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. 2020 Feb 7;6(6):eaay5981.
doi: 10.1126/sciadv.aay5981. eCollection 2020 Feb.

Expansion of known ssRNA phage genomes: From tens to over a thousand

J Callanan  1   2 , S R Stockdale  1 , A Shkoporov  1 , L A Draper  1 , R P Ross  1   2   3 , C Hill  1   2
Affiliations

Expansion of known ssRNA phage genomes: From tens to over a thousand

J Callanan et al. Sci Adv. .

Abstract

The first sequenced genome was that of the 3569-nucleotide single-stranded RNA (ssRNA) bacteriophage MS2. Despite the recent accumulation of vast amounts of DNA and RNA sequence data, only 12 representative ssRNA phage genome sequences are available from the NCBI Genome database (June 2019). The difficulty in detecting RNA phages in metagenomic datasets raises questions as to their abundance, taxonomic structure, and ecological importance. In this study, we iteratively applied profile hidden Markov models to detect conserved ssRNA phage proteins in 82 publicly available metatranscriptomic datasets generated from activated sludge and aquatic environments. We identified 15,611 nonredundant ssRNA phage sequences, including 1015 near-complete genomes. This expansion in the number of known sequences enabled us to complete a phylogenetic assessment of both sequences identified in this study and known ssRNA phage genomes. Our expansion of these viruses from two environments suggests that they have been overlooked within microbiome studies.

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Figures

Fig. 1
Fig. 1. Identification of ssRNA phages in metatranscriptome samples.
(A) The total number of redundant contigs detected per HMM search. (B) The manually curated HMM 5-MC detected 15,611 nonredundant ssRNA phage sequences. Boxplot displays the median value within the 25th and 75th quartiles, with whiskers representing the interquartile range of ±1.5. (C) The number of contigs (near complete or partial) detected per assembly in activated sludge and aquatic samples. Boxplot horizontal lines indicate the mean, while the gray boxes represent 95% highest-density intervals. (D) Two-dimensional ordination of ssRNA compositional abundance across different geographical locations using the Bray-Curtis Dissimilarity index. The colors and shapes of individual samples differentiate study location and environment, respectively. PC, principle component. (E) Linear model of metatranscriptome sequencing coverage and contig length. Contigs included are of minimum length of 750 bp, and the number of core proteins encoded is indicated.
Fig. 2
Fig. 2. Examination of ssRNA phage proteins.
(A) Distribution of protein hits (in parentheses) across MP, CP, and RdRp clusters was identified using HMM 5-MC. (B) Bipartite connection network of contigs (circles) with proteins (squares). Colors are based on the associated CP from (A). (C) Protein cluster co-occurring profiles of ssRNA phages having all three full-length core proteins and (D) the frequently observed positions of hypothetical proteins (genes not drawn to scale).
Fig. 3
Fig. 3. Phylogenetic assessment of ssRNA phages.
Phylogeny of ssRNA phages using their core protein sequences (MP, CP, and RdRp). The 29 previously characterized and 1015 newly identified phages were included. Branch tip shapes highlight specific RdRp protein clusters, while color indicates CP clustering. The encircling annotation ring depicts current ICTV taxonomy. A green arrowhead represents AVE006, which encodes a unique RdRp and CP association. Bootstrap support values shown are for 100 iterations.
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References

    1. Cobián Güemes A. G., Youle M., Cantú V. A., Felts B., Nulton J., Rohwer F., Viruses as winners in the game of life. Annu. Rev. Virol. 3, 197–214 (2016). - PubMed
    1. Clokie M. R. J., Millard A. D., Letarov A. V., Heaphy S., Phages in nature. Bacteriophage 1, 31–45 (2011). - PMC - PubMed
    1. Manrique P., Bolduc B., Walk S. T., van der Oost J., de Vos W. M., Young M. J., Healthy human gut phageome. Proc. Natl. Acad. Sci. U.S.A. 113, 10400–10405 (2016). - PMC - PubMed
    1. Norman J. M., Handley S. A., Baldridge M. T., Droit L., Liu C. Y., Keller B. C., Kambal A., Monaco C. L., Zhao G., Fleshner P., Stappenbeck T. S., McGovern D. P. B., Keshavarzian A., Mutlu E. A., Sauk J., Gevers D., Xavier R. J., Wang D., Parkes M., Virgin H. W., Disease-specific alterations in the enteric virome in inflammatory bowel disease. Cell 160, 447–460 (2015). - PMC - PubMed
    1. Gregory A. C., Zayed A. A., Conceição-Neto N., Temperton B., Bolduc B., Alberti A., Ardyna M., Arkhipova K., Carmichael M., Cruaud C., Dimier C., Domínguez-Huerta G., Ferland J., Kandels S., Liu Y., Marec C., Pesant S., Picheral M., Pisarev S., Poulain J., Tremblay J.-É., Vik D., Acinas S. G., Babin M., Bork P., Boss E., Bowler C., Cochrane G., de Vargas C., Follows M., Gorsky G., Grimsley N., Guidi L., Hingamp P., Iudicone D., Jaillon O., Kandels-Lewis S., Karp-Boss L., Karsenti E., Not F., Ogata H., Pesant S., Poulton N., Raes J., Sardet C., Speich S., Stemmann L., Sullivan M. B., Sunagawa S., Wincker P., Babin M., Bowler C., Culley A. I., de Vargas C., Dutilh B. E., Iudicone D., Karp-Boss L., Roux S., Sunagawa S., Wincker P., Sullivan M. B., Marine DNA viral macro- and microdiversity from Pole to Pole. Cell 177, 1109–1123.e14 (2019). - PMC - PubMed

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