Abstract
A new dsRNA virus from the oomycete Phytophthora pluvialis has been characterized and designated as Phytophthora pluvialis RNA virus 1 (PplRV1). The genome of the PplRV1 reference genome is 6742 bp that encodes two predicted open reading frames (ORFs). ORF1 and ORF2 overlap by a 47 nt “slippery” frameshift sequence. ORF1 encodes a putative protein of unknown function. ORF2 shows high similarity to the RNA-dependent RNA polymerase (RdRp) of other dsRNA viruses. Phylogenetic analysis of the putative PplRV1 RdRp and its most closely related viruses showed PplRV1 is distinct from other known viruses (below 33% amino acid similarity), which indicates this virus may belong to a new virus family. Analyses of the geographical distribution of PplRV1 in relation to two genetically distinct classes of its host revealed two corresponding genotypes of the PplRV1 (termed a and b), which share 92.3% nt identity. The reference genome for the second genotype is 6760 bp long and a prediction of its genetic organization shows three ORFs, with ORF2 being split into two ORFs, ORF2a and ORF2b, that is conserved in seven of eleven genotype b isolates. Additionally, a quick and simple diagnostic method using qPCR has been developed, which is suitable for large scale screens to identify PplRV1 in Phytophthora.
Highlights
Phytophthora is a genus in the family Oomycota, which was previously classified within the fungi domain and separated owing to their highly divergent genome sequence [1]
The three contigs were assembled from dsRNA-derived complementary DNA (cDNA) sequences and translated in silico: contig 1 (3395 nt) and contig 2 (2865 nt) shared approximately 30% amino acid identity with
A BLASTx analysis of the predicted ORF1 amino acid sequence showed similarity to hypothetical proteins found in other RNA viruses, including Phytophthora infestans RNA virus 3 (PiRV-3)
Summary
Phytophthora is a genus in the family Oomycota, which was previously classified within the fungi domain and separated owing to their highly divergent genome sequence [1]. Phytophthora species are plant pathogens and cause enormous economic losses in crops worldwide. The most notorious plant pathogen, Phytophthora infestans, causes potato late blight which in the 1840s triggered a series of events that led to several million people dying from starvation [2]. Another example is Phytophthora agathidicida, the causal agent of the devastating disease kauri dieback which threatens kauri tree (Agathis australis) populations of high ecological and cultural relevance in New Zealand [3,4,5]. Phytophthora pluvialis is a pathogen causing red needle cast disease. A year later, P. pluvialis was first recognized in the North
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