Discovery and characterisation of viral-like sequences and viruses associated with Phytophthora pluvialis in New Zealand

The Phytophthora genus contains species worldwide that are pathogenic to a range of plants. However, little is known of their ecological niche, pathogenicity determinants or management options. Recently, reports have described viruses from various Phytophthora species. To fill the gap in described Phytophthora virus diversity and function, this study characterised viral-like sequences and viruses associated with Phytophthora pluvialis, a pathogen of Pinus radiata, causing red needle cast (RNC) disease in New Zealand, USA, and UK, and assess their impact on their hosts. Mitochondrial genomes of 21 Phytophthora, Nothophytophthora, and Phytopythium species were assembled and analysed for geminivirus-like sequences. Homology searches of customised databases of replication initiation protein sequences of geminiviruses revealed only short spans (28 – 40 nt) that perhaps co-incidentally share sequence similarity to the mitochondrial genomes of seven Phytophthora species. A novel dsRNA virus from P. pluvialis was characterised and designated as Phytophthora pluvialis RNA virus 1 (PplRV1). Two PplRV1 genotypes, PplRV1a and PplRV1b, are exclusively associated with P. pluvialis New Zealand cluster 1 and cluster 2 isolates, respectively. A qPCR diagnostic method was developed and used for large-scale screening for PplRV1 in diverse Phytophthora species, which revealed PplRV1 was specific to P. pluvialis. PplRV1-cured P. pluvialis isolates were generated using antiviral treatments combined with hyphal tipping. Phenotypic assays showed PplRV1-infected isolates produced more aerial hyphae, sporangia, and hyphal swellings compared to PplRV1-cured isolates. To differentiate PplRV1 and P. pluvialis genotypes, a diagnostic method using high-resolution melting (HRM) analysis was developed and used to track horizontal transmission of PplRV1 between P. pluvialis isolates. The HRM results revealed PplRV1b was potentially transmitted between the isogenic isolates of P. pluvialis NZFS 4018, while PplRV1 was not transmitted between P. pluvialis isolates. The vertical transmission of PplRV1 via zoospores was 100%. A detached pine needle assay showed that the RNC symptoms developed on pine needles inoculated with PplRV1b-infected P. pluvialis were more severe than PplRV1b-cured P. pluvialis. These combined results suggest PplRV1b may induce hypervirulence in P. pluvialis. This understanding of PplRV1 may lead to alternative options to control pathogenic P. pluvialis, as well as provide fundamental knowledge about the diversity and ecological niche that Phytophthora and their viruses inhabit.

Name thesis:degree_name

PhD

Level thesis:degree_level

Doctoral

Discipline thesis:degree_discipline

Biological Sciences

Grantor dc:publisher

ResearchSpace@Auckland

Year dc:date.issued

2023

Author dc:creator

• Xu, Zhi

Advisors dc:contributor.advisor

• MacDiarmid, Robin
• Smith, Grant

Statement dc:rights

• Items in ResearchSpace are protected by copyright, with all rights reserved, unless otherwise indicated.

Licence dc:rights.uri

• https://researchspace.auckland.ac.nz/docs/uoa-docs/rights.htm

Handle dc:identifier.uri

https://hdl.handle.net/2292/69282

OAI identifier oai:identifier

oai:researchspace.auckland.ac.nz:2292/69282