Multiple Viral Infections Detected in Phytophthora condilina by Total and Small RNA Sequencing

Abstract

Marine oomycetes have recently been shown to be concurrently infected by (−)ssRNA viruses of the order Bunyavirales. In this work, even higher virus variability was found in a single isolate of Phytophthora condilina, a recently described member of Phytophthora phylogenetic Clade 6a, which was isolated from brackish estuarine waters in southern Portugal. Using total and small RNA-seq the full RdRp of 13 different potential novel bunya-like viruses and two complete toti-like viruses were detected. All these viruses were successfully confirmed by reverse transcription polymerase chain reaction (RT-PCR) using total RNA as template, but complementarily one of the toti-like and five of the bunya-like viruses were confirmed when dsRNA was purified for RT-PCR. In our study, total RNA-seq was by far more efficient for de novo assembling of the virus sequencing but small RNA-seq showed higher read numbers for most viruses. Two main populations of small RNAs (21 nts and 25 nts-long) were identified, which were in accordance with other Phytophthora species. To the best of our knowledge, this is the first study using small RNA sequencing to identify viruses in Phytophthora spp.

Novel Fusari- and Toti-like Viruses, with Probable Different Origins, in the Plant Pathogenic Oomycete Globisporangium ultimum

“…Toti-like oomycete viruses have a phylogenetic relationship with the arthropod GLVlike viruses in the family Totiviridae [8,23,24]. Thus, a ML tree (LG + I + G + F), rooted by Totivirus (ScV-L-A), Victorivirus (RnVV1), Trichomonasvirus (TVV1), and Leishmaniavirus (LRV1) as references, was constructed from the 194 sites of deduced amino acid sequences of the conserved RdRp domain in the ORF2 of PuRV2, PpRV1, PsRV1, PcoRV1, PcRV1, PvlaTLV1, and PvlaTLV2, which were isolated from oomycetes, and those of 32 confirmed and putative GLV-and IMNV-like viruses from family Totiviridae [23,48] (Figure 5, Table S6).…”

“…High-throughput sequence analysis using total and small RNAs revealed 13 different bunya-like viruses and two toti-like viruses from a Ph. condilina single isolate in southern Portugal [8]. A variety of other viruses have been found in Phytophthora spp.…”

“…Since this and our previous studies rely on earlier certified specimens identified before the genus name change, we include "Pythium" in the virus names. Interestingly, toti-like viruses have been detected in all three plantparasitic oomycetes [8,12,13,21,23,24]. Toti-like oomycete viruses, Pythium polare RNA virus 1 (PpRV1), Pythium splendens RNA virus 1 (PsRV1), Phytophthora condilina RNA virus 1 (PcoRV1), Phytophthora cactorum virus 1 (PcRV1), and Plasmopara viticola lesionassociated toti-like virus (PvlaTLV) 1-2 are phylogenetically related based on molecular phylogenetic analysis using deduced amino acid sequences of the RdRp [8].…”

“…Consensus symbols were assigned according to the BLOSUM62 scoring matrix: *, identical; nonidentical with score ≥1; nonidentical with score = 0.3.3.3. Phylogenetic Analysis of PuRV2Toti-like oomycete viruses have a phylogenetic relationship with the arthropod GLVlike viruses in the family Totiviridae[8,23,24]. Thus, a ML tree (LG + I + G + F), rooted by Totivirus (ScV-L-A), Victorivirus (RnVV1), Trichomonasvirus (TVV1), and Leishmaniavirus…”

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

“…Fungal viruses (mycoviruses) have been discovered in many major taxa of phytopathogenic fungi ( Ghabrial et al, 2015 ). In oomycetes, an increasing number of viruses with double-stranded (ds) RNA, positive-sense (+) single-stranded (ss) RNA, and negative-sense (−) single-stranded (ss) RNA genomes have been reported over the last few years ( Shiba et al, 2018 , 2019 ; Cai et al, 2019a , b ; Botella et al, 2020 ; Botella and Jung, 2021 ; Fukunishi et al, 2021 ; Poimala et al, 2021 ). However, many species have yet not been screened for the presence of viruses.…”