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Ho T, Broome JC, Buhler JP, O'Donovan W, Tian T, Diaz-Lara A, Martin RR, Tzanetakis IE. Integration of Rubus yellow net virus in the raspberry genome: A story centuries in the making. Virology 2024; 591:109991. [PMID: 38242059 DOI: 10.1016/j.virol.2024.109991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 12/16/2023] [Accepted: 01/08/2024] [Indexed: 01/21/2024]
Abstract
Rubus yellow net virus (RYNV) belongs to genus Badnavirus. Badnaviruses are found in plants as endogenous, inactive or activatable sequences, and/or in episomal (infectious and active) forms. To assess the state of RYNV in Rubus germplasm, we sequenced the genomes of various cultivars and mined eight raspberry whole genome datasets. Bioinformatics analysis revealed the presence of a diverse array of endogenous RYNV (endoRYNV) sequences that differ significantly in their structure; some lineages have nearly complete, yet non-functional genomes whereas others have rudimentary, short sequence fragments. We developed assays to genotype the main lineages as well as the only known episomal lineage present in the United States. This study discloses the widespread presence of endoRYNVs in commercial raspberries, likely because breeding efforts have focused on a limited pool of germplasm that harbored endoRYNVs.
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Affiliation(s)
- Thien Ho
- Driscoll's Inc., Watsonville, CA, 95076, USA.
| | | | | | | | - Tongyan Tian
- California Department of Food and Agriculture, Sacramento, CA 95832, USA
| | - Alfredo Diaz-Lara
- School of Engineering and Sciences, Tecnologico de Monterrey, Campus Queretaro, Queretaro 76130, Mexico
| | - Robert R Martin
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97330, USA; USDA-ARS Horticultural Crops Research Unit, Corvallis, OR 97330, USA
| | - Ioannis E Tzanetakis
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701, USA.
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