RNA Virome Composition Is Shaped by Sampling Ecotype

Chen, Yanmei; Sadiq, Sabrina; Tian, Jingkui; Chen, Xiao; Lin, Xian-Dan; Shen, Jinjin; Chen, Hao; Hao, Zong-yu; Yang, Weidi; Zhou, Zien; Wu, Jingping; Li, Feng; Wang, Hongwei; Xu, Quangang; Wang, Wen; Gao, Wen-Hua; Holmes, Edward C.; Zhang, Yongzhen

doi:10.2139/ssrn.3934022

Cited by 4 publications

(14 citation statements)

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“…To facilitate and speed the specific detection of RNA virus signals, we provide a comprehensive non-redundant and manually curated viral RdRp protein sequence database. Specifically, we compiled into one location all the RdRp and RdRp-like sequences contained in the nr NCBI protein database, as well as from two major viral metatranscriptomic studies that identified thousands of new RNA viruses 2,37 .…”

Section: Resultsmentioning

confidence: 99%

“…To build our viral RdRp-specific database, we first manually retrieved all the RNA virus encoded RdRps from the nr NCBI database ( https://www.ncbi.nlm.nih.gov/protein ) based on taxonomy (Realm: Riboviria - Kingdom: Orthornavirae - excluding Pararnavirae retro-viruses), keywords and a length cut-off of 300 amino acids (Figure 1). The RdRp sequences from recent metagenomic studies 2,37 were added, and a filtering and manual curation step was employed to remove all non-RdRp sequences. Briefly, the “core” region of the RdRp (i.e., containing the three motifs A, B and C) was located and extracted based on the identification of the A, B and C sequence motifs.…”

Section: Resultsmentioning

confidence: 99%

“…Additional metagenomic-based RdRp sequences were retrieved from recent studies 36,37 and added to the nr RdRp using CD-hit 90% (v4.6.1) 34 .…”

Section: Methodsmentioning

confidence: 99%

“…Additional metagenomic-based RdRp sequences were retrieved from recent studies 36,37 and added to the nr RdRp using CD-hit 90% (v4.6.1) 34 . A comparison against the nr NCBI database was performed using Diamond BLASTp (v2.0.9) 38 (e-value cut-off 1e-05 ; "very-sensitive" option).…”

Section: Addition Of Rdrp Sequences Retrieved From Metagenomic Studiesmentioning

confidence: 99%

“…Revealing the diversity of RNA viruses in metagenomic data sets relies on our ability to compare sequenced and assembled contigs to pre-existing viral nucleotide and protein databases. However, current general protein databases are either too large (NCBI nr) or not comprehensive (NCBI RefSeq), while viral-specific ones such as the Reference Viral Database (RVDB) 47,48 Specifically, we compiled into one location all the RdRp and RdRp-like sequences contained in the nr NCBI protein database, as well as from two major viral metatranscriptomic studies that identified thousands of new RNA viruses 2,37 .…”

Section: A New Curated Viral Rdrp Databasementioning

confidence: 99%

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RdRp-scan: A Bioinformatic Resource to Identify and Annotate Divergent RNA Viruses in Metagenomic Sequence Data

Charon

Buchmann

Sadiq

et al. 2022

Preprint

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Despite a rapid expansion in the number of known RNA viruses following the advent of metagenomic sequencing, the identification and annotation of highly divergent RNA viruses remains challenging, particularly from poorly characterized hosts and environmental samples. Protein structures are more conserved than primary sequence data, such that structure-based comparisons provide an opportunity to reveal the viral “dusk matter”: viral sequences with low, but detectable, levels of sequence identity to known viruses with available protein structures. Here, we present a new open computational and resource – RdRp-scan – that contains a standardized bioinformatic toolkit to identify and annotate divergent RNA viruses in metagenomic sequence data based on the detection of RNA dependent RNA polymerase (RdRp) sequences. By combining RdRp-specific Hidden Markov models (HMM) and structural comparisons we show that RdRp-scan can efficiently detect RdRp sequences with identity levels as low as 10% to those from known viruses and not identifiable using standard sequence-to-sequence comparisons. In addition, to facilitate the annotation and placement of newly detected and divergent virus-like sequences into the known diversity of RNA viruses, RdRp-scan provides new custom and curated databases of viral RdRp sequences and core motif, as well as pre-built RdRp alignments. In parallel, our analysis of the sequence diversity detected by RdRp-scan revealed that while most of the taxonomically unassigned RdRps fell into pre-established clusters, some sequences cluster into potential new orders of RNA viruses related to the Wolframvirales and Tolivirales. Finally, a survey of the conserved A, B and C RdRp motifs within the RdRp-scan sequence database revealed additional variations of both sequence and position, which might provide new insights into the structure, function and evolution of viral RdRps.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

“…Additional metagenomic-based RdRp sequences were retrieved from recent studies 36,37 and added to the nr RdRp using CD-hit 90% (v4.6.1) 34 .…”

Section: Methodsmentioning

confidence: 99%

Section: Addition Of Rdrp Sequences Retrieved From Metagenomic Studiesmentioning

confidence: 99%

Section: A New Curated Viral Rdrp Databasementioning

confidence: 99%

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RdRp-scan: A Bioinformatic Resource to Identify and Annotate Divergent RNA Viruses in Metagenomic Sequence Data

Charon

Buchmann

Sadiq

et al. 2022

Preprint

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The ever-expanding diversity and complexity of the Arenaviridae family

2023

Virulence

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Resolving deep evolutionary relationships within the RNA virus phylum Lenarviricota

et al. 2022

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The RNA virus phylum Lenarviricota is comprised of the fungi-associated families Narnaviridae and Mitoviridae, the RNA bacteriophage Leviviridae, and the plant and fungi-associated Botourmiaviridae. Members of the Lenarviricota are abundant in most environments and boast remarkable phylogenetic and genomic diversity. As this phylum includes both RNA bacteriophage and fungi-and plant-associated species, the Lenarviricota likely mark a major evolutionary transition between those RNA viruses associated with prokaryotes and eukaryotes. Despite the remarkable expansion of this phylum following metagenomic studies, the phylogenetic relationships among the families within the Lenarviricota remain uncertain. Utilising a large data set of relevant viral sequences, we performed phylogenetic and genomic analyses to resolve the complex evolutionary history within this phylum and identify patterns in the evolution of virus genome organisation. Despite limitations reflecting very high levels of sequence diversity, our phylogenetic analyses suggests that the Leviviridae comprise the basal lineage within the Lenarviricota. Our phylogenetic results also support the construction of a new virus family – the Narliviridae – comprising a set of diverse and phylogenetically distinct species, including a number of uniquely encapsidated viruses. We propose a taxonomic restructuring within the Lenarviricota to better reflect the phylogenetic relationships documented here, with the Botourmiaviridae and Narliviridae combined into the order Ourlivirales, the Narnaviridae remaining in the order Wolframvirales, and these orders combined into the single class, the Amabiliviricetes. In sum, this study provides insights into the complex evolutionary relationships among the diverse families that make up the Lenarviricota.

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RNA Virome Composition Is Shaped by Sampling Ecotype

Cited by 4 publications

References 0 publications

RdRp-scan: A Bioinformatic Resource to Identify and Annotate Divergent RNA Viruses in Metagenomic Sequence Data

RdRp-scan: A Bioinformatic Resource to Identify and Annotate Divergent RNA Viruses in Metagenomic Sequence Data

The ever-expanding diversity and complexity of the Arenaviridae family

Resolving deep evolutionary relationships within the RNA virus phylum Lenarviricota

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