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bioRxiv · 10.1101/2023.12.11.571111

Degenerate PCR primers for potexvirus detection in seagrasses

Lim, S. J.·Rosario, K.·Kernbach, M. E.·Gross, A. J.·Furman, B. T.·Breitbart, M.
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Abstract

2.Turtlegrass virus X, which infects the seagrass Thalassia testudinum, is the only potexvirus known to infect marine flowering plants. We investigated potexvirus distribution in seagrasses using a degenerate reverse transcription polymerase chain reaction (RT-PCR) assay originally designed to capture potexvirus diversity in terrestrial plants. The assay, which implements Potex-5 and Potex-2RC primers, successfully amplified a 584 nt RNA-dependent RNA polymerase (RdRp) fragment from TVX-infected seagrasses. Following validation, we screened 74 opportunistically collected, apparently healthy seagrass samples for potexviruses using this RT-PCR assay. The survey examined the host species T. testudinum, Halodule wrightii, Halophila stipulacea, Syringodium filiforme, Ruppia maritima, and Zostera marina. Potexvirus PCR products were successfully generated only from T. testudinum samples and phylogenetic analysis of sequenced PCR products revealed five distinct TVX sequence variants. Although the RT-PCR assay revealed limited potexvirus diversity in seagrasses, the expanded geographic distribution of TVX shown here emphasizes the importance of future studies to investigate T. testudinum populations across its native range and understand how the observed fine-scale genetic diversity a?ects host-virus interactions. 3. Impact statementPotexviruses are widespread in terrestrial plants; however, the recent discovery of TVX in the seagrass Thalassia testudinum extends their host range to marine flowering plants. Here we use existing Potex-5 and Potex-2RC degenerate primers to explore potexvirus infections in several seagrass species. TVX sequence variants were detected in T. testudinum collected from the eastern Gulf of Mexico, uncovering previously unknown genetic diversity of this poorly understood virus. 4. Data summaryAll sequence data are available in NCBI GenBank under the accession numbers OR827692-OR827705, OR854648, OR863396, OR879052-OR879056, and PP430548-PP430571. The authors confirm all supporting data, code and protocols have been provided within the article or through supplementary data files.

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Lim, S. J., Rosario, K., Kernbach, M. E., Gross, A. J., Furman, B. T., Breitbart, M.. 2023-12-11. Degenerate PCR primers for potexvirus detection in seagrasses. https://doi.org/10.1101/2023.12.11.571111

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