Metatranscriptomic Identification of Diverse and Divergent RNA Viruses in Green and Chlorarachniophyte Algae Cultures

Charon, Justine; Marcelino, Vanessa R.; Wetherbee, Richard; Verbruggen, Heroen; Holmes, Edward C.

doi:10.3390/v12101180

Cited by 30 publications

(33 citation statements)

References 98 publications

(110 reference statements)

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“…Likewise, PcoNSRV3 appears to belong to another novel taxon which also includes Shahe bunya-like virus 1 (APG79317), associated with small planktonic crustaceans ( Daphnia magna, D. carinata and Moina macrocopa ) from freshwater ecosystems in China [ 71 ] and bunya-like bridouvirus (QOW97246), detected in Chlorarachnion reptans , a macroalgae collected from marine sand in Victoria, Australia [ 72 ].…”

Section: Resultsmentioning

confidence: 99%

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

Botella

Jung

2021

Viruses

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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.

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Section: Resultsmentioning

confidence: 99%

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

Botella

Jung

2021

Viruses

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“…In addition to the recent association of newly described partiti-and amalgavirus-like viruses in the microalgae Ostreobium sp. (Cholorophyta) 52 , our identification of these novel and divergent…”

Section: The Extension Of Thementioning

confidence: 86%

“…Similarly, the Mitoviridae were considered as exclusively infecting fungi, until the recent discovery of the Chenopodium quinoa mitovirus 1 in a plant 51 and mito-like viruses in the Chlorophyta Osteobium sp. 52 led their host range to be re-evaluated. The three new narna-like viruses in Bacillariophyta discovered here, as well as the proposal of seven new mitovirus-like species in algal lineages as diverse as Haptophyta, Bacillariophyta, Rhodophyta and Chlorophyta, provides further evidence for the ubiquity of these viruses in protists.…”

Section: Narnaviridae-like and Mitoviridae-like Viruses Are Common In Microalgal Culturesmentioning

confidence: 99%

Revealing RNA virus diversity and evolution in unicellular algae transcriptomes

Charon

Murray

Holmes

2021

Preprint

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Remarkably little is known about the diversity and evolution of RNA viruses in unicellular eukaryotes. We screened a total of 570 transcriptomes from the Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP) project that encompasses a wide diversity of microbial eukaryotes, including most major photosynthetic lineages (i.e. the microalgae). From this, we identified 30 new and divergent RNA virus species, occupying a range of phylogenetic positions within the overall diversity of RNA viruses. Approximately one-third of the newly described viruses comprised single-stranded positive-sense RNA viruses from the order Lenarviricota associated with fungi, plants and protists, while another third were related to the order Ghabrivirales, including members of the protist and fungi-associated Totiviridae. Other viral species showed sequence similarity to positive-sense RNA viruses from the algae-associated Marnaviridae, the double-stranded RNA Partitiviridae, as well as a single negative-sense RNA virus related to the Qinviridae. Importantly, we were able to identify divergent RNA viruses from distant host taxa, revealing the ancestry of these viral families and greatly extending our knowledge of the RNA viromes of microalgal cultures. Both the limited number of viruses detected per sample and the low sequence identity to known RNA viruses imply that additional microalgal viruses exist that could not be detected at the current sequencing depth or were too divergent to be identified using sequence similarity. Together, these results highlight the need for further investigation of algal-associated RNA viruses as well as the development of new tools to identify RNA viruses that exhibit very high levels of sequence divergence.

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“…In this study, we have described 25 cryptical viral species associated with three plant taxa in the genus Agave : Agave fourcroydes , Agave sisalana and Agave hybrid 11648 using RNA-sequencing and genomic DNA sequencing for curation. The use of metagenomics-based approaches for the discovery of viral species is seen in research conducted by Charon et al [ 52 ], and Wolf et al [ 53 ], and also reviewed by Greninger [ 54 ], Maclot et al [ 55 ], and Shi et al [ 56 ]. In our methods, we also discarded false-positive results and endogenous elements (EVEs).…”

Section: Discussionmentioning

confidence: 99%

The Sisal Virome: Uncovering the Viral Diversity of Agave Varieties Reveals New and Organ-Specific Viruses

et al. 2021

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Sisal is a common name for different plant varieties in the genus Agave (especially Agave sisalana) used for high-quality natural leaf fiber extraction. Despite the economic value of these plants, we still lack information about the diversity of viruses (virome) in non-tequilana species from the genus Agave. In this work, by associating RNA and DNA deep sequencing we were able to identify 25 putative viral species infecting A. sisalana, A. fourcroydes, and Agave hybrid 11648, including one strain of Cowpea Mild Mottle Virus (CPMMV) and 24 elements likely representing new viruses. Phylogenetic analysis indicated they belong to at least six viral families: Alphaflexiviridae, Betaflexiviridae, Botourmiaviridae, Closteroviridae, Partitiviridae, Virgaviridae, and three distinct unclassified groups. We observed higher viral taxa richness in roots when compared to leaves and stems. Furthermore, leaves and stems are very similar diversity-wise, with a lower number of taxa and dominance of a single viral species. Finally, approximately 50% of the identified viruses were found in all Agave organs investigated, which suggests that they likely produce a systemic infection. This is the first metatranscriptomics study focused on viral identification in species from the genus Agave. Despite having analyzed symptomless individuals, we identified several viruses supposedly infecting Agave species, including organ-specific and systemic species. Surprisingly, some of these putative viruses are probably infecting microorganisms composing the plant microbiota. Altogether, our results reinforce the importance of unbiased strategies for the identification and monitoring of viruses in plant species, including those with asymptomatic phenotypes.

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Metatranscriptomic Identification of Diverse and Divergent RNA Viruses in Green and Chlorarachniophyte Algae Cultures

Cited by 30 publications

References 98 publications

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

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

Revealing RNA virus diversity and evolution in unicellular algae transcriptomes

The Sisal Virome: Uncovering the Viral Diversity of Agave Varieties Reveals New and Organ-Specific Viruses

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