The deep terrestrial virosphere

Network analyses of all viral Äspö HRL contigs were conducted using<br> vConTACT2 (version 0.9.2 (Bolduc et al. 2017;<br> 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,<br> 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;<br> 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;<br> 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,<br> 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 &lt;50, medium circle 50 – 100, and largest circle &gt;100 bp mapped/kb of contig/Mb of metagenome).<br> Black nodes represent isolated bacterial and archaeal viruses obtained from NCBI RefSeq.<br>Files can be opened with Cytoscape v. 3.x (https://cytoscape.org).<br>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.<br>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.<br>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.<br>