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Abrahamian P, Tian T, Posis K, Guo YY, Yu D, Blomquist CL, Wei G, Adducci BA, Vidalakis G, Bodaghi S, Osman F, Roy A, Nunziata S, Nakhla MK, Mavrodieva V, Rivera Y. Genetic analysis of the emerging citrus yellow vein clearing virus reveals a divergent virus population in American isolates. Plant Dis 2023. [PMID: 38127632 DOI: 10.1094/pdis-09-23-1963-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
Citrus yellow vein clearing virus (CYVCV) is a previously reported citrus virus from Asia with widespread distribution in China. In 2022 the California Department of Food and Agriculture (CDFA) conducted a multi-pest citrus survey targeting multiple citrus pathogens including CYVCV. In March 2022, a lemon tree with symptoms of vein clearing, chlorosis and mottling in a private garden in the city of Tulare, California tested positive for CYVCV, which triggered an intensive survey in the surrounding areas. A total of 3,019 plant samples, including citrus and non-citrus species, were collected, and tested for CYVCV using conventional RT-PCR, RT-qPCR, and Sanger sequencing. Five hundred eighty-six citrus trees tested positive for CYVCV, including eight citrus species not previously recorded infected under field conditions. Comparative genomic studies were conducted using seventeen complete viral genomes. Sequence analysis revealed two major phylogenetic groups. Known Asian isolates and five California isolates from this study comprised the first group, whereas all other CYVCV isolates from California formed a second group, distinct from all worldwide isolates. Overall, CYVCV population shows rapid expansion and high differentiation indicating a population bottleneck typical of a recent introduction into a new geographic area. .
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Affiliation(s)
- Peter Abrahamian
- USDA ARS National Germplasm Resources Laboratory, Beltsville, Maryland, United States;
| | - Tongyan Tian
- CDFA, Plant Pest Diagnostics Center, 3294 Meadowview Road, Sacramento, California, United States, 95832;
| | - Katie Posis
- California Department of Food and Agriculture, Plant Pest Diagnostics Center, 3294 Meadowview Rd., Sacramento, California, United States, 95832;
| | - Ying Yi Guo
- California Department of Food and Agriculture, Plant Pest Diagnostics, 3294 Meadowview Road, Sacramento, California, United States, 95832;
| | - Doris Yu
- California Department of Food and Agriculture, , Plant Pest Diagnostics Laboratory (CDFA-PPDC), Sacramento, California, United States;
| | - Cheryl L Blomquist
- California Department of Food and Agriculture, , Plant Pest Diagnostics Laboratory (CDFA-PPDC), 3294 Meadowview Road, Sacramento, California, United States, 95832;
| | - Gang Wei
- APHIS Plant Protection and Quarantine, 171300, S&T PPCDL, Laurel, Maryland, United States;
| | - Benjamin A Adducci
- APHIS Plant Protection and Quarantine, 171300, S&T PPCDL, Laurel, Maryland, United States;
| | - Georgios Vidalakis
- University of California, Plant Pathology, Department of Plant Pathology, University of California, Riverside, California, United States, 92521;
| | - Sohrab Bodaghi
- University of California Riverside, 8790, Microbiology and Plant Pathology, Riverside, California, United States;
| | - Fatima Osman
- University of California Davis, Foundation Plant Services, 455 Hopkins road, Davis, California, United States, 95616;
| | - Avijit Roy
- USDA Agricultural Research Service, 17123, Molecular Plant Pathology Laboratory, Building 004, Room 117, BARC-West, 10300 Baltimore Avenue, Washington, District of Columbia, United States, 20250;
| | - Schyler Nunziata
- PPQ, CPHST, National Plant Germplasm and Biotechnology Laboratory, Laurel, Maryland, United States;
| | - Mark K Nakhla
- USDA, Animal Plant Health Inspection Service; Plant Protection and Quarantine, Science and Technology, Plant Pathogen Confirmatory Diagnostics Laboratory, Laurel, Maryland, United States;
| | - Vessela Mavrodieva
- APHIS Plant Protection and Quarantine, 171300, S&T PPCDL, Laurel, Maryland, United States;
| | - Yazmin Rivera
- USDA, Animal Plant Health Inspection Service; Plant Protection and Quarantine, Science and Technology, Plant Pathogen Confirmatory Diagnostics Laboratory, Plant Pathogen Confirmatory Diagnostics Laboratory, 9901 Powder Mill Rd, Laurel, Maryland, United States, 20705;
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Bin Y, Zhang Q, Su Y, Wang C, Jiang Q, Song Z, Zhou C. Transcriptome analysis of Citrus limon infected with Citrus yellow vein clearing virus. BMC Genomics 2023; 24:65. [PMID: 36750773 PMCID: PMC9903606 DOI: 10.1186/s12864-023-09151-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 01/25/2023] [Indexed: 02/09/2023] Open
Abstract
BACKGROUND Citrus yellow vein clearing virus (CYVCV) is the causative agent of citrus yellow vein clearing disease, and poses a serious threat to the lemon industry in Asia. The common symptoms of CYVCV-infected lemon plants are leaf crinkling, leaf chlorotic mottling, and yellow vein clearing. However, the molecular mechanisms underlying CYVCV-citrus interaction that responsible for symptom occurrence is still unclarified. In this study, RNA-seq was performed to analyze the gene expression patterns of 'Eureka' lemon (Citrus limon Burm. f.) plants in response to CYVCV infection. RESULTS There were 3691 differentially expressed genes (DEGs) identified by comparison between mock and CYVCV-infected lemon plants through RNA-seq. Bioinformatics analyses revealed that these DEGs were components of different pathways involved in phenylpropanoid biosynthesis, brassinosteroid biosynthesis, flavonoid biosynthesis and photosynthesis. Among these, the DEGs related to phytohormone metabolism and photosynthesis pathways were further enriched and analyzed. This study showed that different phytohormone-related genes had different responses toward CYVCV infection, however almost all of the photosynthesis-related DEGs were down-regulated in the CYVCV-infected lemon plants. The obtained RNA-seq data were validated by RT-qPCR using 12 randomly chosen genes, and the results of mRNA expression analysis were consistent with those of RNA-seq. CONCLUSIONS The phytohormone biosynthesis, signaling and photosynthesis-related genes of lemon plants were probably involved in systemic infection and symptom occurrence of CYVCV. Notably, CYVCV infection had regulatory effects on the biosynthesis and signaling of phytohormone, which likely improve systemic infection of CYVCV. Additionally, CYVCV infection could cause structural changes in chloroplast and inhibition of photosynthesis pathway, which probably contribute to the appearance of leaf chlorotic mottling and yellow vein clearing in CYVCV-infected lemon plants. This study illustrates the dynamic nature of the citrus-CYVCV interaction at the transcriptome level and provides new insights into the molecular mechanism underlying the pathogenesis of CYVCV in lemon plants.
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Affiliation(s)
- Yu Bin
- grid.263906.80000 0001 0362 4044Citrus Research Institute, Southwest University, Beibei, Chongqing, 400712 China
| | - Qi Zhang
- grid.263906.80000 0001 0362 4044Citrus Research Institute, Southwest University, Beibei, Chongqing, 400712 China
| | - Yue Su
- grid.263906.80000 0001 0362 4044Citrus Research Institute, Southwest University, Beibei, Chongqing, 400712 China
| | - Chunqing Wang
- grid.263906.80000 0001 0362 4044Citrus Research Institute, Southwest University, Beibei, Chongqing, 400712 China
| | - Qiqi Jiang
- grid.263906.80000 0001 0362 4044Citrus Research Institute, Southwest University, Beibei, Chongqing, 400712 China
| | - Zhen Song
- Citrus Research Institute, Southwest University, Beibei, Chongqing, 400712, China.
| | - Changyong Zhou
- Citrus Research Institute, Southwest University, Beibei, Chongqing, 400712, China.
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