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Venkataravanappa V, Kodandaram MH, Prasanna HC, Reddy MK, Reddy CNL. Unraveling different begomoviruses, DNA satellites and cryptic species of Bemisia tabaci and their endosymbionts in vegetable ecosystem. Microb Pathog 2023; 174:105892. [PMID: 36502993 DOI: 10.1016/j.micpath.2022.105892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 10/16/2022] [Accepted: 11/18/2022] [Indexed: 12/13/2022]
Abstract
Bemisia tabaci species complex contains more than 46 cryptic species. It has emerged as an important pest causing significant yield loss in many cultivated crops. This pest is also a vector for more than 100 species of begomoviruses, that are a major threat for the cultivation of many crops in different regions of the world. The relation between cryptic species of the B. tabaci species complex and associated begomoviruses that infect different crops remains unclear. In the present study, four cryptic species (Asia I, China 3, Asia II 5 and Asia II-1) of B. tabaci and four associated endosymbionts (Arsenophonus, Cardinium, Rickettsia and Wolbachia) were identified in different vegetable crops. The vector-based PCR detection revealed five different begomoviruses such as okra enation leaf curl virus (OELCuV), tomato leaf curl Palampur virus (ToLCPalV), squash leaf curl China virus (SLCCNV), chilli leaf curl virus (ChiLCuV), and tomato leaf curl New Delhi virus (ToLCNDV). Of these begomoviruses, the maximum infection rate was observed (9.1%) for OELCuV, followed by 7.3% for ToLCNDV. The infection rate of the other three viruses (SLCCNV, ChiLCuV, ToLCPalV) ranged from 0.9 to 2.7% in cryptic species of B. tabaci. Further, each cryptic species was infected with multiple virus species and the virus infection rate of Asia I, Asia II-5, China 3 and Asia II-1 was 21.2%, 15.1%, 15.1% and 0.6% respectively. Similarly, in case of betasatellites the highest infection rate was 12% for ToLCBDB, followed by 6% for OLCuB and PaLCB. With regard to alphasatellites, the highest infection rate was 18.2% for AEV and 3% for CLCuMuA. This study demonstrates the distribution of cryptic species of whitefly and their endosymbionts, and associated begomoviruses and DNA satellites in vegetable ecosystem. We believe that the information generated here is useful for evolving an effective pest management strategies for vegetable production.
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Affiliation(s)
- V Venkataravanappa
- ICAR-Indian Institute of Horticultural Research, Hessaraghatta Lake PO, Bengaluru, 560089, Karnataka, India; ICAR-Indian Institute of Vegetable Research, Varanasi, 221305, Uttar Pradesh, India.
| | - M H Kodandaram
- ICAR- Indian Institute of Pulses Research, Regional Research Center, UAS Campus, Dharwad, 580005, Karnataka, India; ICAR-Indian Institute of Vegetable Research, Varanasi, 221305, Uttar Pradesh, India.
| | - H C Prasanna
- ICAR-Indian Institute of Horticultural Research, Hessaraghatta Lake PO, Bengaluru, 560089, Karnataka, India; ICAR-Indian Institute of Vegetable Research, Varanasi, 221305, Uttar Pradesh, India
| | - M Krishna Reddy
- ICAR-Indian Institute of Horticultural Research, Hessaraghatta Lake PO, Bengaluru, 560089, Karnataka, India
| | - C N Lakshminarayana Reddy
- Department of Plant Pathology, College of Agriculture, University of Agricultural Sciences, GKVK, Bengaluru, 560065, Karnataka, India
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Wu H, Liu M, Kang B, Liu L, Hong N, Peng B, Gu Q. AC5 protein encoded by squash leaf curl China virus is an RNA silencing suppressor and a virulence determinant. Front Microbiol 2022; 13:980147. [PMID: 36060769 PMCID: PMC9437540 DOI: 10.3389/fmicb.2022.980147] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 08/05/2022] [Indexed: 11/26/2022] Open
Abstract
Squash leaf curl China virus (SLCCNV) is a bipartite Begomovirus. The function of the protein AC5, which is encoded by SLCCNV, is unknown. Here, we confirmed that the 172-amino acids (aa) long AC5 protein of SLCCNV could suppress single-stranded RNA but not double-stranded RNA-induced post-transcriptional gene silencing (PTGS). Furthermore, we determined that the C-terminal domain (96–172 aa) of the AC5 protein was responsible for RNA silencing suppressor (RSS) activity via deletion mutant analysis. The AC5 protein can reverse GFP silencing and inhibit systemic silencing of GFP by interfering with the systemic spread of the GFP silencing signal. The SLCCNV AC5 protein was localized to both the nucleus and cytoplasm of Nicotiana benthamiana cells. Furthermore, deletion analysis showed that the putative nuclear localization signal (NLS, 102–155 aa) was crucial for the RNA silencing suppression activity of AC5. In addition, the AC5 protein elicited a hypersensitive response and enhanced potoao virus X (PVX) RNA accumulation in infected N. benthamiana plants. Using the infectious clones of the SLCCNV and SLCCNV-AC5 null mutants, mutational analysis confirmed that knockout of the AC5 gene abolished SLCCNV-induced leaf curl symptoms, showing SLCCNV AC5 is also a virulence determinant.
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Affiliation(s)
- Huijie Wu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Mei Liu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Baoshan Kang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Liming Liu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Ni Hong
- College of Plant Science and Technology, Huazhong Agricultural University/Key Lab of Plant Pathology of Hubei Province, Wuhan, China
| | - Bin Peng
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
- Bin Peng,
| | - Qinsheng Gu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
- *Correspondence: Qinsheng Gu,
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Chen YJ, Lai HC, Lin CC, Neoh ZY, Tsai WS. Genetic Diversity, Pathogenicity and Pseudorecombination of Cucurbit-Infecting Begomoviruses in Malaysia. PLANTS (BASEL, SWITZERLAND) 2021; 10:2396. [PMID: 34834759 PMCID: PMC8624487 DOI: 10.3390/plants10112396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 10/28/2021] [Accepted: 11/02/2021] [Indexed: 11/16/2022]
Abstract
Cucurbits are important crops in the world. However, leaf curl disease constrains their production. Here, begomovirus diversity and pathogenicity associated with the disease in Malaysia were studied based on 49 begomovirus-detected out of 69 symptomatic plants from seven cucurbit crops in 15 locations during 2016 and 2017. The presence of Squash leaf curl China virus (SLCCNV) and Tomato leaf curl New Delhi virus (ToLCNDV) were confirmed by virus detection by polymerase chain reaction, viral DNA sequence analysis and specific detection of the viral components. ToLCNDV Malaysian isolates were further distinguished into strains A, B, C and D. Virus co-infection was detected in bitter gourd, bottle gourd and squash. Among them, eight bitter gourd samples were detected without SLCCNV DNA-A. However, one bottle gourd and five squash samples were without ToLCNDV DNA-B. Pseudorecombination of ToLCNDV DNA-A and SLCCNV DNA-B was detected in two bitter gourd samples. The pathogenic viruses and pseudorecombinants were confirmed by agroinoculation. The viral DNA-B influencing on symptomology and host range was also confirmed. The results strengthen the epidemic of cucurbit-infecting begomovirus in Malaysia as well as Southeast Asia. Especially, the natural pseudorecombinant of begomovirus that extends host range and causes severe symptom implies a threat to crops.
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Affiliation(s)
- Yu-Jeng Chen
- Department of Plant Medicine, National Chiayi University, Chiayi City 600355, Taiwan; (Y.-J.C.); (H.-C.L.); (Z.Y.N.)
| | - Hsuan-Chun Lai
- Department of Plant Medicine, National Chiayi University, Chiayi City 600355, Taiwan; (Y.-J.C.); (H.-C.L.); (Z.Y.N.)
| | | | - Zhuan Yi Neoh
- Department of Plant Medicine, National Chiayi University, Chiayi City 600355, Taiwan; (Y.-J.C.); (H.-C.L.); (Z.Y.N.)
| | - Wen-Shi Tsai
- Department of Plant Medicine, National Chiayi University, Chiayi City 600355, Taiwan; (Y.-J.C.); (H.-C.L.); (Z.Y.N.)
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Venkataravanappa V, Reddy CNL, Nandan M, Hiremath S, Ashwathappa KV, Shankarappa KS, Vinay Kumar HD, Reddy MK. Transmission, characterization and occurrence of recombination in Indian strain of squash leaf curl China virus associated with yellow mosaic and leaf curl disease of Summer squash. 3 Biotech 2021; 11:265. [PMID: 33996377 DOI: 10.1007/s13205-021-02821-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 05/04/2021] [Indexed: 11/29/2022] Open
Abstract
Summer squash is one of the important vegetable crops and its production is hampered by various abiotic and biotic stresses. Of the different biotic stresses, viral infections are responsible for causing great losses to this crop. Diseases caused by begomoviruses are becoming a major constraint in the cultivation of summer squash. Samples from summer squash plants exhibiting severe yellow mosaic and leaf curl symptoms were collected from the Varanasi district of Uttar Pradesh (India) and begomovirus associated with these plants was transmitted through whiteflies (Bemisia tabaci) to healthy squash plants. The relationship between causal virus and whitefly vector was determined. The minimum acquisition access period (AAP) and inoculation feeding period (IFP) required by B. tabaci to transmit the virus was determined to be 10 min and female insects have greater efficiency in transmitting virus than male insects. The partial genome of the virus was amplified by PCR (1.2 kb), cloned and sequenced from the ten infected plant samples collected from field. Partial genome sequence analysis (1.2 kb) obtained from the ten samples revealed that they are associated with begomovirus species closely related to the Indian strain of Squash leaf curl China virus (SLCCNV). Therefore, one representative sample (Sq-1) was selected and complete genome of the virus was amplified by rolling circle amplification (RCA) method. Sequence analysis by Sequence Demarcation Tool (SDT) showed that the current isolate has maximum nucleotide (nt) identity of 93.7-98.4% and 89-98.1% with respect to DNA A DNA B, respectively with Indian strains of SLCCNV infecting cucurbits in India. Recombination analysis of genomes (DNA A and DNA B components) showed that a major part of genomes likely to be originated from already known begomoviruses (ToLCNDV, SLCCNV-CN and SLCCNV-IN) are infecting cucurbitaceous crops. Serological assays such as triple antibody sandwich-enzyme-linked immune-sorbent (TAS-ELISA) assay, dot blot immunobinding assay (DIBA), immuno-capture polymerase chain reaction (IC-PCR) were developed for the detection of SLCCNV. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-02821-9.
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Affiliation(s)
- V Venkataravanappa
- Division of Plant Pathology, CHES, ICAR-Indian Institute of Horticultural Research, Chettalli, Madikeri District, Bangalore, Karnataka, 571248 India
| | - C N Lakshminarayana Reddy
- Department of Plant Pathology, College of Agriculture, University of Agricultural Sciences, GKVK, Bengaluru, Karnataka 563125 India
| | - M Nandan
- Department of Plant Pathology, College of Agriculture, University of Agricultural Sciences, GKVK, Bengaluru, Karnataka 563125 India
| | - Shridhar Hiremath
- Department of Plant Pathology, College of Agriculture, University of Agricultural Sciences, GKVK, Bengaluru, Karnataka 563125 India
| | - K V Ashwathappa
- Indian Institute of Horticultural Research, Hessaraghatta Lake PO, Bangalore, Karnataka 560089 India
| | - K S Shankarappa
- Department of Plant Pathology, College of Horticulture, University of Horticultural Sciences, Bagalkot, Bengaluru, Karnataka 560065 India
| | - H D Vinay Kumar
- Department of Plant Pathology, College of Agriculture, University of Agricultural Sciences, GKVK, Bengaluru, Karnataka 563125 India
| | - M Krishna Reddy
- Indian Institute of Horticultural Research, Hessaraghatta Lake PO, Bangalore, Karnataka 560089 India
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Pan LL, Chi Y, Liu C, Fan YY, Liu SS. Mutations in the coat protein of a begomovirus result in altered transmission by different species of whitefly vectors. Virus Evol 2020; 6:veaa014. [PMID: 32153997 PMCID: PMC7055206 DOI: 10.1093/ve/veaa014] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
For many crop pathogens including viruses, high genetic variation provides them with potential to adapt to and prevail in a changing environment. Understanding genetic variation in viruses and their significance is a key to elaborate virus epidemiology and evolution. While genetic variation of plant viruses has been documented to impact virus–host interactions, how it affects virus–insect vector interactions remains elusive. Here, we report the impact of mutations in the coat protein of squash leaf curl China virus (SLCCNV), a begomovirus, on the interaction between the virus and its whitefly vectors. We characterized mutations in the coat protein of SLCCNV and found that some residues exhibited higher mutation frequency than the others. We assayed the impact of mutation on infectivity using agroinoculation and found these mutations marginally affect virus infectivity. We further analyze their functions using virus acquisition and transmission trials and found some of mutations resulted in altered transmission of SLCCNV by different species of the whitefly Bemisia tabaci complex. We then identified the key amino acid residue(s) involved by constructing several mutant viruses and found that a single-residue mutation in the coat protein of SLCCNV was sufficient to significantly alter the whitefly transmission characteristics of SLCCNV. We examined the competition between different genotypes of SLCCNV in plant infection and whitefly transmission. We found that mutations in the coat protein did not alter the fitness of SLCCNV in plants, but they rendered the virus more competitive in transmission by certain species of whiteflies. Our findings indicate that mutations in the coat protein may play a key role in both the adaptation of begomoviruses to the changing vector populations and the evolution of begomoviruses.
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Affiliation(s)
- Li-Long Pan
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yao Chi
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China
| | - Chao Liu
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yun-Yun Fan
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China
| | - Shu-Sheng Liu
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China
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Khatun MF, Hwang HS, Shim JK, Kil EJ, Lee S, Lee KY. Identification of begomoviruses from different cryptic species of Bemisia tabaci in Bangladesh. Microb Pathog 2020; 142:104069. [PMID: 32061918 DOI: 10.1016/j.micpath.2020.104069] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 01/20/2020] [Accepted: 02/12/2020] [Indexed: 11/21/2022]
Abstract
Bemisia tabaci is a global species complex consisting of at least 40 cryptic species. It is also a vector for at least 100 species of begomovirus, many of which cause severe crop damage. The relationship between begomoviruses and cryptic species of the B. tabaci species complex, however, remains unclear. Our previous study [13] was identified four cryptic species (Asia I, Asia II 1, Asia II 5, and Asia II 10) of B. tabaci from Bangladesh. Using those 110 whitefly samples, vector-based PCR analysis identified 8 different begomovirus species: BYVMV, BGYVV, OELCV, SLCCV, SLCV, TbCSV, ToLCBV, and ToLCNDV. The overall rate of virus infection was 26.4%, and BYVMV and ToLCNDV were the most frequently detected in the B. tabaci vector. Virus infection rates for Asia I, Asia II 1, Asia II 5, and Asia II 10 were 22.4% (15/67), 35% (7/20), 27.3% (6/22), and 100% (1/1), respectively. Each cryptic species infected multiple virus species, but SLCCV, TbCSV, and BGYVV were each only detected in, Asia I, Asia II 1, and Asia II 5, respectively. This study demonstrates the geographic distribution of various begomoviruses in Bangladesh and their relationships with cryptic species of B. tabaci.
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Affiliation(s)
- Mst Fatema Khatun
- Division of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, Republic of Korea; Department of Entomology, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Dhaka, Bangladesh
| | - Hwal-Su Hwang
- Division of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, Republic of Korea; Institute of Plant Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Jae-Kyoung Shim
- Division of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, Republic of Korea; Institute of Plant Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Eui-Joon Kil
- Department of Genetic Engineering, Sungkyunkwan University, Suwon, Republic of Korea
| | - Sukchan Lee
- Department of Genetic Engineering, Sungkyunkwan University, Suwon, Republic of Korea
| | - Kyeong-Yeoll Lee
- Division of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, Republic of Korea; Institute of Plant Medicine, Kyungpook National University, Daegu, Republic of Korea; Institute of Agricultural Science and Technology, Kyungpook National University, Daegu, Republic of Korea.
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7
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Maina S, Barbetti MJ, Edwards OR, Minemba D, Areke MW, Jones RAC. Zucchini yellow mosaic virus Genomic Sequences from Papua New Guinea: Lack of Genetic Connectivity with Northern Australian or East Timorese Genomes, and New Recombination Findings. PLANT DISEASE 2019; 103:1326-1336. [PMID: 30995424 DOI: 10.1094/pdis-09-18-1666-re] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Zucchini yellow mosaic virus (ZYMV) isolates were obtained in Papua New Guinea (PNG) from cucumber (Cucumis sativus) or pumpkin (Cucurbita spp.) plants showing mosaic symptoms growing at Kongop in the Mount Hagen District, Western Highlands Province, or Zage in the Goroka District, Eastern Highlands Province. The samples were blotted onto FTA cards, which were sent to Australia, where they were subjected to high-throughput sequencing. When the coding regions of the nine new ZYMV genomic sequences found were compared with those of 64 other ZYMV sequences from elsewhere, they grouped together, forming new minor phylogroup VII within ZYMV's major phylogroup A. Genetic connectivity was lacking between ZYMV genomic sequences from PNG and its neighboring countries, Australia and East Timor; the closest match between a PNG and any other genomic sequence was a 92.8% nucleotide identity with a sequence in major phylogroup A's minor phylogroup VI from Japan. When the RDP5.2 recombination analysis program was used to compare 66 ZYMV sequences, evidence was obtained of 30 firm recombination events involving 41 sequences, and all isolates from PNG were recombinants. There were 21 sequences without recombination events in major phylogroup A, whereas there were only 4 such sequences within major phylogroup B. ZYMV's P1, Cl, N1a-Pro, P3, CP, and NIb regions contained the highest evidence of recombination breakpoints. Following removal of recombinant sequences, seven minor phylogroups were absent (I, III, IV, V, VI, VII, and VIII), leaving only minor phylogroups II and IX. By contrast, when a phylogenetic tree was constructed using recombinant sequences with their recombinationally derived tracts removed before analysis, five previous minor phylogroups remained unchanged within major phylogroup A (II, III, IV, V, and VII) while four formed two new merged phylogroups (I/VI and VIII/IX). Absence of genetic connectivity between PNG, Australian, and East Timorese ZYMV sequences, and the 92.8% nucleotide identity between a PNG sequence and the closest sequence from elsewhere, suggest that a single introduction may have occurred followed by subsequent evolution to adapt to the PNG environment. The need for enhanced biosecurity measures to protect against potentially damaging virus movements crossing the seas separating neighboring countries in this region of the world is discussed.
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Affiliation(s)
- Solomon Maina
- 1 School of Agriculture and Environment, Faculty of Science, and
- 2 UWA Institute of Agriculture, Faculty of Science, The University of Western Australia, Crawley, WA, Australia
- 3 Cooperative Research Centre for Plant Biosecurity, Canberra, Australian Capital Territory, Australia
| | - Martin J Barbetti
- 1 School of Agriculture and Environment, Faculty of Science, and
- 2 UWA Institute of Agriculture, Faculty of Science, The University of Western Australia, Crawley, WA, Australia
- 3 Cooperative Research Centre for Plant Biosecurity, Canberra, Australian Capital Territory, Australia
| | - Owain R Edwards
- 3 Cooperative Research Centre for Plant Biosecurity, Canberra, Australian Capital Territory, Australia
- 4 Commonwealth Scientific and Industrial Research Organisation Land and Water, Floreat Park, WA 6014, Australia
| | - David Minemba
- 1 School of Agriculture and Environment, Faculty of Science, and
- 5 The National Agricultural Research Institute, PO Box 4415, Lae, Morobe Province, Papua New Guinea
| | - Michael W Areke
- 6 National Agriculture Quarantine and Inspection Authority, PO Box 741, Port Moresby, National Capital District, Papua New Guinea; and
| | - Roger A C Jones
- 2 UWA Institute of Agriculture, Faculty of Science, The University of Western Australia, Crawley, WA, Australia
- 3 Cooperative Research Centre for Plant Biosecurity, Canberra, Australian Capital Territory, Australia
- 7 Department of Primary Industries and Regional Development, South Perth, WA, Australia
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Maina S, Barbetti MJ, Edwards OR, Minemba D, Areke MW, Jones RAC. Genetic Connectivity Between Papaya Ringspot Virus Genomes from Papua New Guinea and Northern Australia, and New Recombination Insights. PLANT DISEASE 2019; 103:737-747. [PMID: 30856073 DOI: 10.1094/pdis-07-18-1136-re] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Isolates of papaya ringspot virus (PRSV) were obtained from plants of pumpkin (Cucurbita spp.) or cucumber (Cucumis sativus) showing mosaic symptoms growing at Zage in Goroka District in the Eastern Highland Province of Papua New Guinea (PNG) or Bagl in the Mount Hagen District, Western Highlands Province. The samples were sent to Australia on FTA cards where they were subjected to High Throughput Sequencing (HTS). When the coding regions of the six new PRSV genomic sequences obtained via HTS were compared with those of 54 other complete PRSV sequences from other parts of the world, all six grouped together with the 12 northern Australian sequences within major phylogroup B minor phylogroup I, the Australian sequences coming from three widely dispersed locations spanning the north of the continent. Notably, none of the PNG isolates grouped with genomic sequences from the nearby country of East Timor in phylogroup A. The closest genetic match between Australian and PNG sequences was a nucleotide (nt) sequence identity of 96.9%, whereas between PNG and East Timorese isolates it was only 83.1%. These phylogenetic and nt identity findings demonstrate genetic connectivity between PRSV populations from PNG and Australia. Recombination analysis of the 60 PRSV sequences available revealed evidence of 26 recombination events within 18 isolates, only four of which were within major phylogroup B and none of which were from PNG or Australia. Within the recombinant genomes, the P1, Cl, NIa-Pro, NIb, 6K2, and 5'UTR regions contained the highest numbers of recombination breakpoints. After removal of nonrecombinant sequences, four minor phylogroups were lost (IV, VII, VIII, XV), only one of which was in phylogroup B. When genome regions from which recombinationally derived tracts of sequence were removed from recombinants prior to alignment with nonrecombinant genomes, seven previous minor phylogroups within major phylogroup A, and two within major phylogroup B, merged either partially or entirely forming four merged minor phylogroups. The genetic connectivity between PNG and northern Australian isolates and absence of detectable recombination within either group suggests that PRSV isolates from East Timor, rather than PNG, might pose a biosecurity threat to northern Australian agriculture should they prove more virulent than those already present.
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Affiliation(s)
- Solomon Maina
- 1 School of Agriculture and Environment, Faculty of Science, The University of Western Australia, Crawley, WA, Australia
- 2 UWA Institute of Agriculture, Faculty of Science, The University of Western Australia, Crawley, WA, Australia
- 3 Cooperative Research Centre for Plant Biosecurity, Canberra, ACT, Australia
| | - Martin J Barbetti
- 1 School of Agriculture and Environment, Faculty of Science, The University of Western Australia, Crawley, WA, Australia
- 2 UWA Institute of Agriculture, Faculty of Science, The University of Western Australia, Crawley, WA, Australia
- 3 Cooperative Research Centre for Plant Biosecurity, Canberra, ACT, Australia
| | - Owain R Edwards
- 3 Cooperative Research Centre for Plant Biosecurity, Canberra, ACT, Australia
- 4 CSIRO Land and Water, Floreat Park, WA6014, Australia
| | - David Minemba
- 1 School of Agriculture and Environment, Faculty of Science, The University of Western Australia, Crawley, WA, Australia
- 5 The National Agriculture Research Institute, P.O. Box 4415, Lae, Morobe Province, Papua New Guinea
| | - Michael W Areke
- 6 National Agriculture Quarantine and Inspection Authority, P.O. Box 741, Port Moresby, National Capital District, Papua New Guinea; and
| | - Roger A C Jones
- 2 UWA Institute of Agriculture, Faculty of Science, The University of Western Australia, Crawley, WA, Australia
- 3 Cooperative Research Centre for Plant Biosecurity, Canberra, ACT, Australia
- 7 Department of Primary Industries and Rural Development Food Western Australia, South Perth, WA, Australia
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Maina S, Barbetti MJ, Martin DP, Edwards OR, Jones RAC. New Isolates of Sweet potato feathery mottle virus and Sweet potato virus C: Biological and Molecular Properties, and Recombination Analysis Based on Complete Genomes. PLANT DISEASE 2018; 102:1899-1914. [PMID: 30136885 DOI: 10.1094/pdis-12-17-1972-re] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Sweet potato feathery mottle virus (SPFMV) and Sweet potato virus C (SPVC) isolates were obtained from sweetpotato shoot or tuberous root samples from three widely separated locations in Australia's tropical north (Cairns, Darwin, and Kununurra). The samples were planted in the glasshouse and scions obtained from the plants were graft inoculated to Ipomoea setosa plants. Virus symptoms were recorded in the field in Kununurra and in glasshouse-grown sweetpotato and I. setosa plants. RNA extracts from I. setosa leaf samples were subjected to high-throughput sequencing. New complete SPFMV (n = 17) and SPVC (n = 6) genomic sequences were obtained and compared with 47 sequences from GenBank. Phylogenetic analysis revealed that the 17 new SPFMV genomes all fitted within either major phylogroup A, minor phylogroup II, formerly O; or major phylogroup B, formerly RC. Major phylogroup A's minor phylogroup I, formerly EA, only appeared when recombinants were included. Numbers of SPVC genomes were insufficient to subdivide it into phylogroups. Within phylogroup A's minor phylogroup II, the closest genetic match between an Australian and a Southeast Asian SPFMV sequence was the 97.4% nucleotide identity with an East Timorese sequence. Recombination analysis of the 43 SPFMV and 27 SPVC sequences revealed evidence of 44 recombination events, 16 of which involved interspecies sequence transfers between SPFMV and SPVC and 28 intraspecies transfers, 17 in SPFMV and 11 in SPVC. Within SPFMV, 11 intraspecies recombination events were between different major phylogroups and 6 were between members of the same major phylogroup. Phylogenetic analysis accounting for the detected recombination events within SPFMV sequences yielded evidence of minor phylogroup II and phylogroup B but the five sequences from minor phylogroup I were distributed in two separate groups among the sequences of minor phylogroup II. For the SPVC sequences, phylogenetic analysis accounting for the detected recombination events revealed three major phylogroups (A, B, and C), with major phylogroup A being further subdivided into two minor phylogroups. Within the recombinant genomes of both viruses, their PI, NIa-Pro, NIb, and CP genes contained the highest numbers of recombination breakpoints. The high frequency of interspecies and interphylogroup recombination events reflects the widespread occurrence of mixed SPVC and SPFMV infections within sweetpotato plants. The prevalence of infection in northern Australian sweetpotato samples reinforces the need for improved virus testing in healthy sweetpotato stock programs. Furthermore, evidence of genetic connectivity between Australian and East Timorese SPFMV genomes emphasizes the need for improved biosecurity measures to protect against potentially damaging international virus movements.
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Affiliation(s)
- Solomon Maina
- School of Agriculture and Environment and the University of Western Australia (UWA) Institute of Agriculture, Faculty of Science, UWA, Crawley, WA 6009, Australia; and Cooperative Research Centre for Plant Biosecurity, Canberra, ACT 2617, Australia
| | - Martin J Barbetti
- School of Agriculture and Environment and UWA Institute of Agriculture, Faculty of Science, UWA
| | - Darren P Martin
- Institute of Infectious Diseases and Molecular Medicine, Computational Biology Group, University of Cape Town, Cape Town 7549, South Africa
| | - Owain R Edwards
- CSIRO Land and Water, Floreat Park, WA 6014, Australia; and Cooperative Research Centre for Plant Biosecurity, Canberra, ACT 2617, Australia
| | - Roger A C Jones
- Department of Primary Industries and Rural Development, South Perth, WA 6151, Australia; UWA Institute of Agriculture, Faculty of Science, UWA
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Wamaitha MJ, Nigam D, Maina S, Stomeo F, Wangai A, Njuguna JN, Holton TA, Wanjala BW, Wamalwa M, Lucas T, Djikeng A, Garcia-Ruiz H. Metagenomic analysis of viruses associated with maize lethal necrosis in Kenya. Virol J 2018; 15:90. [PMID: 29792207 PMCID: PMC5966901 DOI: 10.1186/s12985-018-0999-2] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 05/07/2018] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Maize lethal necrosis is caused by a synergistic co-infection of Maize chlorotic mottle virus (MCMV) and a specific member of the Potyviridae, such as Sugarcane mosaic virus (SCMV), Wheat streak mosaic virus (WSMV) or Johnson grass mosaic virus (JGMV). Typical maize lethal necrosis symptoms include severe yellowing and leaf drying from the edges. In Kenya, we detected plants showing typical and atypical symptoms. Both groups of plants often tested negative for SCMV by ELISA. METHODS We used next-generation sequencing to identify viruses associated to maize lethal necrosis in Kenya through a metagenomics analysis. Symptomatic and asymptomatic leaf samples were collected from maize and sorghum representing sixteen counties. RESULTS Complete and partial genomes were assembled for MCMV, SCMV, Maize streak virus (MSV) and Maize yellow dwarf virus-RMV (MYDV-RMV). These four viruses (MCMV, SCMV, MSV and MYDV-RMV) were found together in 30 of 68 samples. A geographic analysis showed that these viruses are widely distributed in Kenya. Phylogenetic analyses of nucleotide sequences showed that MCMV, MYDV-RMV and MSV are similar to isolates from East Africa and other parts of the world. Single nucleotide polymorphism, nucleotide and polyprotein sequence alignments identified three genetically distinct groups of SCMV in Kenya. Variation mapped to sequences at the border of NIb and the coat protein. Partial genome sequences were obtained for other four potyviruses and one polerovirus. CONCLUSION Our results uncover the complexity of the maize lethal necrosis epidemic in Kenya. MCMV, SCMV, MSV and MYDV-RMV are widely distributed and infect both maize and sorghum. SCMV population in Kenya is diverse and consists of numerous strains that are genetically different to isolates from other parts of the world. Several potyviruses, and possibly poleroviruses, are also involved.
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Affiliation(s)
- Mwathi Jane Wamaitha
- Kenya Agricultural and Livestock Research Organization (KALRO), P. O. Box 14733-00800, Nairobi, Kenya
| | - Deepti Nigam
- Department of Plant Pathology and Nebraska Center for Virology, University of Nebraska- Lincoln, Lincoln, NE 68583 USA
| | - Solomon Maina
- School of Agriculture and Environment and UWA Institute of Agriculture, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009 Australia
- Cooperative Research Centre for Plant Biosecurity, Canberra, ACT 2617 Australia
| | - Francesca Stomeo
- Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI), Hub, Nairobi, Kenya
| | - Anne Wangai
- Kenya Agricultural and Livestock Research Organization (KALRO), P. O. Box 14733-00800, Nairobi, Kenya
| | - Joyce Njoki Njuguna
- Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI), Hub, Nairobi, Kenya
| | - Timothy A. Holton
- Plant Innovation Centre, Post-Entry Quarantine, Department of Agriculture and Water Resources, 135 Donnybrook Road, Mickleham, VIC 3064 Australia
| | - Bramwel W. Wanjala
- Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI), Hub, Nairobi, Kenya
| | - Mark Wamalwa
- Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI), Hub, Nairobi, Kenya
| | - Tanui Lucas
- Kenya Agricultural and Livestock Research Organization (KALRO), P. O. Box 14733-00800, Nairobi, Kenya
| | - Appolinaire Djikeng
- Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI), Hub, Nairobi, Kenya
- Centre for Tropical Livestock Genetics and Health (CTLGH), The University of Edinburgh, Edinburgh, Scotland EH25 9RG UK
| | - Hernan Garcia-Ruiz
- Department of Plant Pathology and Nebraska Center for Virology, University of Nebraska- Lincoln, Lincoln, NE 68583 USA
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Maina S, Barbetti MJ, Edwards OR, Minemba D, Areke MW, Jones RAC. First Complete Genome Sequence of Cucurbit aphid-borne yellows virus from Papua New Guinea. GENOME ANNOUNCEMENTS 2018; 6:e00162-18. [PMID: 29545301 PMCID: PMC5854776 DOI: 10.1128/genomea.00162-18] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 02/13/2018] [Indexed: 11/24/2022]
Abstract
Analysis of an RNA-Seq library from cucumber leaf RNA revealed the first complete genome sequence of Cucurbit aphid-borne yellows virus (CABYV) from Papua New Guinea. We compared it with 36 complete CABYV genomes from other world regions. It most resembled the genome of South Korean isolate GS6.
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Affiliation(s)
- Solomon Maina
- School of Agriculture and Environment, Faculty of Science, The University of Western Australia, Crawley, Western Australia, Australia
- Institute of Agriculture, Faculty of Science, The University of Western Australia, Crawley, Western Australia, Australia
- Cooperative Research Centre for Plant Biosecurity, Canberra, Australian Capital Territory, Australia
| | - Martin J Barbetti
- School of Agriculture and Environment, Faculty of Science, The University of Western Australia, Crawley, Western Australia, Australia
- Institute of Agriculture, Faculty of Science, The University of Western Australia, Crawley, Western Australia, Australia
| | - Owain R Edwards
- Cooperative Research Centre for Plant Biosecurity, Canberra, Australian Capital Territory, Australia
- CSIRO Land & Water, Floreat Park, Western Australia, Australia
| | - David Minemba
- School of Agriculture and Environment, Faculty of Science, The University of Western Australia, Crawley, Western Australia, Australia
- Kana Aburu Haus Sir Alkan Tololo Research Centre, PNG National Agriculture Research Institute, Lae, Morobe Province, Papua New Guinea
| | - Michael W Areke
- National Agriculture Quarantine and Inspection Authority, Port Moresby, National Capital District, Papua New Guinea
| | - Roger A C Jones
- Institute of Agriculture, Faculty of Science, The University of Western Australia, Crawley, Western Australia, Australia
- Cooperative Research Centre for Plant Biosecurity, Canberra, Australian Capital Territory, Australia
- Department of Primary Industries and Regional Development, South Perth, Western Australia, Australia
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Maina S, Barbetti MJ, Edwards OR, de Almeida L, Ximenes A, Jones RAC. Sweet potato feathery mottle virus and Sweet potato virus C from East Timorese and Australian Sweetpotato: Biological and Molecular Properties, and Biosecurity Implications. PLANT DISEASE 2018; 102:589-599. [PMID: 30673482 DOI: 10.1094/pdis-08-17-1156-re] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Sweet potato feathery mottle virus (SPFMV) and Sweet potato virus C (SPVC) isolates from sweetpotato were studied to examine genetic connectivity between viruses from Australia and Southeast Asia. East Timorese samples from sweetpotato were sent to Australia on FTA cards. Shoot and tuberous root samples were collected in Australia and planted in the glasshouse, and scions were graft inoculated to Ipomoea setosa plants. Symptoms in infected sweetpotato and I. setosa plants were recorded. RNA extracts from FTA cards and I. setosa leaf samples were subjected to high-throughput sequencing (HTS). Complete genomic sequences (CS) of SPFMV and SPVC (11 each) were obtained by HTS, and coat protein (CP) genes from them were compared with others from GenBank. SPFMV sequences clustered into two major phylogroups (A and B = RC) and two minor phylogroups (EA[I] and O[II]) within A; East Timorese sequences were in EA(I) and O(II), whereas Australian sequences were in O(II) and B(RC). With SPVC, CP trees provided sufficient diversity to distinguish major phylogroups A and B and six minor phylogroups within A (I to VI); East Timorese sequences were in minor phylogroup I, whereas Australian sequences were in minor phylogroups II and VI and in major phylogroup B. With SPFMV, Aus13B grouped with East Timorese sequence TM64B within minor phylogroup O, giving nucleotide sequence identities of 97.4% (CS) and 98.3% (CP). However, the closest match with an Australian sequence was the 97.6% (CS) and 98.7% (CP) nucleotide identity between Aus13B and an Argentinian sequence. With SPVC, closest nucleotide identity matches between Australian and East Timorese sequences were 94.1% with Aus6a and TM68A (CS) and 96.3% with Aus55-4C and TM64A (CP); however neither pair member belonged to the same minor phylogroup. Also, the closest Australian match was 99.1% (CP) nucleotide identity between Aus4C and New Zealand isolate NZ4-4. These first complete genome sequences of SPFMV and SPVC from sweetpotato plantings in the Australian continent and neighboring Southeast Asia suggest at least two (SPFMV) and three (SPVC) separate introductions to Australia since agriculture commenced more than two centuries ago. These findings have major implications for both healthy stock programs and biosecurity management in relation to pathogen entry into Australia and elsewhere.
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Affiliation(s)
- Solomon Maina
- School of Agriculture and Environment and University of Western Australia (UWA) Institute of Agriculture, Faculty of Science, UWA, Crawley, WA 6009, Australia; and Cooperative Research Centre for Plant Biosecurity, Canberra, ACT 2617, Australia
| | - Martin J Barbetti
- School of Agriculture and Environment and UWA Institute of Agriculture, Faculty of Science, UWA; and Cooperative Research Center for Plant Biosecurity, Canberra, Australia
| | - Owain R Edwards
- Commonwealth Scientific and Industrial Research Organisation Land and Water, Floreat Park, WA 6014, Australia; and Cooperative Research Centre for Plant Biosecurity, Canberra
| | - Luis de Almeida
- Seeds of Life Project, Ministry Agriculture and Fisheries, Dili, East Timor
| | - Abel Ximenes
- DNQB-Plant Quarantine, International Airport Nicolau Lobato Comoro, Dili, East Timor
| | - Roger A C Jones
- Department of Agriculture and Food Western Australia, South Perth, WA 6151, Australia; UWA Institute of Agriculture, Faculty of Science, UWA; and Cooperative Research Centre for Plant Biosecurity, Canberra
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Maina S, Edwards OR, Jones RAC. Two Complete Genome Sequences of Squash mosaic virus from 20-Year-Old Cucurbit Leaf Samples from Australia. GENOME ANNOUNCEMENTS 2017; 5:e00778-17. [PMID: 28798181 PMCID: PMC5552990 DOI: 10.1128/genomea.00778-17] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/24/2017] [Accepted: 06/27/2017] [Indexed: 11/20/2022]
Abstract
We present the first complete Australian Squash mosaic virus (SqMV) genome sequences. We compared the 2 Australian genomes from 20-year-old cucurbit samples with 8 other SqMV genomes. The Australian genomes shared >99.0% nucleotide identities, and their RNA1 and RNA2 sequences most closely resembled isolates Y and Kimbe from Japan, respectively.
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Affiliation(s)
- Solomon Maina
- School of Agriculture and Environment, Faculty of Science, The University of Western Australia, Crawley, Western Australia, Australia
- Institute of Agriculture, Faculty of Science, The University of Western Australia, Crawley, Western Australia, Australia
- Cooperative Research Centre for Plant Biosecurity, Canberra, Australian Capital Territory, Australia
| | - Owain R Edwards
- Cooperative Research Centre for Plant Biosecurity, Canberra, Australian Capital Territory, Australia
- CSIRO Land and Water, Floreat Park, Western Australia, Australia
| | - Roger A C Jones
- Institute of Agriculture, Faculty of Science, The University of Western Australia, Crawley, Western Australia, Australia
- Cooperative Research Centre for Plant Biosecurity, Canberra, Australian Capital Territory, Australia
- Department of Agriculture and Food Western Australia, South Perth, Western Australia, Australia
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