Figure 1.
Phylogenetic tree drawn from the major capsid protein multiple alignment.
Linearized genomes are represented for each virus. The open reading frames in each genome are color-coded following the nomenclature used for Chlamydia phage genomes (i.e.VP1 : major capsid protein, VP2 : DNA pilot protein, VP3 : internal scaffolding protein, VP4 : genome replication initiation protein, and VP5 : DNA binding protein). Striped-colored genes encode proteins possessing features characteristic of VP2 proteins, but displaying no significant sequence similarity, as assessed by BLAST. The four Microviridae subgroups are highlighted on the tree. Bootstrap scores greater than 80 are marked with gray dots.
Figure 2.
Major capsid protein (MCP) variation within the Microviridae.
(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 Microviridae. (C) Three-dimensional models of the MCPs from viruses representing the four subgroups of the Microviridae: Microvirus (ΦX174 protein F; PDB ID:1CD3), Gokushovirinae (SpV4 VP1, PDB ID:1KVP), Alpavirinae (Prevotella bucalis prophage BMV5 protein VP1; GI:282877220), Pichovirinae (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.
Figure 3.
Genomic context and phylogenetic analysis of the Peptidase M15 Microviridae sequences.
(A) Organization of the Peptidase M15_3 region in the 11 newly assembled Microviridae genomes. The regions encompassing homologous peptidase genes in three bacterial and two phages (noted with a black circle) genomes are also shown. P2 GpR stands for the P2 phage tail completion protein. (B) Maximum-likelihood tree computed from the multiple alignment of peptidase M15 sequences of the Microvidae 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 Fig. S9.
Figure 4.
Abundance and distribution of VP1-like sequences in the environment.
The number of viromes and the origin of the samples used for virome preparation are indicated. VP1 sequences were affiliated by best BLAST hit against a database including VP1 sequences from both the previously published Microviridae genomes and the complete genomes assembled in this study.