A novel mitovirus detected in Diaporthe rudis, a fungus associated with Phomopsis dieback on grapevines

Characterization of two novel mitoviruses co infecting a single strain of Fusarium pseudograminearum causing wheat crown rot

Wheat crown rot (WCR), caused by Fusarium pseudograminearum, poses a threat to wheat production worldwide. Two mycoviruses, designated as "Fusarium pseudograminearum mitovirus 2" (FupgMV2) and "Fusarium pseudograminearum mitovirus 3" (FupgMV3), were identified in F. pseudograminearum strain YY514-10-2. The two viral genomes are 2,429 and 2,450 nucleotides long, each containing a single open reading frame (ORF) encoding a 724-amino-acid-long RNA-dependent RNA polymerase (RdRp), with 31.98% amino acid sequence identity to each other. BLASTp analysis revealed that the RdRp of FupgMV2 exhibits at least 88.84% amino acid sequence identity to that of Fusarium mitovirus 1, while the RdRp of FupgMV3 shows 80.19% amino acid sequence identity to that of Fusarium mitovirus 2. Phylogenetic analysis indicated that FupgMV2 and FupgMV3 both belong to the genus Unuamitovirus of the family Mitoviridae. This is the first report of two mitoviruses hosted by the same strain of the plant-pathogenic fungus F. pseudograminearum.

Mycovirome of Diaporthe helianthi and D. gulyae, causal agents of Phomopsis stem canker of sunflower (Helianthus annuus L.)

Diaporthe gulyae and D. helianthi cause Phomopsis stem canker, which is a yield-limiting fungal disease of sunflower (Helianthus annuus L.) in the United States. In this study, the mycovirus population was characterized in D. gulyae and D. helianthi using 52 and 42 isolates, respectively, that were recovered from diseased sunflower plants randomly sampled from commercial sunflower fields in the U.S. states of Minnesota, Nebraska, North Dakota, and South Dakota. Total RNA extracts depleted of rRNA from each fungus were pooled to construct one library for sequencing to obtain 20 GB per library of raw reads using a metatranscriptomics approach. Only the family Mitoviridae was present in both Diaporthe species. Twelve and nine novel viral contigs were discovered infecting D. gulyae and D. helianthi, respectively. Additionally, we detected two of the same viruses infecting D. helianthi, Helianthus annuus leaf-associated partitivirus 3 and 5, that were detected in a direct sunflower metatranscriptome reported before. Interestingly, Qinvirus, which is mostly known as a group of insect viruses, was found in a contig. An ambivirus that is rarely reported in the phylum Ascomycota was also discovered in this study. Besides an understanding of virome diversity, the mycovirome survey provides the first clue of biological molecules that can be further developed for antifungal purposes.

Identification of a novel mitovirus in grapevine through high-throughput sequencing

BACKGROUND

Transcriptome data from a plant sample frequently include numerous reads originating from RNA virus genomes that were concurrently isolated during RNA preparation. These high-throughput sequencing reads from the virus can be assembled to form a new sequence for the plant RNA genome.

METHODS AND RESULTS

Here, we identify putative novel mitovirus, grapevine mitovirus 1 (GMV1) through high-throughput sequencing (HTS) of grapevine rootstocks (Vitis spp.), and the identified virus was confirmed using virus-specific primers in RT-PCR assay. The genomic RNA of GMV1 encodes complete open reading frame (ORF) of 2,496 nucleotides (nts) in length. RNA-dependent RNA polymerase (RdRp) encoded by the viral genome contained one RdRp conserved domain. BLASTx analysis of GMV1 genome showed sequence identity of 33.18-56.75% with the existing mitovirus sequences. Phylogenetic analysis based on genome sequences showed that GMV1 clustered in a distinct clade to other mitoviruses.

CONCLUSION

Grapevine mitovirus 1 represents a newly discovered species within the Unuamitovirus genus of the Mitoviridae family, targeting fungal mitochondria. While the majority of recognized mitoviruses typically lack a functional RdRp as per the plant mitochondrial genetic code, GMV1 encodes a complete RdRp in accordance with both fungal and plant mitochondrial genetic codes.

Expanding the knowledge frontier of mitoviruses in Cannabis sativa

Mitoviruses were initially known for their presence in the mitochondria of fungi and were considered exclusive to these organisms. However, recent studies have shown that they are also present in a large number of plant species. Despite the potential impact that mitoviruses might have on the mitochondria of plant cells, there is a lack of information about these ancient RNA viruses, especially within the Cannabaceae family. Cannabis sativa has been in the spotlight in recent years due to the growing industrial applications of plant derivatives, such as fiber and secondary metabolites. Given the importance of Cannabis in today's agriculture, our study aimed to expand the knowledge frontier of Mitoviruses in C. sativa by increasing the number of reference genomes of CasaMV1 available in public databases and representing a larger number of crops in countries where its industrial-scale growth is legalized. To achieve this goal, we used transcriptomics to sequence the first mitoviral genomes of Colombian crops and analyzed RNA-seq datasets available in the SRA databank. Additionally, the evolutionary analysis performed using the mitovirus genomes revealed two main lineages of CasaMV1, termed CasaMV1_L1 and CasaMV1_L2. These mitoviral lineages showed strong clustering based on the geographic location of the crops and differential expression intensities.

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

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.

Characterization of a Novel Mitovirus Infecting Melanconiella theae Isolated From Tea Plants

A dsRNA segment was identified in the fungus Melanconiella theae isolated from tea plants. The complete dsRNA sequence, determined by random cloning together with RACE protocol, is 2,461 bp in length with an AU-rich content (62.37%) and comprises a single ORF of 2,265-nucleotides encoding an RNA-dependent RNA-polymerase (RdRp, 754 amino acids in size). The terminus sequences can fold into predicted stable stem-loop structures. A BLASTX and phylogenetic analysis revealed the dsRNA genome shows similarities with the RdRp sequences of mitoviruses, with the highest identity of 48% with those of grapevine-associated mitovirus 20 and Colletotrichum fructicola mitovirus 1. Our results reveal a novel member, tentatively named Melanconiella theae mitovirus 1 (MtMV1), belongs to the family Mitoviridae. MtMV1 is capsidless as examined by transmission electron microscope, efficiently transmitted through conidia as 100 conidium-generated colonies were analyzed, and easily eliminated by hyphal tipping method combined with green-leaf tea powder. MtMV1 has a genomic sequence obviously divergent from those of most members in the family Mitoviridae and some unique characteristics unreported in known members. This is the first report of a mycovirus infecting Melanconiella fungi to date.