Next generation sequencing of oomycete communities in nursery irrigation waterAuthor(s): Joyce Eberhart; Fumiaki Funahashi; Zachary S.L. Foster; Jennifer Parke
Source: Proceedings of the sudden oak death sixth science symposium. Gen. Tech. Rep. GTR-PSW-255. Albany, CA: U.S. Department of Agriculture, Forest Service, Pacific Southwest Research Station: 66-69.
Publication Series: General Technical Report (GTR)
Station: Pacific Southwest Research Station
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Horticultural nurseries are under increasing pressure to reduce, remediate, and recycle irrigation water. A major constraint for reusing irrigation water is contamination by waterborne plant pathogenic Phytophthora and Pythium species. Current research is focused on helping plant nurseries monitor oomycete pathogens in their irrigation water to determine the need for water treatment, evaluate effectiveness of treatment options, and enable selection of cost-effective ways to disinfest water.
A sensitive method to identify waterborne oomycetes present at low concentrations was needed. A semiquantitative method that would allow for determining the relative frequency of diverse, co-occurring species was also desired (Parke and others 2014). Next generation sequencing has the potential to accomplish both goals. Vannini and others (2013) developed an ITS6 and ITS7 primer set that was successful at amplifying oomycetes with the Roche 454 platform. Because Illumina has higher throughput capabilities and is becoming the standard for next generation sequencing, we investigated modifications that would allow us to use the same primers with the Illumina MiSeq platform. Each primer was designed with the appropriate Nextera XT adapter and the forward primer included a spacer designed to raise the annealing temperature to the recommended level.
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CitationEberhart, Joyce; Funahashi, Fumiaki; Foster, Zachary S.L.; Parke, Jennifer. 2017. Next generation sequencing of oomycete communities in nursery irrigation water. In: Frankel, Susan J.; Harrell, Katharine M., tech. coords. Proceedings of the sudden oak death sixth science symposium. Gen. Tech. Rep. GTR-PSW-255. Albany, CA: U.S. Department of Agriculture, Forest Service, Pacific Southwest Research Station: 66-69.
- Phytophthora diversity in Lake Mathews, the irrigation water source for a southern California nursery
- Restoration outplantings of nursery-origin Californian flora are heavily infested with Phytophthora
- Development of reagents for immunoassay of Phytophthora ramorum in nursery water samples
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