Research ArticleMICROBIOLOGY

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

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Science Advances  07 Feb 2020:
Vol. 6, no. 6, eaay5981
DOI: 10.1126/sciadv.aay5981
  • 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 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 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.

Supplementary Materials

  • Supplementary material for this article is available at http://advances.sciencemag.org/cgi/content/full/6/6/eaay5981/DC1

    Supplementary Text

    Fig. S1. Workflow depiction of known ssRNA phage sequences.

    Fig. S2. Workflow depiction of the study pipeline.

    Fig. S3. Identification of ssRNA phage contigs within 82 metatranscriptome samples.

    Fig. S4. Genome architecture of ssRNA phages.

    Fig. S5. Taxonomic cutoff values for ssRNA phage genera and species.

    Fig. S6. Potential taxonomic restructuring for ssRNA phages.

    Fig. S7. Analysis of microbial community complexity.

    Fig. S8. Structural investigation of ssRNA phage–host interactions.

    Data S1. ssRNA phage finding hidden Markov model and associated sequences.

    Data S2. Bioinformatic scripts used during data analysis.

    References (6078)

  • Supplementary Materials

    The PDFset includes:

    • Supplementary Text
    • Fig. S1. Workflow depiction of known ssRNA phage sequences.
    • Fig. S2. Workflow depiction of the study pipeline.
    • Fig. S3. Identification of ssRNA phage contigs within 82 metatranscriptome samples.
    • Fig. S4. Genome architecture of ssRNA phages.
    • Fig. S5. Taxonomic cutoff values for ssRNA phage genera and species.
    • Fig. S6. Potential taxonomic restructuring for ssRNA phages.
    • Fig. S7. Analysis of microbial community complexity.
    • Fig. S8. Structural investigation of ssRNA phage–host interactions.
    • References (6078)

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    Other Supplementary Material for this manuscript includes the following:

    • Data S1 (.rar format). ssRNA phage finding hidden Markov model and associated sequences.
    • Data S2 (.rar format). Bioinformatic scripts used during data analysis.

    Files in this Data Supplement:

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