D. Hanold

Nucleotide sequence of a circular single-stranded DNA associated with coconut foliar decay virus

A circular single-stranded (ss) covalently closed (ccc) DNA associated with coconut foliar decay virus (CFDV) was purified, amplified by the polymerase chain reaction, and subcloned and its sequence established by analysis of overlapping subgenomic cDNA clones. The complete CFDV sequence comprised 1291 nucleotides and contained open reading frames for six proteins of molecular weight larger than 5 kDa. One of these (ORF1, 33.4 kDa) codes for a leucine-rich protein with the nucleoside triphosphate-binding motif GXGKS and may possibly participate in virus replication. The putative viral protein encoded by ORF3 (6.4 kDa) is a positively charged arginine-rich protein with homology to the capsid protein of nuclear polyhedrosis virus, and may represent the CFDV coat protein. CFDV DNA can form a stable stem structure of 10 GC base pairs subtending a loop sequence which in one orientation closely resembles the motif TAATATTAC conserved in a similar structural arrangement within the geminivirus group. Otherwise no sequence homology to DNA-containing plant viruses of the gemini- or caulimovirus groups was found. CFDV therefore represents a new taxonomic group of plant viruses.

Variants of Coconut cadang-cadang viroid isolated from an African oil palm (Elaies guineensis Jacq.) in Malaysia

Summary.Variants of Coconut cadang-cadang viroid have been identified in a plantation oil palm growing in Malaysia. Three size classes are described, comprising 297, 293, and 270 nt. Compared with the 296-nt form of coconut cadang-cadang viroid (CCCVd), all variants substituted C31 → U in the pathogenicity domain and A175 → C in the right-hand terminus. Other mutations and deletions accounted for the different sizes. These are the first sequences reported for variants of Coconut cadang-cadang viroid in a species other than coconut palm, and this is the first evidence that variants closely related to CCCVd occur outside the Philippines.

Detection and diagnosis of coconut foliar decay disease

Plant viruses axe the second most important group of plant pathogens and may cause losses exceeding US

Chapter 34 – Gel Electrophoresis

60 billion per year (Matthews, 1991). Their effects are most severe in agrarian economies where major staple crops are grown intensively. There are no direct control measures available for most crops, and resistance is available for only a few virus diseases where good crop research facilities are in place. Control is usually attempted through modification of cultural practices, but this requires an extensive knowledge of the disease cycle of the virus, including factors such as where the virus survives, the type of vector which transfers it from plant to plant, and the time and pattern of spread. A fundamental difficulty in working with viruses is that although their accurate identification is essential, the means of achieving this relies on laboratory based procedures. Symptoms are unreliable as either an indicator of the presence of a virus in a plant, or its identity.

Coconut cadang-cadang disease and its viroid agent.

Gel electrophoresis (GE) is a versatile tool for research on viroids and other small circular nucleic acids. GE systems can be adapted to suit specific applications by adjusting variables of matrix and running conditions. Since sequence information is not required, GE is suitable for identifying that a viroid is associated with a disease of unknown etiology and for characterization of new viroids or viroid variants. For routine viroid diagnosis, sensitive, reliable, and robust systems can be designed. If sequence information and specific probes are available, GE can be combined with either gel-blotting to increase specificity and sensitivity of detection, or ribonuclease protection assay to analyze populations of viroid variants and quasispecies.