1
|
Li C, Guo S, Sun M, Niu J, Yin C, Du W, Zhao J, Liu D, Yue A. A Colorimetric RT-LAMP Assay for Rapid Detection of Soybean mosaic Virus SC15. ACS OMEGA 2024; 9:29765-29775. [PMID: 39005798 PMCID: PMC11238210 DOI: 10.1021/acsomega.4c03372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 05/19/2024] [Accepted: 06/10/2024] [Indexed: 07/16/2024]
Abstract
Soybean mosaic virus (SMV) represents one of the most devastating viral diseases affecting soybeans worldwide. Among its strains, SMV-SC15 is notable for its virulence, predominance, and widespread occurrence. Rapid and on-site diagnosis is important for controlling the spread of SMV-SC15. In this study, we proposed a colorimetric reverse-transcription loop-mediated isothermal amplification (RT-LAMP) assay for the detection of SMV-SC15 using three color indicators for visual interpretation: Neutral Red (N-Red), Bromothymol Blue (BTB), and SYBR Green I. The SMV-SC15 in the soybean tissue was detected with remarkable sensitivity and specificity within 30 min, achieving a detection limit as low as 10-4 ng/μL. 200 soybean leaf samples from the field were analyzed by the colorimetric RT-LAMP assays, holding significant potential for rapid screening of SMV-SC15-resistant cultivars, thereby contributing to effective SMV control.
Collapse
Affiliation(s)
- Chen Li
- Department
of Basic Sciences, Shanxi Agricultural University, Taigu, Shanxi 030801, China
| | - Shuixian Guo
- Department
of Basic Sciences, Shanxi Agricultural University, Taigu, Shanxi 030801, China
| | - Min Sun
- College
of Agronomy, Shanxi Agricultural University, Taigu, Shanxi 030801, China
| | - Jingping Niu
- College
of Life Science, Shanxi Agricultural University, Taigu, Shanxi 030801, China
| | - Congcong Yin
- Department
of Basic Sciences, Shanxi Agricultural University, Taigu, Shanxi 030801, China
| | - Weijun Du
- College
of Agronomy, Shanxi Agricultural University, Taigu, Shanxi 030801, China
| | - Jinzhong Zhao
- Department
of Basic Sciences, Shanxi Agricultural University, Taigu, Shanxi 030801, China
| | - Dingbin Liu
- College
of Chemistry, Nankai University, Tianjin 300071, China
| | - Aiqin Yue
- College
of Agronomy, Shanxi Agricultural University, Taigu, Shanxi 030801, China
| |
Collapse
|
2
|
Wei Y, Xie H, Xu L, Cheng X, Zhu B, Zeng H, Shi H. Coat protein of cassava common mosaic virus targets RAV1 and RAV2 transcription factors to subvert immunity in cassava. PLANT PHYSIOLOGY 2024; 194:1218-1232. [PMID: 37874769 DOI: 10.1093/plphys/kiad569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 09/26/2023] [Accepted: 10/03/2023] [Indexed: 10/26/2023]
Abstract
Cassava common mosaic virus (CsCMV, genus Potexvirus) is a prevalent virus associated with cassava mosaic disease, so it is essential to elucidate the underlying molecular mechanisms of the coevolutionary arms race between viral pathogenesis and the cassava (Manihot esculenta Crantz) defense response. However, the molecular mechanism underlying CsCMV infection is largely unclear. Here, we revealed that coat protein (CP) acts as a major pathogenicity determinant of CsCMV via a mutant infectious clone. Moreover, we identified the target proteins of CP-related to abscisic acid insensitive3 (ABI3)/viviparous1 (VP1) (MeRAV1) and MeRAV2 transcription factors, which positively regulated disease resistance against CsCMV via transcriptional activation of melatonin biosynthetic genes (tryptophan decarboxylase 2 (MeTDC2), tryptamine 5-hydroxylase (MeT5H), N-aceylserotonin O-methyltransferase 1 (MeASMT1)) and MeCatalase6 (MeCAT6) and MeCAT7. Notably, the interaction between CP, MeRAV1, and MeRAV2 interfered with the protein phosphorylation of MeRAV1 and MeRAV2 individually at Ser45 and Ser44 by the protein kinase, thereby weakening the transcriptional activation activity of MeRAV1 and MeRAV2 on melatonin biosynthetic genes, MeCAT6 and MeCAT7 dependent on the protein phosphorylation of MeRAV1 and MeRAV2. Taken together, the identification of the CP-MeRAV1 and CP-MeRAV2 interaction module not only illustrates a molecular mechanism by which CsCMV orchestrates the host defense system to benefit its infection and development but also provides a gene network with potential value for the genetic improvement of cassava disease resistance.
Collapse
Affiliation(s)
- Yunxie Wei
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), National Key Laboratory for Tropical Crop Breeding, Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, School of Tropical Agriculture and Forestry, Hainan University, Sanya, Hainan Province 572025, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan Province 572025, China
| | - Haoqi Xie
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), National Key Laboratory for Tropical Crop Breeding, Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, School of Tropical Agriculture and Forestry, Hainan University, Sanya, Hainan Province 572025, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan Province 572025, China
| | - Lulu Xu
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), National Key Laboratory for Tropical Crop Breeding, Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, School of Tropical Agriculture and Forestry, Hainan University, Sanya, Hainan Province 572025, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan Province 572025, China
| | - Xiao Cheng
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), National Key Laboratory for Tropical Crop Breeding, Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, School of Tropical Agriculture and Forestry, Hainan University, Sanya, Hainan Province 572025, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan Province 572025, China
| | - Binbin Zhu
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), National Key Laboratory for Tropical Crop Breeding, Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, School of Tropical Agriculture and Forestry, Hainan University, Sanya, Hainan Province 572025, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan Province 572025, China
| | - Hongqiu Zeng
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), National Key Laboratory for Tropical Crop Breeding, Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, School of Tropical Agriculture and Forestry, Hainan University, Sanya, Hainan Province 572025, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan Province 572025, China
| | - Haitao Shi
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), National Key Laboratory for Tropical Crop Breeding, Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, School of Tropical Agriculture and Forestry, Hainan University, Sanya, Hainan Province 572025, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan Province 572025, China
| |
Collapse
|
3
|
Leiva AM, Pardo JM, Arinaitwe W, Newby J, Vongphachanh P, Chittarath K, Oeurn S, Thi Hang L, Gil-Ordóñez A, Rodriguez R, Cuellar WJ. Ceratobasidium sp. is associated with cassava witches' broom disease, a re-emerging threat to cassava cultivation in Southeast Asia. Sci Rep 2023; 13:22500. [PMID: 38110543 PMCID: PMC10728180 DOI: 10.1038/s41598-023-49735-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 12/11/2023] [Indexed: 12/20/2023] Open
Abstract
Cassava witches' broom disease (CWBD) is a devastating disease of cassava in Southeast Asia (SEA), of unknown etiology. Affected plants show reduced internodal length, proliferation of leaves and weakening of stems. This results in poor germination of infected stem cuttings (i.e., planting material) and significant reductions in fresh root yields and starch content, causing economic losses for farmers and processors. Using a metagenomic approach, we identified a fungus belonging to the Ceratobasidium genus, sharing more than 98.3-99.7% nucleotide identity at the Internal Transcribed Spacer (ITS), with Ceratobasidium theobromae a pathogen causing similar symptoms in cacao. Microscopy analysis confirmed the identity of the fungus and specific designed PCR tests readily showed (1) Ceratobasidium sp. of cassava is strongly associated with CWBD symptoms, (2) the fungus is present in diseased samples collected since the first recorded CWBD outbreaks in SEA and (3) the fungus is transmissible by grafting. No phytoplasma sequences were detected in diseased plants. Current disease management efforts include adjustment of quarantine protocols and guarantee the production and distribution of Ceratobasidium-free planting material. Implications of related Ceratobasidium fungi, infecting cassava, and cacao in SEA and in other potential risk areas are discussed.
Collapse
Affiliation(s)
- Ana M Leiva
- Virology and Crop Protection Laboratory, Cassava Program, International Center for Tropical Agriculture (CIAT), Crops for Nutrition and Health Research Area, The Americas Hub, Km 17 Recta Cali, 763537, Palmira, Colombia
| | - Juan M Pardo
- Virology and Crop Protection Laboratory, Cassava Program, International Center for Tropical Agriculture (CIAT), Crops for Nutrition and Health Research Area, The Americas Hub, Km 17 Recta Cali, 763537, Palmira, Colombia
| | - Warren Arinaitwe
- Crops for Nutrition and Health, International Center for Tropical Agriculture (CIAT), Cassava Program Asia Office, P.O. Box 783, Vientiane, Lao PDR
| | - Jonathan Newby
- Crops for Nutrition and Health, International Center for Tropical Agriculture (CIAT), Cassava Program Asia Office, P.O. Box 783, Vientiane, Lao PDR
| | - Pinkham Vongphachanh
- Plant Protection Center (PPC), Department of Agriculture, Ministry of Agriculture and Forestry, P.O. Box 811, Vientiane, Lao PDR
| | - Khonesavanh Chittarath
- Plant Protection Center (PPC), Department of Agriculture, Ministry of Agriculture and Forestry, P.O. Box 811, Vientiane, Lao PDR
| | - Samoul Oeurn
- Plant Protection Sanitary and Phytosanitary Department, General Directorate of Agriculture (GDA), Phnom Penh, 120406, Cambodia
| | - Le Thi Hang
- Plant Protection Research Institute (PPRI), Duc Thang Bac Tu Liem, Hanoi, 100000, Vietnam
| | - Alejandra Gil-Ordóñez
- Virology and Crop Protection Laboratory, Cassava Program, International Center for Tropical Agriculture (CIAT), Crops for Nutrition and Health Research Area, The Americas Hub, Km 17 Recta Cali, 763537, Palmira, Colombia
| | - Rafael Rodriguez
- Virology and Crop Protection Laboratory, Cassava Program, International Center for Tropical Agriculture (CIAT), Crops for Nutrition and Health Research Area, The Americas Hub, Km 17 Recta Cali, 763537, Palmira, Colombia
| | - Wilmer J Cuellar
- Virology and Crop Protection Laboratory, Cassava Program, International Center for Tropical Agriculture (CIAT), Crops for Nutrition and Health Research Area, The Americas Hub, Km 17 Recta Cali, 763537, Palmira, Colombia.
| |
Collapse
|
4
|
Carvajal-Yepes M, Jimenez J, Belalcazar J, Cuasquer JB, Lozano I, Olaya CA, Cuellar WJ. Genome Analysis and Pathobiology of Cassava-Infecting Torradoviruses Containing a Putative Maf/HAM1 Pyrophosphatase Domain. PLANT DISEASE 2022; 106:2808-2816. [PMID: 35471077 DOI: 10.1094/pdis-11-21-2520-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: 06/14/2023]
Abstract
Next generation sequencing has been used to identify and characterize the full genome sequence of a cassava-infecting torradovirus, revealing the presence of a Maf/HAM1 domain downstream of the RNA-dependent RNA-polymerase (RdRp) domain in RNA1 in all isolates sequenced. A similar domain is also found in unrelated potyvirids infecting Euphorbiaceae hosts in the Americas and cassava in Africa. Even though cassava torrado-like virus (CsTLV) could not be mechanically transmitted to a series of herbaceous hosts, it can be efficiently transmitted by bud graft-inoculation to different cassava landraces. Our bioassays show that CsTLV has a narrow host range. Crystal-like structures of isometric virus-like particles were observed in cells of plants with single infection by CsTLV, and consistently induced chlorotic leaf spots and affected root yields significantly. Moreover, CsTLV infection induces changes in the accumulation of total sugars in storage roots. Field surveys indicated the presence of CsTLV in the main cassava growing regions of Colombia, and the occurrence of two different cassava-infecting torradovirus species. Profiles of small RNAs of 21 to 24 nucleotides in length, derived from CsTLV RNAs targeted by cassava RNA silencing defense mechanisms, are also reported.
Collapse
Affiliation(s)
| | - Jenyfer Jimenez
- International Center for Tropical Agriculture (CIAT), AA 6713, Cali, Colombia
- Facultad de Ciencias Agropecuarias, Universidad Nacional de Colombia (UNAL), Palmira, Colombia
| | - John Belalcazar
- International Center for Tropical Agriculture (CIAT), AA 6713, Cali, Colombia
| | - Juan B Cuasquer
- International Center for Tropical Agriculture (CIAT), AA 6713, Cali, Colombia
| | - Ivan Lozano
- International Center for Tropical Agriculture (CIAT), AA 6713, Cali, Colombia
| | - Cristian A Olaya
- International Center for Tropical Agriculture (CIAT), AA 6713, Cali, Colombia
| | - Wilmer J Cuellar
- International Center for Tropical Agriculture (CIAT), AA 6713, Cali, Colombia
| |
Collapse
|
5
|
Cassava Frogskin Disease: Current Knowledge on a Re-Emerging Disease in the Americas. PLANTS 2022; 11:plants11141841. [PMID: 35890475 PMCID: PMC9318364 DOI: 10.3390/plants11141841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 06/29/2022] [Accepted: 06/30/2022] [Indexed: 11/17/2022]
Abstract
Cassava frogskin disease (CFSD) is a graft-transmissible disease of cassava reported for the first time in the 1970s, in Colombia. The disease is characterized by the formation of longitudinal lip-like fissures on the peel of the cassava storage roots and a progressive reduction in fresh weight and starch content. Since its first report, different pathogens have been identified in CFSD-affected plants and improved sequencing technologies have unraveled complex mixed infections building up in plants with severe root symptoms. The re-emergence of the disease in Colombia during 2019–2020 is again threatening the food security of low-income farmers and the growing local cassava starch industry. Here, we review some results obtained over several years of CFSD pathology research at CIAT, and provide insights on the biology of the disease coming from works on symptoms’ characterization, associated pathogens, means of transmission, carbohydrate accumulation, and management. We expect this work will contribute to a better understanding of the disease, which will reflect on lowering its impact in the Americas and minimize the risk of its spread elsewhere.
Collapse
|
6
|
Doski S, Bolus S, Grinstead S, Juszczak S, Groth-Helms D, Mollov D. Complete sequence and genome characterization of a new potexvirus isolated from Chaenostoma cordatum. Arch Virol 2022; 167:2089-2092. [PMID: 35796833 DOI: 10.1007/s00705-022-05520-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 05/20/2022] [Indexed: 11/29/2022]
Abstract
Leaves from the ornamental plant Chaenostoma cordatum (Thunb.) Benth. expressing virus-like symptoms were collected for pathogen testing. A virus with features consistent with those of members of the genus Potexvirus was identified by high-throughput sequencing. The genome sequence was confirmed and completed using RT-PCR, cloning, rapid amplification of cDNA ends kits, and Sanger sequencing, revealing a complete viral genome of 6,071 nucleotides, excluding the poly-A tail. Phylogenetic analysis of the RNA-dependent RNA polymerase sequence from the viral genome indicated that its closest relative is Plantago asiatica mosaic virus. Further analysis of the nucleotide and amino acid sequences revealed that it had diverged enough from other potexviruses to be considered a member of a new species.
Collapse
Affiliation(s)
- Shadin Doski
- USDA-ARS National Germplasm Resources Laboratory, Beltsville, MD, 20705, USA
| | - Stephen Bolus
- USDA-ARS National Germplasm Resources Laboratory, Beltsville, MD, 20705, USA
| | - Samuel Grinstead
- USDA-ARS National Germplasm Resources Laboratory, Beltsville, MD, 20705, USA
| | | | | | - Dimitre Mollov
- USDA-ARS Horticultural Crops Research Unit, Corvallis, OR, 97330, USA.
| |
Collapse
|
7
|
Jimenez J, Leiva AM, Olaya C, Acosta-Trujillo D, Cuellar WJ. An optimized nucleic acid isolation protocol for virus diagnostics in cassava ( Manihot esculenta Crantz.). MethodsX 2021; 8:101496. [PMID: 34754767 PMCID: PMC8563463 DOI: 10.1016/j.mex.2021.101496] [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: 05/27/2021] [Accepted: 08/20/2021] [Indexed: 11/15/2022] Open
Abstract
Our group works on the detection and characterization of cassava viruses, supporting projects that involve large scale pathogen surveillance activities and resistance screening assays in multiple and remote locations. In order to comply with these applications, nucleic acid isolation protocols need to be cost effective, adjusted for samples that will stand long distance transport and harsh storage conditions, while maximizing the yield and quality of the nucleic acid extracts obtained. The method we describe here has been widely used and validated using different downstream tests (including, but not limited to, Rolling Circle Amplification and Illumina and Nanopore sequencing), but is currently unpublished. The protocol begins with milligram amounts of dry leaf samples stored in silica gel, does not require liquid Nitrogen nor phenol extraction and produces an average of 2.11 µg of nucleic acids per mg of dry tissue.•DNA purity estimations reveal OD260/280 ratios above 2.0 and OD260/230 ratios above 1.7, even for samples stored in silica gel for several months.•The high quality of the extracts is suitable for detection of DNA and RNA viruses, with high efficiency.•We suggest this method could be used as part of a gold standard kit for virus detection in cassava.
Collapse
Affiliation(s)
- Jenyfer Jimenez
- Virology Laboratory, Crops for Nutrition and Health, International Center for Tropical Agriculture (CIAT), AA 6713, Cali, Colombia
| | - Ana Maria Leiva
- Virology Laboratory, Crops for Nutrition and Health, International Center for Tropical Agriculture (CIAT), AA 6713, Cali, Colombia
| | | | - Daniela Acosta-Trujillo
- Virology Laboratory, Crops for Nutrition and Health, International Center for Tropical Agriculture (CIAT), AA 6713, Cali, Colombia
| | - Wilmer Jose Cuellar
- Virology Laboratory, Crops for Nutrition and Health, International Center for Tropical Agriculture (CIAT), AA 6713, Cali, Colombia
| |
Collapse
|
8
|
Morozov SY, Solovyev AG. Small hydrophobic viral proteins involved in intercellular movement of diverse plant virus genomes. AIMS Microbiol 2020; 6:305-329. [PMID: 33134746 PMCID: PMC7595835 DOI: 10.3934/microbiol.2020019] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 09/13/2020] [Indexed: 12/12/2022] Open
Abstract
Most plant viruses code for movement proteins (MPs) targeting plasmodesmata to enable cell-to-cell and systemic spread in infected plants. Small membrane-embedded MPs have been first identified in two viral transport gene modules, triple gene block (TGB) coding for an RNA-binding helicase TGB1 and two small hydrophobic proteins TGB2 and TGB3 and double gene block (DGB) encoding two small polypeptides representing an RNA-binding protein and a membrane protein. These findings indicated that movement gene modules composed of two or more cistrons may encode the nucleic acid-binding protein and at least one membrane-bound movement protein. The same rule was revealed for small DNA-containing plant viruses, namely, viruses belonging to genus Mastrevirus (family Geminiviridae) and the family Nanoviridae. In multi-component transport modules the nucleic acid-binding MP can be viral capsid protein(s), as in RNA-containing viruses of the families Closteroviridae and Potyviridae. However, membrane proteins are always found among MPs of these multicomponent viral transport systems. Moreover, it was found that small membrane MPs encoded by many viruses can be involved in coupling viral replication and cell-to-cell movement. Currently, the studies of evolutionary origin and functioning of small membrane MPs is regarded as an important pre-requisite for understanding of the evolution of the existing plant virus transport systems. This paper represents the first comprehensive review which describes the whole diversity of small membrane MPs and presents the current views on their role in plant virus movement.
Collapse
Affiliation(s)
- Sergey Y Morozov
- A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia.,Department of Virology, Biological Faculty, Moscow State University, Moscow, Russia
| | - Andrey G Solovyev
- A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia.,Department of Virology, Biological Faculty, Moscow State University, Moscow, Russia.,Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Moscow, Russia
| |
Collapse
|
9
|
Xing Y, Hernandez Nopsa JF, Andersen KF, Andrade-Piedra JL, Beed FD, Blomme G, Carvajal-Yepes M, Coyne DL, Cuellar WJ, Forbes GA, Kreuze JF, Kroschel J, Kumar PL, Legg JP, Parker M, Schulte-Geldermann E, Sharma K, Garrett KA. Global Cropland Connectivity: A Risk Factor for Invasion and Saturation by Emerging Pathogens and Pests. Bioscience 2020; 70:744-758. [PMID: 32973407 PMCID: PMC7498352 DOI: 10.1093/biosci/biaa067] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The geographic pattern of cropland is an important risk factor for invasion and saturation by crop-specific pathogens and arthropods. Understanding cropland networks supports smart pest sampling and mitigation strategies. We evaluate global networks of cropland connectivity for key vegetatively propagated crops (banana and plantain, cassava, potato, sweet potato, and yam) important for food security in the tropics. For each crop, potential movement between geographic location pairs was evaluated using a gravity model, with associated uncertainty quantification. The highly linked hub and bridge locations in cropland connectivity risk maps are likely priorities for surveillance and management, and for tracing intraregion movement of pathogens and pests. Important locations are identified beyond those locations that simply have high crop density. Cropland connectivity risk maps provide a new risk component for integration with other factors-such as climatic suitability, genetic resistance, and global trade routes-to inform pest risk assessment and mitigation.
Collapse
Affiliation(s)
- Yanru Xing
- Plant Pathology Department, Institute for Sustainable Food Systems, and Emerging Pathogens Institute at University of Florida, Gainesville, USA
- Yanru Xing and John F. Hernandez Nopsa contributed equally to this work
| | - John F Hernandez Nopsa
- Corporación Colombiana de Investigación Agropecuaria, AGROSAVIA, Mosquera-Bogota, Colombia
- Yanru Xing and John F. Hernandez Nopsa contributed equally to this work
| | - Kelsey F Andersen
- Plant Pathology Department, Institute for Sustainable Food Systems, and Emerging Pathogens Institute at University of Florida, Gainesville, USA
- CGIAR Research Program on Roots, Tubers, and Bananas
| | - Jorge L Andrade-Piedra
- International Potato Center (CIP), P.O. Box 1558, Lima 12, Peru
- CGIAR Research Program on Roots, Tubers, and Bananas
| | - Fenton D Beed
- Plant Production and Protection Division, Food and Agriculture Organization, United Nations (FAO), 00153 Roma, Italy
- CGIAR Research Program on Roots, Tubers, and Bananas
| | - Guy Blomme
- Bioversity International, c/o ILRI, Addis Ababa, Ethiopia
- CGIAR Research Program on Roots, Tubers, and Bananas
| | - Mónica Carvajal-Yepes
- International Center for Tropical Agriculture (CIAT), AA6713, Cali, Colombia
- CGIAR Research Program on Roots, Tubers, and Bananas
| | - Danny L Coyne
- International Institute of Tropical Agriculture (IITA), Nairobi, Kenya
- CGIAR Research Program on Roots, Tubers, and Bananas
| | - Wilmer J Cuellar
- International Center for Tropical Agriculture (CIAT), AA6713, Cali, Colombia
- CGIAR Research Program on Roots, Tubers, and Bananas
| | - Gregory A Forbes
- International Potato Center (CIP), P.O. Box 1558, Lima 12, Peru
- CGIAR Research Program on Roots, Tubers, and Bananas
| | - Jan F Kreuze
- International Potato Center (CIP), P.O. Box 1558, Lima 12, Peru
- CGIAR Research Program on Roots, Tubers, and Bananas
| | - Jürgen Kroschel
- International Potato Center (CIP), P.O. Box 1558, Lima 12, Peru
- CGIAR Research Program on Roots, Tubers, and Bananas
| | - P Lava Kumar
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
- CGIAR Research Program on Roots, Tubers, and Bananas
| | - James P Legg
- International Institute of Tropical Agriculture (IITA), Dar es Salaam, Tanzania
- CGIAR Research Program on Roots, Tubers, and Bananas
| | - Monica Parker
- International Potato Center (CIP), Nairobi, Kenya
- CGIAR Research Program on Roots, Tubers, and Bananas
| | - Elmar Schulte-Geldermann
- International Potato Center (CIP), Nairobi, Kenya
- CGIAR Research Program on Roots, Tubers, and Bananas
| | - Kalpana Sharma
- International Potato Center (CIP), Nairobi, Kenya
- CGIAR Research Program on Roots, Tubers, and Bananas
| | - Karen A Garrett
- Plant Pathology Department, Institute for Sustainable Food Systems, and Emerging Pathogens Institute at University of Florida, Gainesville, USA
- CGIAR Research Program on Roots, Tubers, and Bananas
| |
Collapse
|
10
|
Siriwan W, Jimenez J, Hemniam N, Saokham K, Lopez-Alvarez D, Leiva AM, Martinez A, Mwanzia L, Becerra Lopez-Lavalle LA, Cuellar WJ. Surveillance and diagnostics of the emergent Sri Lankan cassava mosaic virus (Fam. Geminiviridae) in Southeast Asia. Virus Res 2020; 285:197959. [PMID: 32407870 DOI: 10.1016/j.virusres.2020.197959] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 03/31/2020] [Accepted: 03/31/2020] [Indexed: 12/17/2022]
Abstract
Emergent agricultural pathogens cause severe damage worldwide and their invasive potential is significantly increased by global trade, crop intensification and climate change. Standard surveillance and diagnostic protocols need to be evaluated and implemented, particularly with diseases caused by a wide range of pathogens that induce similar symptoms. Such is the case with Cassava Mosaic Disease (CMD) present in Africa and Asia, and associated with mixed virus infections and recombinant and re-assorted virus strains. CMD has been recently reported in Southeast Asia (SEA) and is already widely spread throughout this region. This communication offers an update on protocols and tools used to track the distribution of CMD and to characterize the pathogen associated with it in SEA.
Collapse
Affiliation(s)
| | - Jenyfer Jimenez
- Virology Laboratory, International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | | | - Kingkan Saokham
- Center for Agricultural Biotechnology, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom, 73140, Thailand; Center of Excellence on Agricultural Biotechnology: (AG-BIO/PERDO-CHE), Bangkok, 10900, Thailand
| | - Diana Lopez-Alvarez
- Virology Laboratory, International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Ana M Leiva
- Virology Laboratory, International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Andres Martinez
- Data Management Group, International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Leroy Mwanzia
- Data Management Group, International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | | | - Wilmer J Cuellar
- Virology Laboratory, International Center for Tropical Agriculture (CIAT), Cali, Colombia.
| |
Collapse
|
11
|
Nanopore-Based Complete Genome Sequence of a Sri Lankan Cassava Mosaic Virus ( Geminivirus) Strain from Thailand. Microbiol Resour Announc 2020; 9:9/6/e01274-19. [PMID: 32029567 PMCID: PMC7005115 DOI: 10.1128/mra.01274-19] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Sri Lankan cassava mosaic virus is an emerging pathogen in Southeast Asia. Here, we report the complete genome of a Thai isolate obtained using Nanopore technology. The isolate was collected in 2019 from the northeastern province of Surin, soon after disease eradication was reported in the country. Sri Lankan cassava mosaic virus is an emerging pathogen in Southeast Asia. Here, we report the complete genome of a Thai isolate obtained using Nanopore technology. The isolate was collected in 2019 from the northeastern province of Surin, soon after disease eradication was reported in the country.
Collapse
|
12
|
Solovyev AG, Morozov SY. Non-replicative Integral Membrane Proteins Encoded by Plant Alpha-Like Viruses: Emergence of Diverse Orphan ORFs and Movement Protein Genes. FRONTIERS IN PLANT SCIENCE 2017; 8:1820. [PMID: 29163564 PMCID: PMC5663686 DOI: 10.3389/fpls.2017.01820] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2017] [Accepted: 10/06/2017] [Indexed: 06/07/2023]
Abstract
Fast accumulation of sequencing data on plant virus genomes and plant transcriptomes demands periodic re-evaluation of current views on the genome evolution of viruses. Here, we substantiate and further detail our previously mostly speculative model on the origin and evolution of triple gene block (TGB) encoding plant virus movement proteins TGB1, TGB2, and TGB3. Recent experimental data on functional competence of transport gene modules consisting of two proteins related to TGB1 and TGB2, as well as sequence analysis data on similarity of TGB2 and TGB3 encoded by a viral genome and virus-like RNAs identified in a plant transcriptomes, suggest that TGB evolution involved events of gene duplication and gene transfer between viruses. In addition, our analysis identified that plant RNA-seq data assembled into RNA virus-like contigs encode a significant variety of hydrophobic proteins. Functions of these orphan proteins are still obscure; however, some of them are obviously related to hydrophobic virion proteins of recently sequenced invertebrate (mostly insect) viruses, therefore supporting the current view on a common origin for many groups of plant and insect RNA-containing viruses. Moreover, these findings may suggest that the function of at least some orphan hydrophobic proteins is to provide plant viruses with the ability to infect insect hosts. In general, our observations emphasize that comparison of RNA virus sequences in a large variety of land plants and algae isolated geographically and ecologically may lead to experimental confirmation of previously purely speculative schemes of evolution of single genes, gene modules, and whole genomes.
Collapse
Affiliation(s)
- Andrey G. Solovyev
- A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Moscow, Russia
| | - Sergey Y. Morozov
- A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia
- Department of Virology, Biological Faculty, Moscow State University, Moscow, Russia
| |
Collapse
|