1
|
Maina S, Zheng L, Rodoni BC. Targeted Genome Sequencing (TG-Seq) Approaches to Detect Plant Viruses. Viruses 2021; 13:583. [PMID: 33808381 PMCID: PMC8066983 DOI: 10.3390/v13040583] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 03/22/2021] [Accepted: 03/27/2021] [Indexed: 12/18/2022] Open
Abstract
Globally, high-throughput sequencing (HTS) has been used for virus detection in germplasm certification programs. However, sequencing costs have impeded its implementation as a routine diagnostic certification tool. In this study, the targeted genome sequencing (TG-Seq) approach was developed to simultaneously detect multiple (four) viral species of; Pea early browning virus (PEBV), Cucumber mosaic virus (CMV), Bean yellow mosaic virus (BYMV) and Pea seedborne mosaic virus (PSbMV). TG-Seq detected all the expected viral amplicons within multiplex PCR (mPCR) reactions. In contrast, the expected PCR amplicons were not detected by gel electrophoresis (GE). For example, for CMV, GE only detected RNA1 and RNA2 while TG-Seq detected all the three RNA components of CMV. In an mPCR to amplify all four viruses, TG-Seq readily detected each virus with more than 732,277 sequence reads mapping to each amplicon. In addition, TG-Seq also detected all four amplicons within a 10-8 serial dilution that were not detectable by GE. Our current findings reveal that the TG-Seq approach offers significant potential and is a highly sensitive targeted approach for detecting multiple plant viruses within a given biological sample. This is the first study describing direct HTS of plant virus mPCR products. These findings have major implications for grain germplasm healthy certification programs and biosecurity management in relation to pathogen entry into Australia and elsewhere.
Collapse
Affiliation(s)
- Solomon Maina
- Microbial Sciences, Pests & Diseases, Agriculture Victoria, 110 Natimuk Road, Horsham, Victoria 3400, Australia
- Australian Grains Genebank, Agriculture Victoria, 110 Natimuk Road, Horsham, Victoria 3400, Australia
| | - Linda Zheng
- Microbial Sciences, Pests & Diseases, Agriculture Victoria, AgriBio, 5 Ring Road, Bundoora, Victoria 3083, Australia; (L.Z.); (B.C.R.)
| | - Brendan C. Rodoni
- Microbial Sciences, Pests & Diseases, Agriculture Victoria, AgriBio, 5 Ring Road, Bundoora, Victoria 3083, Australia; (L.Z.); (B.C.R.)
- School of Applied Systems Biology (SASB), La Trobe University, Bundoora, Victoria 3083, Australia
| |
Collapse
|
2
|
Ranawaka B, Hayashi S, Waterhouse PM, de Felippes FF. Homo sapiens: The Superspreader of Plant Viral Diseases. Viruses 2020; 12:E1462. [PMID: 33348905 PMCID: PMC7766621 DOI: 10.3390/v12121462] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 12/15/2020] [Indexed: 02/05/2023] Open
Abstract
Plant viruses are commonly vectored by flying or crawling animals, such as aphids and beetles, and cause serious losses in major agricultural and horticultural crops. Controlling virus spread is often achieved by minimizing a crop's exposure to the vector, or by reducing vector numbers with compounds such as insecticides. A major, but less obvious, factor not controlled by these measures is Homo sapiens. Here, we discuss the inconvenient truth of how humans have become superspreaders of plant viruses on both a local and a global scale.
Collapse
Affiliation(s)
| | - Satomi Hayashi
- Centre for Agriculture and the Bioeconomy, Institute for Future Environments, Queensland University of Technology (QUT), 2 George Street, Brisbane, QLD 4000, Australia; (B.R.); (P.M.W.)
| | | | - Felipe F. de Felippes
- Centre for Agriculture and the Bioeconomy, Institute for Future Environments, Queensland University of Technology (QUT), 2 George Street, Brisbane, QLD 4000, Australia; (B.R.); (P.M.W.)
| |
Collapse
|
3
|
Tibiri EB, Pita JS, Tiendrébéogo F, Bangratz M, Néya JB, Brugidou C, Somé K, Barro N. Characterization of virus species associated with sweetpotato virus diseases in Burkina Faso. PLANT PATHOLOGY 2020; 69:1003-1017. [PMID: 32742024 PMCID: PMC7386933 DOI: 10.1111/ppa.13190] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 03/28/2020] [Indexed: 06/11/2023]
Abstract
Sweetpotato (Ipomoea batatas) production in sub-Saharan Africa is severely affected by viral diseases caused by several interacting viruses, including sweet potato feathery mottle virus (SPFMV), sweet potato chlorotic stunt virus (SPCSV), and sweet potato leaf curl virus (SPLCV). However, the aetiology of viral symptoms on sweetpotato is rarely established in most countries in Africa. Here, we aimed to investigate and characterize the incidence of sweetpotato viruses in Burkina Faso. We performed a countrywide survey in 18 districts of Burkina Faso and collected 600 plants, with and without symptoms, from 80 fields. Viral strains were identified using nitrocellulose membrane-ELISA, PCR, and reverse transcription-PCR. Three scions from each of 50 selected plants with symptoms were grafted to healthy Ipomoea setosa and then serological and molecular tests were performed on the 150 recorded samples. Three viruses were detected: 24% of samples were positive for SPFMV, 18% for SPLCV, and 2% for SPCSV. Across all diagnostic tests, 40% of all plant samples were virus-negative. Coinfections were found in 16% of samples. Partial sequences were obtained, including 13 that matched SPFMV, one that matched SPLCV, and one that matched SPCSV. All identified SPFMV isolates belonged to either phylogroup B or A-II. The SPCSV-positive isolates had 98% gene sequence homology with SPCSV-West Africa for the coat protein. Begomovirus-positive isolates clustered with SPLCV-United States. This first study of sweetpotato viral diseases in Burkina Faso indicates widespread occurrence and suggests a need for further epidemiological investigations, breeding programmes focused on virus-resistant varieties, and improved farming practices to control disease spread.
Collapse
Affiliation(s)
- Ezechiel B. Tibiri
- Laboratoire de Virologie et de Biotechnologies VégétalesInstitut de l’Environnement et de Recherches Agricoles (INERA)OuagadougouBurkina Faso
- Laboratoire de Génétique et de Biotechnologies VégétalesInstitut de l’Environnement et de Recherches Agricoles (INERA)OuagadougouBurkina Faso
- Laboratoire Mixte International Patho‐BiosIRD‐INERAOuagadougouBurkina Faso
- Laboratoire d’Epidémiologie et de Surveillance des bactéries et virus Transmissibles par les Aliments et l’eauLabESTA/UFR/SVTUniversité Joseph Ki‐ZerboOuagadougouBurkina Faso
| | - Justin S. Pita
- Central and West African Virus Epidemiology (WAVE), Pôle Scientifique et d’innovation de BingervilleUniversité Félix Houphouët‐Boigny (UFHB)BingervilleCôte d’Ivoire
| | - Fidèle Tiendrébéogo
- Laboratoire de Virologie et de Biotechnologies VégétalesInstitut de l’Environnement et de Recherches Agricoles (INERA)OuagadougouBurkina Faso
- Laboratoire Mixte International Patho‐BiosIRD‐INERAOuagadougouBurkina Faso
| | - Martine Bangratz
- Laboratoire Mixte International Patho‐BiosIRD‐INERAOuagadougouBurkina Faso
- Interactions Plants Microorganismes et Environnement (IPME)IRD, CiradUniversité MontpellierMontpellierCedexFrance
| | - James B. Néya
- Laboratoire de Virologie et de Biotechnologies VégétalesInstitut de l’Environnement et de Recherches Agricoles (INERA)OuagadougouBurkina Faso
- Laboratoire Mixte International Patho‐BiosIRD‐INERAOuagadougouBurkina Faso
| | - Christophe Brugidou
- Laboratoire Mixte International Patho‐BiosIRD‐INERAOuagadougouBurkina Faso
- Interactions Plants Microorganismes et Environnement (IPME)IRD, CiradUniversité MontpellierMontpellierCedexFrance
| | - Koussao Somé
- Laboratoire de Génétique et de Biotechnologies VégétalesInstitut de l’Environnement et de Recherches Agricoles (INERA)OuagadougouBurkina Faso
- Laboratoire Mixte International Patho‐BiosIRD‐INERAOuagadougouBurkina Faso
| | - Nicolas Barro
- Laboratoire d’Epidémiologie et de Surveillance des bactéries et virus Transmissibles par les Aliments et l’eauLabESTA/UFR/SVTUniversité Joseph Ki‐ZerboOuagadougouBurkina Faso
| |
Collapse
|
4
|
Trebicki P. Climate change and plant virus epidemiology. Virus Res 2020; 286:198059. [PMID: 32561376 DOI: 10.1016/j.virusres.2020.198059] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 04/20/2020] [Accepted: 06/10/2020] [Indexed: 10/24/2022]
Abstract
Changes in global climate driven by anthropogenic activities, especially the burning of fossil fuels and deforestation, have been progressively increasing and are projected to intensify. Increasing concentrations of atmospheric carbon dioxide and temperature will have significant consequences for future food production, quality, distribution and security. The epidemiology of plant viruses will be altered in the future as a result of climate change. Elevated atmospheric carbon dioxide, increased temperature, changes to water availability and more frequent extreme weather events will have direct and indirect effects on plant viruses through changes in hosts and vectors. Predicted climatic changes will affect the distribution and survival of plant viruses and their vectors, which are expected to increase in many geographic regions. Furthermore, climate change can affect the virulence and pathogenicity of plant viruses, consequently increasing the frequency and scale of disease outbreaks. Thus, greater understanding of plant virus epidemiology is needed to better anticipate challenges ahead and to develop effective and robust control strategies that will aid in securing global food production for the future.
Collapse
Affiliation(s)
- Piotr Trebicki
- Agriculture Victoria, 110 Natimuk Rd, Horsham, Victoria, 3400, Australia.
| |
Collapse
|
5
|
Wokorach G, Otim G, Njuguna J, Edema H, Njung'e V, Machuka EM, Yao N, Stomeo F, Echodu R. Genomic analysis of Sweet potato feathery mottle virus from East Africa. PHYSIOLOGICAL AND MOLECULAR PLANT PATHOLOGY 2020; 110:101473. [PMID: 32454559 PMCID: PMC7233136 DOI: 10.1016/j.pmpp.2020.101473] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 02/07/2020] [Accepted: 02/10/2020] [Indexed: 06/11/2023]
Abstract
Sweet potato feathery mottle virus is a potyvirus that infect sweet potato. The genome of the virus was analysed to understand genetic diversity, evolution and gene flow. Motifs, nucleotide identity and a phylogenetic tree were used to determine phylogroup of the isolates. Gene flow and genetic diversity were tested using DnaSP v.5. Codons evolution were tested using three methods embedded in Datamonkey. The results indicate occurrence of an isolate of phylogroup B within East Africa. Low genetic differentiation was observed between isolates from Kenya and Uganda indicating evidence of gene flow between the two countries. Four genes were found to have positively selected codons bordering or occurring within functional motifs. A motif within P1 gene evolved differently between phylogroup A and B. The evidence of gene flow indicates frequent exchange of the virus between the two countries and P1 gene motif provide a possible marker that can be used for mapping the distribution of the phylogroups.
Collapse
Affiliation(s)
- Godfrey Wokorach
- Biosciences Research Laboratory, Gulu University, P.O. Box 166, Gulu, Uganda
| | - Geoffrey Otim
- Biosciences Research Laboratory, Gulu University, P.O. Box 166, Gulu, Uganda
- Faculty of Agriculture, Gulu University, P.O. Box 166, Gulu, Uganda
| | - Joyce Njuguna
- Biosciences Eastern and Central Africa, International Livestock Research Institute (BecA-ILRI) Hub, P.O. Box 30709, Nairobi, 00100, Kenya
| | - Hilary Edema
- Biosciences Research Laboratory, Gulu University, P.O. Box 166, Gulu, Uganda
| | - Vincent Njung'e
- Biosciences Eastern and Central Africa, International Livestock Research Institute (BecA-ILRI) Hub, P.O. Box 30709, Nairobi, 00100, Kenya
| | - Eunice M. Machuka
- Biosciences Eastern and Central Africa, International Livestock Research Institute (BecA-ILRI) Hub, P.O. Box 30709, Nairobi, 00100, Kenya
| | - Nasser Yao
- Biosciences Eastern and Central Africa, International Livestock Research Institute (BecA-ILRI) Hub, P.O. Box 30709, Nairobi, 00100, Kenya
| | - Francesca Stomeo
- Biosciences Eastern and Central Africa, International Livestock Research Institute (BecA-ILRI) Hub, P.O. Box 30709, Nairobi, 00100, Kenya
| | - Richard Echodu
- Biosciences Research Laboratory, Gulu University, P.O. Box 166, Gulu, Uganda
- Faculty of Agriculture, Gulu University, P.O. Box 166, Gulu, Uganda
- Department of Biology, Faculty of Science, Gulu University, P.O. Box 166, Gulu, Uganda
| |
Collapse
|
6
|
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.
Collapse
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
| |
Collapse
|
7
|
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.
Collapse
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
| |
Collapse
|
8
|
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.
Collapse
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
| |
Collapse
|
9
|
Wainaina JM, Ateka E, Makori T, Kehoe MA, Boykin LM. Phylogenomic relationship and evolutionary insights of sweet potato viruses from the western highlands of Kenya. PeerJ 2018; 6:e5254. [PMID: 30038869 PMCID: PMC6054865 DOI: 10.7717/peerj.5254] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 06/24/2018] [Indexed: 11/20/2022] Open
Abstract
Sweet potato is a major food security crop within sub-Saharan Africa where 90% of Africa production occurs. One of the major limitations of sweet potato production are viral infections. In this study, we used a combination of whole genome sequences from a field isolate obtained from Kenya and those available in GenBank. Sequences of four sweet potato viruses: Sweet potato feathery mottle virus (SPFMV), Sweet potato virus C (SPVC), Sweet potato chlorotic stunt virus (SPCSV), Sweet potato chlorotic fleck virus (SPCFV) were obtained from the Kenyan sample. SPFMV sequences both from this study and from GenBank were found to be recombinant. Recombination breakpoints were found within the Nla-Pro, coat protein and P1 genes. The SPCSV, SPVC, and SPCFV viruses from this study were non-recombinant. Bayesian phylogenomic relationships across whole genome trees showed variation in the number of well-supported clades; within SPCSV (RNA1 and RNA2) and SPFMV two well-supported clades (I and II) were resolved. The SPCFV tree resolved three well-supported clades (I-III) while four well-supported clades were resolved in SPVC (I-IV). Similar clades were resolved within the coalescent species trees. However, there were disagreements between the clades resolved in the gene trees compared to those from the whole genome tree and coalescent species trees. However the coat protein gene tree of SPCSV and SPCFV resolved similar clades to the genome and coalescent species tree while this was not the case in SPFMV and SPVC. In addition, we report variation in selective pressure within sites of individual genes across all four viruses; overall all viruses were under purifying selection. We report the first complete genomes of SPFMV, SPVC, SPCFV, and a partial SPCSV from Kenya as a mixed infection in one sample. Our findings provide a snap shot on the evolutionary relationship of sweet potato viruses (SPFMV, SPVC, SPCFV, and SPCSV) from Kenya as well as assessing whether selection pressure has an effect on their evolution.
Collapse
Affiliation(s)
- James M. Wainaina
- School of Molecular Sciences/ARC CoE Plant Energy Biology, The University of Western Australia, Crawley, WA, Australia
| | - Elijah Ateka
- Department of Horticulture, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Timothy Makori
- Department of Horticulture, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Monica A. Kehoe
- Plant Pathology, Department of Primary Industries and Regional Development Diagnostic Laboratory Service, South Perth, WA, Australia
| | - Laura M. Boykin
- School of Molecular Sciences/ARC CoE Plant Energy Biology, The University of Western Australia, Crawley, WA, Australia
| |
Collapse
|
10
|
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.
Collapse
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
| |
Collapse
|