1
|
ÇELİK A. Incidence and coat protein characterization of apple stem pitting virus isolates from Isparta province of Turkey. ULUSLARARASI TARIM VE YABAN HAYATI BILIMLERI DERGISI 2022. [DOI: 10.24180/ijaws.1180101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Turkey is one of the major countries in the world in terms of fruit growing due to its climate diversity and geographical features. Apple, which is one of these fruits, is grown intensively in Turkey, and especially the Mediterranean Region is important for apple agriculture. Today, viral diseases are considered as an important yield loss factor in apple farming. This study investigated the incidence and molecular characterization of apple stem pitting virus (ASPV) in Isparta province, a significant apple-producing region in Turkey. By using the DAS-ELISA and RT-PCR methods, ASPV infection was found in 7 out of 70 collected apple leaf samples. The partial nucleotid sequences of ASPV were obtained and registered in GenBank for accession numbers. The generated similarity matrix by using the representative isolates revealed that the new ASPV isolates shared 79–93% of their nucleotide sequences with GenBank reference acessions. The isolates collected in this research were clustered in group 1 of the phylogenetic tree that was created by selecting a specific number of isolates from GenBank and thought to be reliable in the phylogenetic differentiation of ASPV. This is the first study to examine the prevalence of ASPV in the Isparta region and its phylogeny. It is possible that the results of the research will contribute to a better understanding of the situation of ASPV in Turkey.
Collapse
Affiliation(s)
- Ali ÇELİK
- Bolu Abant İzzet Baysal Üniversitesi
| |
Collapse
|
2
|
Kim NY, Lee HJ, Kim HS, Lee SH, Moon JS, Jeong RD. Identification of Plant Viruses Infecting Pear Using RNA Sequencing. THE PLANT PATHOLOGY JOURNAL 2021; 37:258-267. [PMID: 34111915 PMCID: PMC8200581 DOI: 10.5423/ppj.oa.01.2021.0009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 03/30/2021] [Accepted: 04/23/2021] [Indexed: 06/12/2023]
Abstract
Asian pear (Pyrus pyrifolia) is a widely cultivated and commercially important fruit crop, which is occasionally subject to severe economic losses due to latent viral infections. Thus, the aim of the present study was to examine and provide a comprehensive overview of virus populations infecting a major pear cultivar ('Singo') in Korea. From June 2017 to October 2019, leaf samples (n = 110) of pear trees from 35 orchards in five major pear-producing regions were collected and subjected to RNA sequencing. Most virus-associated contigs matched the sequences of known viruses, including apple stem grooving virus (ASGV) and apple stem pitting virus (ASPV). However, some contigs matched the sequences of apple green crinkle-associated virus and cucumber mosaic virus. In addition, three complete or nearly complete genomes were constructed based on transcriptome data and subjected to phylogenetic analyses. Based on the number of virus-associated reads, ASGV and ASPV were identified as the dominant viruses of 'Singo.' The present study describes the virome of a major pear cultivar in Korea, and looks into the diversity of viral communities in this cultivar. This study can provide valuable information on the complexity of genetic variability of viruses infecting pear trees.
Collapse
Affiliation(s)
- Nam-Yeon Kim
- Department of Applied Biology, Institute of Environmentally Friendly Agriculture, Chonnam National University, Gwangju 61185, Korea
| | - Hyo-Jeong Lee
- Department of Applied Biology, Institute of Environmentally Friendly Agriculture, Chonnam National University, Gwangju 61185, Korea
| | - Hong-Sup Kim
- Seed Testing & Research Center, Korea Seed & Variety Service, Gimcheon 39660, Korea
| | - Su-Heon Lee
- School of Applied Biosciences, Kyungpook National University, Daegu 98411, Korea
| | - Jae-Sun Moon
- Plant Genome Research Center, Korea Research Institute of Biosciences & Biotechnology, Daejeon 34141, Korea
| | - Rae-Dong Jeong
- Department of Applied Biology, Institute of Environmentally Friendly Agriculture, Chonnam National University, Gwangju 61185, Korea
| |
Collapse
|
3
|
Jiao J, Kong K, Han J, Song S, Bai T, Song C, Wang M, Yan Z, Zhang H, Zhang R, Feng J, Zheng X. Field detection of multiple RNA viruses/viroids in apple using a CRISPR/Cas12a-based visual assay. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:394-405. [PMID: 32886837 PMCID: PMC7868969 DOI: 10.1111/pbi.13474] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 08/20/2020] [Indexed: 05/18/2023]
Abstract
Co-infection of apple trees with several viruses/viroids is common and decreases fruit yield and quality. Accurate and rapid detection of these viral pathogens helps to reduce losses and prevent virus spread. Current molecular detection assays used for apple viruses require specialized and expensive equipment. Here, we optimized a CRISPR/Cas12a-based nucleic acid detection platform for the diagnosis of the most prevalent RNA viruses/viroid in apple, namely Apple necrotic mosaic virus (ApNMV), Apple stem pitting virus (ASPV), Apple stem grooving virus (ASGV), Apple chlorotic leaf spot virus (ACLSV) and Apple scar skin viroid (ASSVd). We detected each RNA virus/viroid directly from crude leaf extracts after simultaneous multiplex reverse transcription-recombinase polymerase amplification (RT-RPA) with high specificity. Positive results can be distinguished by the naked eye via oligonucleotide-conjugated gold nanoparticles. The CRISPR/Cas12a-RT-RPA platform exhibited comparable sensitivity to RT-qPCR, with limits of detection reaching 250 viral copies per reaction for ASPV and ASGV and 2500 copies for the others. However, this protocol was faster and simpler, requiring an hour or less from leaf harvest. Field tests showed 100% agreement with RT-PCR detection for 52 samples. This novel Cas12a-based method is ideal for rapid and reliable detection of apple viruses in the orchard without the need to send samples to a specialized laboratory.
Collapse
Affiliation(s)
- Jian Jiao
- College of HorticultureHenan Agricultural UniversityZhengzhouChina
| | - Kangkang Kong
- College of HorticultureHenan Agricultural UniversityZhengzhouChina
| | - Jinmeng Han
- College of HorticultureHenan Agricultural UniversityZhengzhouChina
| | - Shangwei Song
- College of HorticultureHenan Agricultural UniversityZhengzhouChina
| | - Tuanhui Bai
- College of HorticultureHenan Agricultural UniversityZhengzhouChina
| | - Chunhui Song
- College of HorticultureHenan Agricultural UniversityZhengzhouChina
| | - Miaomiao Wang
- College of HorticultureHenan Agricultural UniversityZhengzhouChina
| | - Zhenli Yan
- Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouHenanChina
| | - Hengtao Zhang
- Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouHenanChina
| | - Ruiping Zhang
- Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouHenanChina
| | - Jiancan Feng
- College of HorticultureHenan Agricultural UniversityZhengzhouChina
| | - Xianbo Zheng
- College of HorticultureHenan Agricultural UniversityZhengzhouChina
| |
Collapse
|
4
|
Determination of Protein Interactions among Replication Components of Apple Necrotic Mosaic Virus. Viruses 2020; 12:v12040474. [PMID: 32331324 PMCID: PMC7232516 DOI: 10.3390/v12040474] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 04/18/2020] [Accepted: 04/20/2020] [Indexed: 11/30/2022] Open
Abstract
Apple mosaic disease is one of the most widely distributed and destructive diseases in apple cultivation worldwide, especially in China, whose apple yields account for more than 50% of the global total. Apple necrotic mosaic virus (ApNMV) is a newly identified ilarvirus that is closely associated with apple mosaic disease in China; however, basic viral protein interactions that play key roles in virus replication and the viral life cycle have not been determined in ApNMV. Here, we first identify an ApNMV–Lw isolate that belongs to subgroup 3 in the genus Ilarvirus. ApNMV–Lw was used to investigate interactions among viral components. ApNMV 1a and 2apol, encoded by RNA1 and RNA2, respectively, were co-localized in plant cell cytoplasm. ApNMV 1a interacted with itself at both the inter- and intramolecular levels, and its N-terminal portion played a key role in these interactions. 1a also interacted with 2apol, and 1a’s C-terminal, together with 2apol’s N-terminal, was required for this interaction. Moreover, the first 115 amino acids of 2apol were sufficient for permitting the 1a–2apol interaction. This study provides insight into the protein interactions among viral replication components of ApNMV, facilitating future investigations on its pathogenicity, as well as the development of strategies to control the virus and disease.
Collapse
|
5
|
Shi W, Yao R, Sunwu R, Huang K, Liu Z, Li X, Yang Y, Wang J. Incidence and Molecular Identification of Apple Necrotic Mosaic Virus (ApNMV) in Southwest China. PLANTS 2020; 9:plants9040415. [PMID: 32231064 PMCID: PMC7237995 DOI: 10.3390/plants9040415] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 03/25/2020] [Accepted: 03/25/2020] [Indexed: 11/30/2022]
Abstract
Apple mosaic disease has a great influence on apple production. In this study, an investigation into the incidence of apple mosaic disease in southwest China was performed, and the pathogen associated with the disease was detected. The results show that 2869 apple trees with mosaic disease were found in the Sichuan, Yunnan, and Guizhou Provinces, with an average incidence of 9.6%. Although apple mosaic virus (ApMV) is widespread in apples worldwide, the diseased samples were negative when tested for ApMV. However, a novel ilarvirus (apple necrotic mosaic virus, ApNMV) was identified in mosaic apple leaves which tested negative for ApMV. RT-PCR analysis indicated that ApNMV was detected in 322 out of 357 samples with mosaic symptoms. Phylogenetic analysis of coat protein (CP) sequences of ApNMV isolates suggested that, compared with ApMV, ApNMV was closer to prunus necrotic ringspot virus (PNRSV). The CP sequences of the isolates showed the diversity of ApNMV, which may enable the virus to adapt to the changeable environments. In addition, the pathology of mosaic disease was observed by microscope, and the result showed that the arrangement of the tissue and the shape of the cell, including the organelle, were seriously destroyed or drastically changed.
Collapse
|
6
|
Bi X, Li X, Yu H, An M, Li R, Xia Z, Wu Y. Development of a multiplex RT-PCR assay for simultaneous detection of Cucumber green mottle mosaic virus and Acidovorax citrulli in watermelon. PeerJ 2019; 7:e7539. [PMID: 31497401 PMCID: PMC6708580 DOI: 10.7717/peerj.7539] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 07/23/2019] [Indexed: 11/20/2022] Open
Abstract
Watermelon (Citrullus lanatus Thunb.) is considered as a popular and nutritious fruit crop worldwide. Watermelon blood flesh disease caused by Cucumber green mottle mosaic virus (CGMMV) and bacterial fruit blotch caused by Acidovorax citrulli, are two major quarantine diseases of watermelon and result in considerable losses to global watermelon production. In this study, a multiplex reverse-transcription polymerase chain reaction (RT-PCR) method was developed for simultaneous detection of CGMMV and A. citrulli in both watermelon leaves and seeds. Two pairs of specific primers were designed based on the conserved sequences of the genomic RNA of CGMMV and the internal transcribed spacer of A. citrulli, respectively. Transcriptional elongation factor-1α from watermelon was added as an internal reference gene to prevent false negatives. No cross-reactivity was detected with other viral or bacterial pathogens infecting watermelon. Moreover, the multiplex RT-PCR showed high sensitivity and could simultaneously detect CGMMV and A. citrulli as little as 102 copies of plasmid DNA. This method was successfully applied to test field-collected watermelon leaves and stored seeds of cucurbitaceous crops. These results suggested that the developed multiplex RT-PCR technique is a rapid, efficient, and sensitive method for simultaneous detection of CGMMV and A. citrulli, providing technical support for monitoring, predicting, and preventing these two quarantine diseases. To our knowledge, this is the first report on simultaneous detection of a virus and a bacterium by multiplex RT-PCR in watermelon.
Collapse
Affiliation(s)
- Xinyue Bi
- College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Xiaodong Li
- College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning, China
- General Station of Forest and Grassland Pest and Diseases Control, National Forestry and Grassland Administration, Shenyang, Liaoning, China
| | - Haibo Yu
- College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Mengnan An
- College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Rui Li
- College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Zihao Xia
- College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Yuanhua Wu
- College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning, China
| |
Collapse
|
7
|
Kim NY, Oh J, Lee SH, Kim H, Moon JS, Jeong RD. Rapid and Specific Detection of Apple stem grooving virus by Reverse Transcription-recombinase Polymerase Amplification. THE PLANT PATHOLOGY JOURNAL 2018; 34:575-579. [PMID: 30588230 PMCID: PMC6305176 DOI: 10.5423/ppj.nt.06.2018.0108] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 08/26/2018] [Accepted: 08/26/2018] [Indexed: 05/24/2023]
Abstract
Apple stem grooving virus (ASGV) is considered to cause the most economically important viral disease in pears in Korea. The current PCR-based methods used to diagnose ASGV are time-consuming in terms of target detection. In this study, a novel assay for specific ASGV detection that is based on reverse transcription-recombinase polymerase amplification is described. This assay has been shown to be reproducible and able to detect as little as 4.7 ng/μl of purified RNA obtained from an ASGV-infected plant. The major advantage of this assay is that the reaction for the target virus is completed in 1 min, and amplification only requires an incubation temperature of 42°C. This assay is a promising alternative method for pear breeding programs or virus-free certification laboratories.
Collapse
Affiliation(s)
- Nam-Yeon Kim
- Department of Applied Biology, Institute of Environmentally Friendly Agriculture, Chonnam National University, Gwangju 61185,
Korea
| | - Jonghee Oh
- School of Applied Biosciences, Kyungpook National University, Daegu 98411,
Korea
| | - Su-Heon Lee
- School of Applied Biosciences, Kyungpook National University, Daegu 98411,
Korea
| | - Hongsup Kim
- Seed Testing & Research Center, Korea Seed & Variety Service, Gimcheon,
Korea
| | - Jae Sun Moon
- Plant Genome Research Center, Korea Research Institute of Bioscience & Biotechnology, Daejeon,
Korea
| | - Rae-Dong Jeong
- Department of Applied Biology, Institute of Environmentally Friendly Agriculture, Chonnam National University, Gwangju 61185,
Korea
| |
Collapse
|
8
|
Xing F, Robe BL, Zhang Z, Wang H, Li S. Genomic Analysis, Sequence Diversity, and Occurrence of Apple necrotic mosaic virus, a Novel Ilarvirus Associated with Mosaic Disease of Apple Trees in China. PLANT DISEASE 2018; 102:1841-1847. [PMID: 30125152 DOI: 10.1094/pdis-10-17-1580-re] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
China accounts for over 50% of apple production worldwide. Very recently, a novel ilarvirus, Apple necrotic mosaic virus (ApNMV), was isolated from apple trees showing mosaic symptoms in Japan. This study compared different types of mosaic symptoms observed in apple trees in China under field conditions. Complete nucleotide sequences were obtained for six isolates of ApNMV. The genomic components varied in size from 3,378 to 3,380 nt (RNA1), 2,778 to 2,786 nt (RNA2), and 1,909 to 1,955 nt (RNA3), respectively. Although nucleotide sequence similarities with subgroup 3 ilarviruses were low (49.2 to 64.3%), results of phylogenetic analysis indicated that Chinese ApNMV isolates were clustered in subgroup 3 together with Prunus necrotic ring spot virus (PNRSV) and Apple mosaic virus (ApMV). Apple mosaic disease occurred widely in apple producing areas of China with a very high percentage (92.1%, 268 out of 291) of symptomatic trees being infected with ApNMV but not with ApMV. The data suggested that ApNMV might be the main pathogen causing apple mosaic disease in China. The genomes of the six studied Chinese ApNMV isolates demonstrated substantial sequence diversity. Here, we demonstrated a strong association of ApNMV with the mosaic disease of apple trees in China.
Collapse
Affiliation(s)
- Fei Xing
- College of Horticulture, China Agricultural University, Beijing 100193; and Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193
| | - Berhanu Lemma Robe
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193
| | - Zhixiang Zhang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193
| | - Hongqing Wang
- College of Horticulture, China Agricultural University, Beijing 100193
| | - Shifang Li
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193
| |
Collapse
|
9
|
Zhao L, Wang MR, Cui ZH, Chen L, Volk GM, Wang QC. Combining Thermotherapy with Cryotherapy for Efficient Eradication of Apple stem grooving virus from Infected In-vitro-cultured Apple Shoots. PLANT DISEASE 2018; 102:1574-1580. [PMID: 30673422 DOI: 10.1094/pdis-11-17-1753-re] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Apple stem grooving virus (ASGV), a difficult-to-eradicate virus from apple propagative materials, causes serious damage to apple production. The use of virus-free plants has been and is an effective strategy for control of plant viral diseases. This study aimed to eradicate ASGV from virus-infected in-vitro-cultured shoots of four apple cultivars and one rootstock by combining thermotherapy with cryotherapy. In vitro stock shoots infected with ASGV were thermo-treated using an alternating temperature of 36°C (day) and 32°C (night). Shoot tips were excised from the treated stock shoots and subjected to cryotherapy. Results showed that, although thermotherapy did not influence shoot survival rates, it reduced shoot growth and proliferation of in vitro shoots. Shoot regrowth rates decreased while virus eradication frequencies increased in cryo-treated shoot tips as time durations of thermotherapy increased from 0 to 6 weeks. Shoot regrowth and frequency of virus eradication were positively and negatively correlated, respectively, with the size of shoot tips. The protocol established here yielded shoot regrowth rates and virus eradication frequencies of 33 to 76% and 30 to 100%, respectively, in the four apple cultivars and one rootstock. Thermotherapy altered virus distribution patterns, subsequently resulting in production of a larger virus-free area in the thermo-treated shoot tips. Many cells in the top layers of apical dome and some cells in the youngest leaf primordia survived in cryo-treated shoot tips; these cells were most likely free of virus infection. Thus, plants regenerated from the procedure of combining thermotherapy with cryotherapy were free of ASGV, as judged by reverse-transcription polymerase chain reaction. To the best of our knowledge, this is the widest-spectrum technique reported thus far for the production of ASGV-free plants and provides a novel biotechnology for the production of virus-free plants in Malus spp.
Collapse
Affiliation(s)
- Lei Zhao
- College of Plant Protection, Northwest A&F University
| | - Min-Rui Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Zhen-Hua Cui
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of College of Horticulture, Northwest A&F University
| | - Long Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of College of Horticulture, Northwest A&F University
| | - Gayle M Volk
- United States Department of Agriculture-Agricultural Research Service National Laboratory for Genetic Resources Preservation, Fort Collins, CO 80521
| | - Qiao-Chun Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of College of Horticulture, Northwest A&F University
| |
Collapse
|
10
|
Jo Y, Choi H, Kim SM, Kim SL, Lee BC, Cho WK. Integrated analyses using RNA-Seq data reveal viral genomes, single nucleotide variations, the phylogenetic relationship, and recombination for Apple stem grooving virus. BMC Genomics 2016; 17:579. [PMID: 27507588 PMCID: PMC4977635 DOI: 10.1186/s12864-016-2994-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 08/03/2016] [Indexed: 02/08/2023] Open
Abstract
Background Next-generation sequencing (NGS) provides many possibilities for plant virology research. In this study, we performed integrated analyses using plant transcriptome data for plant virus identification using Apple stem grooving virus (ASGV) as an exemplar virus. We used 15 publicly available transcriptome libraries from three different studies, two mRNA-Seq studies and a small RNA-Seq study. Results We de novo assembled nearly complete genomes of ASGV isolates Fuji and Cuiguan from apple and pear transcriptomes, respectively, and identified single nucleotide variations (SNVs) of ASGV within the transcriptomes. We demonstrated the application of NGS raw data to confirm viral infections in the plant transcriptomes. In addition, we compared the usability of two de novo assemblers, Trinity and Velvet, for virus identification and genome assembly. A phylogenetic tree revealed that ASGV and Citrus tatter leaf virus (CTLV) are the same virus, which was divided into two clades. Recombination analyses identified six recombination events from 21 viral genomes. Conclusions Taken together, our in silico analyses using NGS data provide a successful application of plant transcriptomes to reveal extensive information associated with viral genome assembly, SNVs, phylogenetic relationships, and genetic recombination. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2994-6) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Yeonhwa Jo
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Hoseong Choi
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Sang-Min Kim
- Crop Foundation Division, National Institute of Crop Science, RDA, Wanju, 55365, South Korea
| | - Sun-Lim Kim
- Crop Foundation Division, National Institute of Crop Science, RDA, Wanju, 55365, South Korea
| | - Bong Choon Lee
- Crop Foundation Division, National Institute of Crop Science, RDA, Wanju, 55365, South Korea
| | - Won Kyong Cho
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea. .,The Taejin Genome Institute, Gadam-gil 61, Hoeongseong, 25239, Republic of Korea.
| |
Collapse
|
11
|
Liang P, Navarro B, Zhang Z, Wang H, Lu M, Xiao H, Wu Q, Zhou X, Di Serio F, Li S. Identification and characterization of a novel geminivirus with a monopartite genome infecting apple trees. J Gen Virol 2015; 96:2411-2420. [PMID: 25934791 DOI: 10.1099/vir.0.000173] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel circular DNA virus sequence has been identified through next-generation sequencing and in silico assembly of small RNAs of 21-24 nt from an apple tree grown in China. The virus genome was cloned using two independent approaches and sequenced. With a size of 2932 nt, it showed the same genomic structure and conserved origin of replication reported for members of the family Geminiviridae. However, the low nucleotide and amino acid sequence identity with known geminiviruses indicated that it was a novel virus, for which the provisional name apple geminivirus (AGV) is proposed. Rolling circle amplification followed by RFLP analyses indicated that AGV was a virus with a monopartite DNA genome. This result was in line with bioassays showing that the cloned viral genome was infectious in several herbaceous plants (Nicotiana bethamiana, Nicotiana glutinosa and Solanum lycopersicum), thus confirming it was complete and biologically active, although no symptoms were observed in these experimental hosts. AGV genome structure and phylogenetic analyses did not support the inclusion of this novel species in any of the established genera in the family Geminiviridae. A survey of 165 apple trees grown in four Chinese provinces showed a prevalence of 7.2% for AGV, confirming its presence in several cultivars and geographical areas in China, although no obvious relationship between virus infection and specific symptoms was found.
Collapse
Affiliation(s)
- Pengbo Liang
- State Key Laboratory of Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Yuanmingyuan West Road No. 2, Haidian District, Beijing 100193, PR China.,College of Agronomy and Biotechnology, China Agricultural University, Yuanmingyuan West Road No. 2, Haidian District, Beijing 100193, PR China
| | - Beatriz Navarro
- Istituto per la Protezione Sostenibile delle Piante, UOS Bari, Consiglio Nazionale delle Ricerche (IPSP-CNR), Via Amendola, 70126 Bari, Italy
| | - Zhixiang Zhang
- State Key Laboratory of Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Yuanmingyuan West Road No. 2, Haidian District, Beijing 100193, PR China
| | - Hongqing Wang
- College of Agronomy and Biotechnology, China Agricultural University, Yuanmingyuan West Road No. 2, Haidian District, Beijing 100193, PR China
| | - Meiguang Lu
- State Key Laboratory of Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Yuanmingyuan West Road No. 2, Haidian District, Beijing 100193, PR China
| | - Hong Xiao
- State Key Laboratory of Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Yuanmingyuan West Road No. 2, Haidian District, Beijing 100193, PR China
| | - Qingfa Wu
- School of Life Sciences, University of Science and Technology of China, Hefei 230026, Anhui, PR China
| | - Xueping Zhou
- State Key Laboratory of Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Yuanmingyuan West Road No. 2, Haidian District, Beijing 100193, PR China
| | - Francesco Di Serio
- Istituto per la Protezione Sostenibile delle Piante, UOS Bari, Consiglio Nazionale delle Ricerche (IPSP-CNR), Via Amendola, 70126 Bari, Italy
| | - Shifang Li
- State Key Laboratory of Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Yuanmingyuan West Road No. 2, Haidian District, Beijing 100193, PR China
| |
Collapse
|