Mining metatranscriptomes reveals a vast world of viroid-like circular RNAs

Lee, Benjamin D.; Neri, Uri; Roux, Simon; Wolf, Yuri I.; Camargo, Antônio Pedro; Krupovìč, Mart; Simmonds, Peter; Kyrpides, Nikos; Gophna, Uri; Dolja, Valerian V.; Koonin, Eugene V.

doi:10.1016/j.cell.2022.12.039

Cited by 55 publications

(51 citation statements)

References 96 publications

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“…Moreover, besides viruses, we also attempted to uncover new viroid-like agents, to uncover their still vastly undiscovered diversity [94]. We obtained five candidate viroids (out of >300 initial candidates), including one that was experimentally confirmed to be circular and structurally similar to members of Avsunviroidae due to the presence of a hammerhead ribozyme [95].…”

Section: Discussionmentioning

confidence: 99%

“…We obtained five candidate viroids (out of >300 initial candidates), including one that was experimentally confirmed to be circular and structurally similar to members of Avsunviroidae due to the presence of a hammerhead ribozyme [95]. Development of bioinformatics tools for viroid discovery could possibly uncover their largely hidden diversity and their further characterization could reveal their unknown roles in ecosystems [94].…”

Section: Discussionmentioning

confidence: 99%

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In-depth study of tomato and weed viromes reveals undiscovered plant virus diversity in an agroecosystem

et al. 2023

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Background In agroecosystems, viruses are well known to influence crop health and some cause phytosanitary and economic problems, but their diversity in non-crop plants and role outside the disease perspective is less known. Extensive virome explorations that include both crop and diverse weed plants are therefore needed to better understand roles of viruses in agroecosystems. Such unbiased exploration is available through viromics, which could generate biological and ecological insights from immense high-throughput sequencing (HTS) data. Results Here, we implemented HTS-based viromics to explore viral diversity in tomatoes and weeds in farming areas at a nation-wide scale. We detected 125 viruses, including 79 novel species, wherein 65 were found exclusively in weeds. This spanned 21 higher-level plant virus taxa dominated by Potyviridae, Rhabdoviridae, and Tombusviridae, and four non-plant virus families. We detected viruses of non-plant hosts and viroid-like sequences and demonstrated infectivity of a novel tobamovirus in plants of Solanaceae family. Diversities of predominant tomato viruses were variable, in some cases, comparable to that of global isolates of the same species. We phylogenetically classified novel viruses and showed links between a subgroup of phylogenetically related rhabdoviruses to their taxonomically related host plants. Ten classified viruses detected in tomatoes were also detected in weeds, which might indicate possible role of weeds as their reservoirs and that these viruses could be exchanged between the two compartments. Conclusions We showed that even in relatively well studied agroecosystems, such as tomato farms, a large part of very diverse plant viromes can still be unknown and is mostly present in understudied non-crop plants. The overlapping presence of viruses in tomatoes and weeds implicate possible presence of virus reservoir and possible exchange between the weed and crop compartments, which may influence weed management decisions. The observed variability and widespread presence of predominant tomato viruses and the infectivity of a novel tobamovirus in solanaceous plants, provided foundation for further investigation of virus disease dynamics and their effect on tomato health. The extensive insights we generated from such in-depth agroecosystem virome exploration will be valuable in anticipating possible emergences of plant virus diseases and would serve as baseline for further post-discovery characterization studies.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

In-depth study of tomato and weed viromes reveals undiscovered plant virus diversity in an agroecosystem

et al. 2023

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“… Callanan et al 2020 ). Approaches based on predicted secondary or tertiary protein structure such as HHpred ( Zimmermann et al 2018 ), Phyre2 ( Kelley et al 2015 ), or AlphaFold ( Jumper et al 2021 ) could also be useful to find more divergent RdRp sequences ( Wolf et al 2020 ; Charon et al 2022 ; Forgia, Chiapello, et al 2022 ; Lee et al 2022 ). For example, homology of the quenyavirus RdRp to previously known RNA virus RdRps was detectable with HHpred but not with BLASTP ( Obbard et al 2020 ) or our approach.…”

Section: Discussionmentioning

confidence: 99%

“…In most cases, the data sets were obtained for purposes completely different from virus identification—for example, the divergent axolotl-associated orthomyxo-like sequence came from a transcriptomic data set for a study on limb regeneration ( Bryant et al 2017 ). A variety of other studies have also searched for RNA viruses in the NCBI TSA database or other transcriptomic studies generated without the express purpose of virus discovery, including Cook et al (2013) , Longdon et al (2015) , Mushegian et al (2016) , Olendraite et al (2017) , Gilbert et al (2019) , Käfer et al (2019) , Lauber et al (2019 , 2021 ), Rosani et al (2019) , Starr et al (2019) , Callanan et al (2020) , Obbard et al (2020) , Ott Rutar and Kordis (2020) , Parry et al (2020) , Wu et al (2020) , Chang et al (2021) , Charon et al (2021) , Paraskevopoulou et al (2021) , Bejerman and Debat (2022) , Dheilly et al (2022) , Lee et al (2022) , Mifsud et al (2022) , Neri et al (2022) , Sidharthan et al (2022) , and Zayed et al (2022) . Most of these studies have been limited to certain virus groups and/or certain host groups.…”

Section: Discussionmentioning

confidence: 99%

“…A small proportion of viruses lack capsids, and here, the appropriate Baltimore group is determined by phylogenetic relatedness to viruses with capsids. Depending on species, RNA viruses can have segmented or nonsegmented genomes that are almost always linear, but in a few cases (notably chuviruses and the recently discovered ambiviruses) are or appear to be circular ( Li et al 2015 ; Forgia, Navarro, et al 2022 ; Lee et al 2022 ).…”

Section: Introductionmentioning

confidence: 99%

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Identification of RNA Virus–Derived RdRp Sequences in Publicly Available Transcriptomic Data Sets

Olendraitė

Brown

Firth

2023

Molecular Biology and Evolution

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RNA viruses are abundant, highly diverse, and infect all or most eukaryotic organisms. However, only a tiny fraction of the number and diversity of RNA virus species have been catalogued. To cost effectively expand the diversity of known RNA virus sequences we mined publicly available transcriptomic datasets. We developed 77 family-level Hidden Markov Model profiles for the viral RNA dependent RNA polymerase – the only universal “hall-mark” gene of RNA viruses. By using these to search the NCBI Transcriptome Shotgun Assembly database, we identified 5,867 contigs encoding RNA virus RdRps or fragments thereof and analysed their diversity, taxonomic classification, phylogeny and host associations. Our study expands the known diversity of RNA viruses, and the 77 curated RdRp pHMMs provide a useful resource for the virus discovery community.

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Discovery of a novel viroid‐like circular RNA in colorectal cancer

Wu,

Li,

et al. 2024

Cancer Communications

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Mining metatranscriptomes reveals a vast world of viroid-like circular RNAs

Cited by 55 publications

References 96 publications

In-depth study of tomato and weed viromes reveals undiscovered plant virus diversity in an agroecosystem

In-depth study of tomato and weed viromes reveals undiscovered plant virus diversity in an agroecosystem

Identification of RNA Virus–Derived RdRp Sequences in Publicly Available Transcriptomic Data Sets

Discovery of a novel viroid‐like circular RNA in colorectal cancer

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