Clean pyrosequencing data

These sequences were checked against the following quality criteria: (i) no Ns, (ii) quality score ≥ 23 according to the PANGEA process (Giongo et al., 2010), (iii) a minimum sequence length of 200 bp, and (iv) no sequencing error in the forward primer. The scripts used were quality.pl and preprocess.pl implemented in the pipeline PANAM (http://code.google.com/p/panam-phylogenetic-annotation /downloads /list) described more in detail in the related paper (Taib et al. 2013)

Phylogeny_fasttree_files

This compressed file aggregates the FastTree files (newick format) generated by the script panam.p

Table1_data

Similarity and phylogenetic indices determined for each phylogenetic units (PUs) presented in the table

synthese_OTU_RNA_DNA

OTUs with the taxonomies, the DNA and RNA abundances (tab delimited

Alignments and Phylogenies

Alignments and Phylogenie

Genomic context and phylogenetic analysis of the Peptidase M15 <i>Microviridae</i> sequences.

<p><b>(</b>A) Organization of the Peptidase M15_3 region in the 11 newly assembled <i>Microviridae</i> genomes. The regions encompassing homologous peptidase genes in three bacterial and two phages (noted with a black circle) genomes are also shown. <i>P2 GpR</i> stands for the P2 phage tail completion protein. (B) Maximum-likelihood tree computed from the multiple alignment of peptidase M15 sequences of the <i>Microvidae</i> and their closest homologues in viral and bacterial genomes. Bootstrap support values are indicated on each node. A fully expanded view of this tree is available as <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0040418#pone.0040418.s009" target="_blank">Fig. S9</a>.</p

Cleaned sequences

Cleaned sequence

Major capsid protein (MCP) variation within the <i>Microviridae</i>.

<p> (A) Three-dimensional model of the SpV4 virion (PDB ID:1KVP). Three capsomers donating long insertion loops to form the ‘mushroom-like’ protrusions at the three-fold axes of symmetry of the icosahedral capsid are highlighted in blue, green, and red. (B) A boxplot illustrating the variation of MCP sizes between the four subgroups of the <i>Microviridae</i>. (C) Three-dimensional models of the MCPs from viruses representing the four subgroups of the <i>Microviridae</i>: <i>Microvirus</i> (ΦX174 protein F; PDB ID:1CD3), <i>Gokushovirinae</i> (SpV4 VP1, PDB ID:1KVP), <i>Alpavirinae</i> (<i>Prevotella bucalis</i> prophage BMV5 protein VP1; GI:282877220), <i>Pichovirinae</i> (Pavin_279 protein VP1). The insertions within the VP1 proteins of gokusho-, alpa- and pichoviruses relative to the F protein of ΦX174 are highlighted in green.</p

Accuracy of the phylogenetic affiliation of PANAM compared to different approaches and on different regions

<p>. 1.A. Accuracy of the phylogenetic affiliation of PANAM-LCA, PANAM-NN, STAP, BLAST and RDP Classifier. 1,000 near-full-length sequences were randomly picked from the reference database and removed from it for the simulations. For PANAM, simulations were repeated 5 times and the standard variation is less than 0.03. 1.B. Accuracy of the phylogenetic affiliation in relation with the variable region targeted. The specificity was tested with PANAM-LCA and a sequence length equal to 400 bp.</p

The specificity percentage values at the genus level for BLAST, RDP, STAP and PANAM (NN and LCA).

<p>The specificity corresponds to the number of genus correctly affiliated among the detected ones, computed from forward primers for 200 bp and 400 bp amplicons. These values correspond to the mean computed from five samples of 1000 sequences (with the exception of V9 region computed with 300 sequences). The standard variation is less than 0.05.</p