Abstract
The experience with a diagnostic technology based on rolling circle amplification (RCA), restriction fragment length polymorphism (RFLP) analyses, and direct or deep sequencing (Circomics) over the past 15 years is surveyed for the plant infecting geminiviruses, nanoviruses and associated satellite DNAs, which have had increasing impact on agricultural and horticultural losses due to global transportation and recombination-aided diversification. Current state methods for quarantine measures are described to identify individual DNA components with great accuracy and to recognize the crucial role of the molecular viral population structure as an important factor for sustainable plant protection.
Highlights
The symptoms of plant viruses, later known to contain circular single-stranded DNA, were already described in ancient times: 752 ACE, in a poem, and 1868 ACE, in garden literature [1–3].Only in more recent decades have they become devastating pests in agriculture and horticulture due to intensified farming and global transportation of plant material, as well as recombination and pseudo-recombination of viruses [4]
The detection of single-stranded circles by rolling circle amplification (RCA)/restriction fragment length polymorphism (RFLP) in a plant is a first good diagnostic hint for a virus infection in most plants, but some plant species harbor small circular mitochondrial plasmids that may be misinterpreted as viral agents
The samples are stored dry at room temperature in the dark to avoid hydrolytic DNA base deamination and oxidation and they may be analyzed several years later for RCA/RFLP without any loss of resolution [2,26,72,96]
Summary
The symptoms of plant viruses, later known to contain circular single-stranded DNA, were already described in ancient times: 752 ACE, in a poem, and 1868 ACE, in garden literature [1–3]. It is necessary to emphasize that geminiviruses may be prone to generate defective DNAs (“D-DNA”) depending on the virus and the host plant. The detection of single-stranded (ssDNA) circles by RCA/restriction fragment length polymorphism (RFLP) in a plant is a first good diagnostic hint for a virus infection in most plants, but some plant species harbor small circular mitochondrial plasmids that may be misinterpreted as viral agents. Such plasmids might be useful as internal standards. The nomenclature of aSats has become more and more complex, with an ICTV-approved family Alphasatellitidae including two subfamilies (Geminialalphasatellitinae and Nanoalphasatellitinae) [17]
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