The deep terrestrial virosphere

Network analyses of all viral Äspö HRL contigs were conducted using

vConTACT2 (version 0.9.2 (Bolduc et al. 2017;

https://dx.doi.org/10.7717/peerj.3243)) within the Cyverse Discovery Environment, following procedures available at protocols.io (https://dx.doi.org/10.17504/protocols.io.wigfcbw,

https://dx.doi.org/10.17504/protocols.io.wijfccn).
Here, the amino acid sequences of the predicted proteins were compared
to isolated, genome-sequenced bacterial and archaeal viruses (NCBI
Bacterial and Archaeal Viral RefSeq V85) using Diamond (Buchfink et al.
2015;

https://dx.doi.org/10.1038/nmeth.3176)
with e-value cut-off of 0.001 and default vConTACT2 settings. To
visualize the network, the produced c1.ntw file was imported into
Cytoscape (v3.7.2 (Shannon 2003;

https://dx.doi.org/10.1101/gr.1239303)) following the procedure on protocols.io
where column 1 was selected as Source Node, column 2 as Target Node,
and column 3 as Edge Attribute and duplicate edges were removed. The
Äspö HRL contig names in the Cytoscape file are defined as MM-171.3 =
MM,

MM-415.2 = UM, and TM-448.2 = OS. Node sizes for Äspö HRL viral contigs
are based on bp reads recruited divided by the contig size in kb and the
metagenome size in Mb (smallest circle <50, medium circle 50 – 100,
and largest circle >100 bp mapped/kb of contig/Mb of metagenome).

Black nodes represent isolated bacterial and archaeal viruses obtained from NCBI RefSeq.
Files can be opened with Cytoscape v. 3.x (https://cytoscape.org).
Fig. S2, MM-171.3_MM-415.2_TM-448.2_network.groundwater_detected.cys: Nodes coloured according to groundwater that the viral contigs were detected in.
Fig. S5, MMMM-171.3_MM-415.2_TM-448.2_network.groundwater_originated.cys: Nodes coloured according to groundwater that the viral contig originated from.
Fig. S6,MM-171.3_MM-415.2_TM-448.2_network.host_prediction.cys : Nodes coloured according to predicted microbial hosts based upon kmer analysis.