Genome Analysis and Geographical Distribution of a Novel Emaravirus in Karaka
Rabbidge, Lee Owen
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Chlorotic spot symptoms were observed on a specimen of a tree endemic to New Zealand, karaka (Corynocarpus laevigatus), leading to an investigation of the potential viruses associated with the symptoms. RNA-seq analysis identified a new-to-science emaravirus along with two other novel DNA sequences. Full genome sequencing, a survey to identify the distribution of symptomatic karaka trees, and symptom correlation studies were undertaken. Emaravirus is an established genus of viruses with plant hosts. Each species within the genus has a segmented, negative-sense monocistronic RNA genome comprising five to eight segments, and is vectored by eriophyid mites. Five negative sense segments were identified by high throughput sequencing, which were all confirmed by Sanger sequencing. The sequence of each segment was completed following rapid amplification of cDNA ends (RACE). Sequence comparison with other established emaravirus sequences revealed that this represents a unique virus, with only 31.4% amino acid identity within the replicase of its closest relative European mountain ash ringspot-associated virus. A diagnostic test was developed and implemented to assess the virus’ distribution across New Zealand. The novel virus was primarily found throughout Auckland in both naturally occurring and planted karaka trees, with only a few examples identified beyond this region. Using the diagnostic test, the presence of virus was confirmed to be highly correlated with the chlorotic spot symptoms. In addition, the virus was found to be only detectable within symptomatic regions of the leaf and not systematic. Systemic movement may be dependent on the suspected eriophyid mite vector, the endemic karaka gall mite. Evidence is presented for the sequence of a unique emaravirus, that represents the first endemic plant virus reported in New Zealand. The virus is strongly associated with the observed symptoms; therefore, we suggest the name Karaka Okahu purepure virus, which describes the chlorotic spots in te reo Māori.