High Diversity of Novel Viruses in the Tree Pathogen Phytophthora castaneae Revealed by High-Throughput Sequencing of Total and Small RNA

Abstract

Phytophthora castaneae, an oomycete pathogen causing root and trunk rot of different tree species in Asia, was shown to harbor a rich diversity of novel viruses from different families. Four P. castaneae isolates collected from Chamaecyparis hodginsii in a semi-natural montane forest site in Vietnam were investigated for viral presence by traditional and next-generation sequencing (NGS) techniques, i.e., double-stranded RNA (dsRNA) extraction and high-throughput sequencing (HTS) of small RNAs (sRNAs) and total RNA. Genome organization, sequence similarity, and phylogenetic analyses indicated that the viruses were related to members of the order Bunyavirales and families Endornaviridae, Megabirnaviridae, Narnaviridae, Totiviridae, and the proposed family “Fusagraviridae.” The study describes six novel viruses: Phytophthora castaneae RNA virus 1–5 (PcaRV1-5) and Phytophthora castaneae negative-stranded RNA virus 1 (PcaNSRV1). All six viruses were detected by sRNA sequencing, which demonstrates an active RNA interference (RNAi) system targeting viruses in P. castaneae. To our knowledge, this is the first report of viruses in P. castaneae and the whole Phytophthora major Clade 5, as well as of the activity of an RNAi mechanism targeting viral genomes among Clade 5 species. PcaRV1 is the first megabirnavirus described in oomycetes and the genus Phytophthora.

Bunyaviruses Affect Growth, Sporulation, and Elicitin Production in Phytophthora cactorum

“…A novel virus with a resemblance to members of Ghabrivirales was also recently reported from Phytophthora pluvialis [19]. In addition, multiple novel viruses were recorded recently in Phytophthora castaneae, including viruses with phylogenetic affinities to families Endornaviridae, Narnaviridae, Totiviridae, Megabirnaviridae, and "Fusagraviridae" in addition to members of Bunyavirales [20]. A giant virus has also been found integrated in the Phytophthora parasitica genome [21].…”

“…The presence and absence of the bunyaviruses in PhF66 and PhF66-, respectively, was also re-checked before morphological, sporulation, and proteomic analyses. Here, RNAzol (Sigma-Aldrich) was used for RNA extraction and a High-capacity cDNA kit (Thermo Fisher) for reverse transcription, as in Raco et al [20].…”

“…Bunya-like viruses were also reported from Plasmopara viticola lesions in grapevine [48]. Furthermore, 13 bunya-like viruses have been detected in P. condilina [13], three in P. cactorum [10], and one in P. castaneae [20]. No direct effects of bunyavirus infection on the growth or virulence of their fungal or oomycete hosts have been recorded.…”

New Insights on the Integrated Management of Plant Diseases by RNA Strategies: Mycoviruses and RNA Interference

“…Furthermore, this system is only useful for the control of plant diseases caused by fungi. Nevertheless, with the advent of new sequencing techniques, numerous novel mycoviruses are being identified in a multitude of fungi, offering new possibilities in this field [ 5 ].…”

“…In recent years, the emergence of high-throughput sequencing technologies has made possible the identification of an unexpected number of new mycoviruses among fungi ( Table 1 ), a trend expected to continue in the future [ 5 , 36 , 37 , 38 ]. This stream of new findings is improving our understanding of the evolution and diversity of viruses.…”