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Jailani AAK, Chattopadhyay A, Kumar P, Singh OW, Mukherjee SK, Roy A, Sanan-Mishra N, Mandal B. Accelerated Long-Fragment Circular PCR for Genetic Manipulation of Plant Viruses in Unveiling Functional Genomics. Viruses 2023; 15:2332. [PMID: 38140572 PMCID: PMC10747169 DOI: 10.3390/v15122332] [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: 09/29/2023] [Revised: 11/14/2023] [Accepted: 11/24/2023] [Indexed: 12/24/2023] Open
Abstract
Molecular cloning, a crucial prerequisite for engineering plasmid constructs intended for functional genomic studies, relies on successful restriction and ligation processes. However, the lack of unique restriction sites often hinders construct preparation, necessitating multiple modifications. Moreover, achieving the successful ligation of large plasmid constructs is frequently challenging. To address these limitations, we present a novel PCR strategy in this study, termed 'long-fragment circular-efficient PCR' (LC-PCR). This technique involves one or two rounds of PCR with an additional third-long primer that complements both ends of the newly synthesized strand of a plasmid construct. This results in self-circularization with a nick-gap in each newly formed strand. The LC-PCR technique was successfully employed to insert a partial sequence (210 nucleotides) of the phytoene desaturase gene from Nicotiana benthamiana and a full capsid protein gene (770 nucleotides) of a begomovirus (tomato leaf curl New Delhi virus) into a 16.4 kb infectious construct of a tobamovirus, cucumber green mottle mosaic virus (CGMMV), cloned in pCambia. This was done to develop the virus-induced gene silencing vector (VIGS) and an expression vector for a foreign protein in plants, respectively. Furthermore, the LC-PCR could be applied for the deletion of a large region (replicase enzyme) and the substitution of a single amino acid in the CGMMV genome. Various in planta assays of these constructs validate their biological functionality, highlighting the utility of the LC-PCR technique in deciphering plant-virus functional genomics. The LC-PCR is not only suitable for modifying plant viral genomes but also applicable to a wide range of plant, animal, and human gene engineering under in-vitro conditions. Additionally, the LC-PCR technique provides an alternative to expensive kits, enabling quick introduction of modifications in any part of the nucleotide within a couple of days. Thus, the LC-PCR proves to be a suitable 'all in one' technique for modifying large plasmid constructs through site-directed gene insertion, deletion, and mutation, eliminating the need for restriction and ligation.
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Affiliation(s)
- A. Abdul Kader Jailani
- Advanced Centre for Plant Virology, Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi 110012, India; (A.C.); (P.K.); (O.W.S.); (S.K.M.); (A.R.)
- International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India;
- Plant Pathology Department, University of Florida, North Florida Research and Education Centre, Quincy, FL 32351, USA
| | - Anirudha Chattopadhyay
- Advanced Centre for Plant Virology, Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi 110012, India; (A.C.); (P.K.); (O.W.S.); (S.K.M.); (A.R.)
- Pulses Research Station, Sardarkrushinagar Dantiwada Agricultural University, Sardarkrushinagar 385506, India
| | - Pradeep Kumar
- Advanced Centre for Plant Virology, Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi 110012, India; (A.C.); (P.K.); (O.W.S.); (S.K.M.); (A.R.)
| | - Oinam Washington Singh
- Advanced Centre for Plant Virology, Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi 110012, India; (A.C.); (P.K.); (O.W.S.); (S.K.M.); (A.R.)
| | - Sunil Kumar Mukherjee
- Advanced Centre for Plant Virology, Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi 110012, India; (A.C.); (P.K.); (O.W.S.); (S.K.M.); (A.R.)
| | - Anirban Roy
- Advanced Centre for Plant Virology, Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi 110012, India; (A.C.); (P.K.); (O.W.S.); (S.K.M.); (A.R.)
| | - Neeti Sanan-Mishra
- International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India;
| | - Bikash Mandal
- Advanced Centre for Plant Virology, Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi 110012, India; (A.C.); (P.K.); (O.W.S.); (S.K.M.); (A.R.)
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Devendran R, Kavalappara SR, Simmons AM, Bag S. Whitefly-Transmitted Viruses of Cucurbits in the Southern United States. Viruses 2023; 15:2278. [PMID: 38005954 PMCID: PMC10675411 DOI: 10.3390/v15112278] [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: 10/24/2023] [Revised: 11/16/2023] [Accepted: 11/17/2023] [Indexed: 11/26/2023] Open
Abstract
Cucurbits are economically important crops that are widely cultivated in many parts of the world, including the southern US. In recent years, higher temperatures have favored the rapid build-up of whiteflies in the fall-grown cucurbits in this region. As a result, whitefly-transmitted viruses (WTVs) have severely impacted the marketable yield of cucurbits. In this review, we discuss three major groups of WTVs negatively impacting cucurbit cultivation in the southern US, including begomoviruses, criniviruses, and ipomoviruses. Here, we discuss the available information on the biology, epidemiology and advances made toward detecting and managing these viruses, including sources of resistance and cultural practices.
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Affiliation(s)
| | | | - Alvin M. Simmons
- U.S. Vegetable Laboratory, Agricultural Research Service, United States Department of Agriculture, Charleston, SC 29414, USA
| | - Sudeep Bag
- Department of Plant Pathology, University of Georgia, Tifton, GA 31793, USA
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Che H, Ma Y, Lin Y, Feng T, Luo D, Long H. Virome Profiling, New Virus Identification and the Prevalence and Distribution of Viruses Infecting Chieh-Qua ( Benincasa hispida Cogn. var. chieh-qua How) in China. Viruses 2023; 15:1396. [PMID: 37376695 DOI: 10.3390/v15061396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 06/29/2023] Open
Abstract
The cucurbit vegetable chieh-qua (Benincasa hispida var. chieh-qua How) is an important crop in South China and southeast Asian countries. Viral diseases cause substantial loss of chieh-qua yield. To identify the viruses that affect chieh-qua in China, ribosomal RNA-depleted total RNA sequencing was performed using chieh-qua leaf samples with typical viral symptoms. The virome of chieh-qua comprises four known viruses (melon yellow spot virus (MYSV), cucurbit chlorotic yellows virus (CCYV), papaya ringspot virus (PRSV) and watermelon silver mottle virus (WSMoV) and two novel viruses: cucurbit chlorotic virus (CuCV) in the genus Crinivirus and chieh-qua endornavirus (CqEV) in the genus Alphaendornavirus. The complete genomes of the two novel viruses in chieh-qua and three other isolates of CuCV in pumpkin, watermelon and cucumber were determined and the recombination signals of pumpkin and watermelon isolates of CuCV were detected. A reverse transcriptase PCR indicated that the dominant viruses of chieh-qua in Hainan are MYSV (66.67%) and CCYV (55.56%), followed by CuCV (27.41%), WSMoV (7.41%), cucumber mosaic virus (8.15%), zucchini yellow mosaic virus (6.67%), PRSV (6.67%) and CqEV (35.56%). Our findings support diagnostic and prevalence studies of viruses infecting chieh-qua in China, enabling sustainable control strategies for cucurbit viruses worldwide.
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Affiliation(s)
- Haiyan Che
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Key Laboratory of Pests Comprehensive Governance for Tropical Crops, Ministry of Agriculture and Rural Affairs, Haikou 571101, China
| | - Yuxin Ma
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Key Laboratory of Pests Comprehensive Governance for Tropical Crops, Ministry of Agriculture and Rural Affairs, Haikou 571101, China
| | - Yating Lin
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Key Laboratory of Pests Comprehensive Governance for Tropical Crops, Ministry of Agriculture and Rural Affairs, Haikou 571101, China
| | - Tuizi Feng
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Key Laboratory of Pests Comprehensive Governance for Tropical Crops, Ministry of Agriculture and Rural Affairs, Haikou 571101, China
| | - Daquan Luo
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Key Laboratory of Pests Comprehensive Governance for Tropical Crops, Ministry of Agriculture and Rural Affairs, Haikou 571101, China
| | - Haibo Long
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Hainan Key Laboratory for Monitoring and Control of Tropical Agricultural Pests, Haikou 571101, China
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Alfaro-Fernández A, Espino de Paz AI, Botella-Guillén M, Font-San-Ambrosio I, Sanauja E, Galipienso L, Rubio L. First Report of Cucurbit Chlorotic Yellows Virus Infecting Watermelon and Zucchini in the Canary Islands, Spain. PLANT DISEASE 2022; 106:PDIS10212296PDN. [PMID: 34931898 DOI: 10.1094/pdis-10-21-2296-pdn] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Affiliation(s)
- A Alfaro-Fernández
- Grupo de Virología, Instituto Agroforestal Mediterráneo, Universitat Politècnica de València, 46022 Valencia, Spain
| | - A I Espino de Paz
- Laboratorio de Sanidad Vegetal, Servicio de Sanidad Vegetal de la Consejería de Agricultura, Ganadería, Pesca y Aguas del Gobierno de Canarias, 38270 Tenerife, Canary Islands, Spain
| | - M Botella-Guillén
- Laboratorio de Sanidad Vegetal, Servicio de Sanidad Vegetal de la Consejería de Agricultura, Ganadería, Pesca y Aguas del Gobierno de Canarias, 38270 Tenerife, Canary Islands, Spain
| | - I Font-San-Ambrosio
- Grupo de Virología, Instituto Agroforestal Mediterráneo, Universitat Politècnica de València, 46022 Valencia, Spain
| | - E Sanauja
- Grupo de Virología, Instituto Agroforestal Mediterráneo, Universitat Politècnica de València, 46022 Valencia, Spain
| | - L Galipienso
- Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113 Moncada, Valencia, Spain
| | - L Rubio
- Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113 Moncada, Valencia, Spain
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Wild Radish (Raphanus raphanistrum L.) Is a Potential Reservoir Host of Cucurbit Chlorotic Yellows Virus. Viruses 2022; 14:v14030593. [PMID: 35337000 PMCID: PMC8950442 DOI: 10.3390/v14030593] [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: 02/02/2022] [Revised: 03/08/2022] [Accepted: 03/10/2022] [Indexed: 02/04/2023] Open
Abstract
Cucurbit chlorotic yellows virus (CCYV) belongs to the genus Crinivirus and is part of a complex of whitefly-transmitted viruses that cause yellowing disease in cucurbits. In the southeastern USA, heavy incidences of CCYV have been observed on all cucurbits grown in the fall. CCYV was detected from wild radish (Raphanus raphanistrum L.), a common weed that grows in the southeastern USA by high-throughput sequencing as well as RT-PCR. CCYV sequence from wild radish was 99.90% and 99.95%, identical to RNA 1 and RNA 2 of cucurbit isolates of CCYV from the region. Transmission assays using whiteflies demonstrated that wild radish is a good host for CCYV. Whiteflies were also able to acquire CCYV from wild radish and transmit the virus to cucurbit hosts, which developed typical symptoms associated with CCYV. Using quantitative PCR, the titer of CCYV in wild radish was also estimated to be on par with that of cucurbit hosts of the virus. Whitefly bioassays revealed that wild radish is an acceptable feeding and reproductive host plant. These results indicate that wild radish could serve as a reservoir host for CCYV in the USA and other parts of the world where similar conditions exist.
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