Diversity of putative archaeal RNA viruses in metagenomic datasets of a yellowstone acidic hot spring
Open accessAbstract
Two genomic fragments (5,662 and 1,269 nt in size, GenBank accession no. JQ756122 and JQ756123, respectively) of novel, positive-strand RNA viruses that infect archaea were first discovered in an acidic hot spring in Yellowstone National Park (Bolduc et al., 2012). To investigate the diversity of these newly identified putative archaeal RNA viruses, global metagenomic datasets were searched for sequences that were significantly similar to those of the viruses. A total of 3,757 associated reads were retrieved solely from the Yellowstone datasets and were used to assemble the genomes of the putative archaeal RNA viruses. Nine contigs with lengths ranging from 417 to 5,866 nt were obtained, 4 of which were longer than 2,200 nt; one contig was 204 nt longer than JQ756122, representing the longest genomic sequence of the putative archaeal RNA viruses. These contigs revealed more than 50% sequence similarity to JQ756122 or JQ756123 and may be partial or nearly complete genomes of novel genogroups or genotypes of the putative archaeal RNA viruses. Sequence and phylogenetic analyses indicated that the archaeal RNA viruses are genetically diverse, with at least 3 related viral lineages in the Yellowstone acidic hot spring environment.
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Chemical structure mapping showed that the long-lived LinearDesign-1 was significantly more highly structured than Yellowstone, as assessed by DMS and SHAPE reactivities.
“Chemical structure mapping showed that the long-lived LinearDesign-1 was significantly more highly structured than Yellowstone, as assessed by dimethyl sulfate (DMS) and selective 2’-hydroxyl acylation with primer extension (SHAPE) reactivities59,60 (Fig. 2H, Fig. S3) and structure models guided by these data (Fig. 2I).”
From Combinatorial optimization of mRNA structure, stability, and translation for RNA-based therapeutics (2022) · cites this paper as [60]
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Combinatorial optimization of mRNA structure, stability, and translation for RNA-based therapeutics
Leppek, K., Byeon, G. W., Kladwang, W., Wayment-Steele, H. K., Kerr, C. H., Xu, A. F., Kim, D. S., Topkar, V. V., Choe, C., Rothschild, D., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-28776-w · Cited by 399 · see citing works
Combinatorial optimization of mRNA structure, stability, and translation for RNA-based therapeutics
Leppek, K., Byeon, G. W., Kladwang, W., Wayment-Steele, H. K., Kerr, C. H., Xu, A. F., Kim, D. S., Topkar, V. V., Choe, C., Rothschild, D., et al. (2021) · doi:10.1101/2021.03.29.437587 · Cited by 399 · see citing works
- Authors
- Wang, H., Yu, Y., Liu, T., Pan, Y., Yan, S., & Wang, Y.
- Affiliations
- Shanghai Ocean University (CN)
- Corresponding author
- Wang, Yongjie
- Venue
- SpringerPlus
- Published
- 2015-04-18
- Volume
- 4
- Issue
- 1
- Pages
- 189-189
- ISSN
- 2193-1801 (ISSN-L)
- PMC
- PMC4405519
- OpenAlex
- W2157346239
- Cited by
- 7
- References
- 0
- Citations by year
- 2023: 1 · 2022: 2 · 2019: 2 · 2017: 2
- FWCI
- 0.60
- Type
- journal article
- Language
- en
- Open access
- diamond
- doi.org
- Locations
- SpringerPlus (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- GRO (publishedVersion, other-oa)
- GoeScholar The Publication Server of the Georg-August-Universität Göttingen (Georg-August-Universität Göttingen) (submittedVersion, cc-by)
- Funders
- National Natural Science Foundation of China (41376135)
- Ministry of Education of the People's Republic of China (20133104110006, 14ZZ144)
- Shanghai Municipal Education Commission (14ZZ144)
- Topics
- Physical Sciences › Environmental Science › Ecology › Bacteriophages and microbial interactions
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Endocrinology › Plant and Fungal Interactions Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- positive-strand RNA viruses, viral diversity, viral genome assembly, metagenomics, acidic hot springs, Yellowstone National Park, viral phylogeny, novel viral lineages
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