a Cucurbit aphid-borne yellows virus (CABYV) (genus Polerovirus, family Luteoviridae) population was evaluated by determining the nucleotide sequences of two genomic regions of CABYV isolates collected in open-field melon and squash crops during three consecutive years in Murcia (southeastern Spain). A phylogenetic analysis showed the existence of two major clades. The sequences did not cluster according to host, year, or locality of collection, and nucleotide similarities among isolates were 97 to 100 and 94 to 97% within and between clades, respectively. The ratio of nonsynonymous to synonymous nucleotide substitutions reflected that all open reading frames have been under purifying selection. Estimates of the population's genetic diversity were of the same magnitude as those previously reported for other plant virus populations sampled at larger spatial and temporal scales, suggesting either the presence of CABYV in the surveyed area long before it was first described, multiple introductions, or a particularly rapid diversification. We also determined the full-length sequences of three isolates, identifying the occurrence and location of recombination events along the CABYV genome. Furthermore, our field surveys indicated that Aphis gossypii was the major vector species of CABYV and the most abundant aphid species colonizing melon fields in the Murcia (Spain) region. Our surveys also suggested the importance of the weed species Ecballium elaterium as an alternative host and potential virus reservoir.
Collapse
|
23
|
Knierim D, Tsai WS, Kenyon L. Analysis of sequences from field samples reveals the presence of the recently described pepper vein yellows virus (genus Polerovirus) in six additional countries. Arch Virol 2013; 158:1337-41. [PMID: 23307365 DOI: 10.1007/s00705-012-1598-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2012] [Accepted: 11/29/2012] [Indexed: 11/25/2022]
Abstract
Polerovirus infection was detected by reverse transcription polymerase chain reaction (RT-PCR) in 29 pepper plants (Capsicum spp.) and one black nightshade plant (Solanum nigrum) sample collected from fields in India, Indonesia, Mali, Philippines, Thailand and Taiwan. At least two representative samples for each country were selected to generate a general polerovirus RT-PCR product of 1.4 kb length for sequencing. Sequence analysis of the partial genome sequences revealed the presence of pepper vein yellows virus (PeVYV) in all 13 samples. A 1990 Australian herbarium sample of pepper described by serological means as infected with capsicum yellows virus (CYV) was identified by sequence analysis of a partial CP sequence as probably infected with a potato leaf roll virus (PLRV) isolate.
Collapse
Affiliation(s)
- Dennis Knierim
- AVRDC-The World Vegetable Center, PO Box 42, Shanhua, Tainan 74199, Taiwan
| | | | | |
Collapse
|
24
|
Bujarski JJ. Genetic recombination in plant-infecting messenger-sense RNA viruses: overview and research perspectives. FRONTIERS IN PLANT SCIENCE 2013; 4:68. [PMID: 23533000 PMCID: PMC3607795 DOI: 10.3389/fpls.2013.00068] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Accepted: 03/11/2013] [Indexed: 05/09/2023]
Abstract
RNA recombination is one of the driving forces of genetic variability in (+)-strand RNA viruses. Various types of RNA-RNA crossovers were described including crosses between the same or different viral RNAs or between viral and cellular RNAs. Likewise, a variety of molecular mechanisms are known to support RNA recombination, such as replicative events (based on internal or end-to-end replicase switchings) along with non-replicative joining among RNA fragments of viral and/or cellular origin. Such mechanisms as RNA decay or RNA interference are responsible for RNA fragmentation and trans-esterification reactions which are likely accountable for ligation of RNA fragments. Numerous host factors were found to affect the profiles of viral RNA recombinants and significant differences in recombination frequency were observed among various RNA viruses. Comparative analyses of viral sequences allowed for the development of evolutionary models in order to explain adaptive phenotypic changes and co-evolving sites. Many questions remain to be answered by forthcoming RNA recombination research. (1) How various factors modulate the ability of viral replicase to switch templates, (2) What is the intracellular location of RNA-RNA template switchings, (3) Mechanisms and factors responsible for non-replicative RNA recombination, (4) Mechanisms of integration of RNA viral sequences with cellular genomic DNA, and (5) What is the role of RNA splicing and ribozyme activity. From an evolutionary stand point, it is not known how RNA viruses parasitize new host species via recombination, nor is it obvious what the contribution of RNA recombination is among other RNA modification pathways. We do not understand why the frequency of RNA recombination varies so much among RNA viruses and the status of RNA recombination as a form of sex is not well documented.
Collapse
Affiliation(s)
- Jozef J. Bujarski
- Plant Molecular Biology Center and the Department of Biological Sciences, Northern Illinois UniversityDeKalb, IL, USA
- Laboratory of Molecular and Systems Biology, Institute of Bioorganic Chemistry, Polish Academy of SciencesPoznan, Poland
- *Correspondence: Jozef J. Bujarski, Plant Molecular Biology Center and the Department of Biological Sciences, Northern Illinois University, Montgomery Hall, DeKalb, IL 60115, USA. e-mail:
| |
Collapse
|
25
|
Romanel E, Silva TF, Corrêa RL, Farinelli L, Hawkins JS, Schrago CEG, Vaslin MFS. Global alteration of microRNAs and transposon-derived small RNAs in cotton (Gossypium hirsutum) during Cotton leafroll dwarf polerovirus (CLRDV) infection. PLANT MOLECULAR BIOLOGY 2012; 80:443-60. [PMID: 22987114 DOI: 10.1007/s11103-012-9959-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2012] [Accepted: 08/22/2012] [Indexed: 05/13/2023]
Abstract
Small RNAs (sRNAs) are a class of non-coding RNAs ranging from 20- to 40-nucleotides (nts) that are present in most eukaryotic organisms. In plants, sRNAs are involved in the regulation of development, the maintenance of genome stability and the antiviral response. Viruses, however, can interfere with and exploit the silencing-based regulatory networks, causing the deregulation of sRNAs, including small interfering RNAs (siRNAs) and microRNAs (miRNAs). To understand the impact of viral infection on the plant sRNA pathway, we deep sequenced the sRNAs in cotton leaves infected with Cotton leafroll dwarf virus (CLRDV), which is a member of the economically important virus family Luteoviridae. A total of 60 putative conserved cotton miRNAs were identified, including 19 new miRNA families that had not been previously described in cotton. Some of these miRNAs were clearly misregulated during viral infection, and their possible role in symptom development and disease progression is discussed. Furthermore, we found that the 24-nt heterochromatin-associated siRNAs were quantitatively and qualitatively altered in the infected plant, leading to the reactivation of at least one cotton transposable element. This is the first study to explore the global alterations of sRNAs in virus-infected cotton plants. Our results indicate that some CLRDV-induced symptoms may be correlated with the deregulation of miRNA and/or epigenetic networks.
Collapse
Affiliation(s)
- Elisson Romanel
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
| | | | | | | | | | | | | |
Collapse
|
26
|
Profile of small interfering RNAs from cotton plants infected with the polerovirus Cotton leafroll dwarf virus. BMC Mol Biol 2011; 12:40. [PMID: 21864377 PMCID: PMC3189115 DOI: 10.1186/1471-2199-12-40] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2011] [Accepted: 08/24/2011] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND In response to infection, viral genomes are processed by Dicer-like (DCL) ribonuclease proteins into viral small RNAs (vsRNAs) of discrete sizes. vsRNAs are then used as guides for silencing the viral genome. The profile of vsRNAs produced during the infection process has been extensively studied for some groups of viruses. However, nothing is known about the vsRNAs produced during infections of members of the economically important family Luteoviridae, a group of phloem-restricted viruses. Here, we report the characterization of a population of vsRNAs from cotton plants infected with Cotton leafroll dwarf virus (CLRDV), a member of the genus Polerovirus, family Luteoviridae. RESULTS Deep sequencing of small RNAs (sRNAs) from leaves of CLRDV-infected cotton plants revealed that the vsRNAs were 21- to 24-nucleotides (nt) long and that their sequences matched the viral genome, with higher frequencies of matches in the 3- region. There were equivalent amounts of sense and antisense vsRNAs, and the 22-nt class of small RNAs was predominant. During infection, cotton Dcl transcripts appeared to be up-regulated, while Dcl2 appeared to be down-regulated. CONCLUSIONS This is the first report on the profile of sRNAs in a plant infected with a virus from the family Luteoviridae. Our sequence data strongly suggest that virus-derived double-stranded RNA functions as one of the main precursors of vsRNAs. Judging by the profiled size classes, all cotton DCLs might be working to silence the virus. The possible causes for the unexpectedly high accumulation of 22-nt vsRNAs are discussed. CLRDV is the causal agent of Cotton blue disease, which occurs worldwide. Our results are an important contribution for understanding the molecular mechanisms involved in this and related diseases.
Collapse
|
27
|
Schneider WL, Damsteegt VD, Stone AL, Kuhlmann M, Bunyard BA, Sherman DJ, Graves MV, Smythers G, Smith OP, Hatziloukas E. Molecular analysis of soybean dwarf virus isolates in the eastern United States confirms the presence of both D and Y strains and provides evidence of mixed infections and recombination. Virology 2011; 412:46-54. [PMID: 21256532 DOI: 10.1016/j.virol.2011.01.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2010] [Revised: 10/24/2010] [Accepted: 01/04/2011] [Indexed: 11/28/2022]
Abstract
Soybean dwarf virus (SbDV), first identified as an agricultural problem in Japan, has emerged as a growing problem in the Midwestern United States. The majority of research on SbDV had been limited to four lab maintained strains from Japan. SbDV had been found in clover in the eastern United States, but these isolates rarely emerged into soybeans. These isolates were analyzed by multiplex PCR and sequencing, revealing that some were infections of both Y and D components, including a recombinant subisolate. Phylogenetic analyses for the US isolates revealed a broad diversity of SbDV, with selection pressure greater on the movement protein than the coat protein. The field isolates from the Eastern United States showed differences in symptoms, aphid transmission and host range, demonstrating that a study of field isolates is an important complement to laboratory maintained strains in understanding the biology and evolution of plant viruses.
Collapse
Affiliation(s)
- William L Schneider
- USDA-ARS Foreign Disease Weed Science Research Unit, U.S. Department of Agriculture, 1301 Ditto Avenue, Fort Detrick, MD 21702, USA.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
28
|
Sztuba-Solińska J, Urbanowicz A, Figlerowicz M, Bujarski JJ. RNA-RNA recombination in plant virus replication and evolution. ANNUAL REVIEW OF PHYTOPATHOLOGY 2011; 49:415-43. [PMID: 21529157 DOI: 10.1146/annurev-phyto-072910-095351] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
RNA-RNA recombination is one of the strongest forces shaping the genomes of plant RNA viruses. The detection of recombination is a challenging task that prompted the development of both in vitro and in vivo experimental systems. In the divided genome of Brome mosaic virus system, both inter- and intrasegmental crossovers are described. Other systems utilize satellite or defective interfering RNAs (DI-RNAs) of Turnip crinkle virus, Tomato bushy stunt virus, Cucumber necrosis virus, and Potato virus X. These assays identified the mechanistic details of the recombination process, revealing the role of RNA structure and proteins in the replicase-mediated copy-choice mechanism. In copy choice, the polymerase and the nascent RNA chain from which it is synthesized switch from one RNA template to another. RNA recombination was found to mediate the rearrangement of viral genes, the repair of deleterious mutations, and the acquisition of nonself sequences influencing the phylogenetics of viral taxa. The evidence for recombination, not only between related viruses but also among distantly related viruses, and even with host RNAs, suggests that plant viruses unabashedly test recombination with any genetic material at hand.
Collapse
Affiliation(s)
- Joanna Sztuba-Solińska
- Plant Molecular Biology Center, Department of Biological Sciences, Northern Illinois University, DeKalb, Illinois 60115, USA
| | | | | | | |
Collapse
|
29
|
The complete genome sequence of a virus associated with cotton blue disease, cotton leafroll dwarf virus, confirms that it is a new member of the genus Polerovirus. Arch Virol 2010; 155:1849-54. [PMID: 20677026 DOI: 10.1007/s00705-010-0764-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2010] [Accepted: 07/17/2010] [Indexed: 10/19/2022]
Abstract
Cotton blue disease is the most important virus disease of cotton in the southern part of America. The complete nucleotide sequence of the ssRNA genome of the cotton blue disease-associated virus was determined for the first time. It comprised 5,866 nucleotides, and the deduced genomic organization resembled that of members of the genus Polerovirus. Sequence homology comparison and phylogenetic analysis confirm that this virus (previous proposed name cotton leafroll dwarf virus) is a member of a new species within the genus Polerovirus.
Collapse
|
30
|
Fang DD, Xiao J, Canci PC, Cantrell RG. A new SNP haplotype associated with blue disease resistance gene in cotton (Gossypium hirsutum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2010; 120:943-53. [PMID: 19960336 DOI: 10.1007/s00122-009-1223-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2009] [Accepted: 11/12/2009] [Indexed: 05/10/2023]
Abstract
Resistance to cotton blue disease (CBD) was evaluated in 364 F(2.3) families of three populations derived from resistant variety 'Delta Opal'. The CBD resistance in 'Delta Opal' was controlled by one single dominant gene designated Cbd. Two simple sequence repeat (SSR) markers were identified as linked to Cbd by bulked segregant analysis. Cbd resides at the telomere region of chromosome 10. SSR marker DC20027 was 0.75 cM away from Cbd. DC20027 marker fragments amplified from 3 diploid species and 13 cotton varieties whose CBD resistance was known were cloned and sequenced. One single nucleotide polymorphism (SNP) was identified at the 136 th position by sequence alignment analysis. Screening SNP markers previously mapped on chromosome 10 identified an additional 3 SNP markers that were associated with Cbd. A strong association between a haplotype based on four SNP markers and Cbd was developed. This demonstrates one of the first examples in cotton where SNP markers were used to effectively tag a trait enabling marker-assisted selection for high levels of CBD resistance in breeding programs.
Collapse
Affiliation(s)
- David D Fang
- Cotton Fiber Bioscience Research Unit, USDA-ARS-SRRC, 1100 Robert E. Lee Blvd., New Orleans, LA 70124, USA
| | | | | | | |
Collapse
|