Viruses of the Nahant Collection, characterization of 251 marine Vibrionaceae viruses

Abstract

Viruses are highly discriminating in their interactions with host cells and are thought to play a major role in maintaining diversity of environmental microbes. However, large-scale ecological and genomic studies of co-occurring virus-host pairs, required to characterize the mechanistic and genomic foundations of virus-host interactions, are lacking. Here, we present the largest dataset of cultivated and sequenced co-occurring virus-host pairs that captures ecologically representative fine-scale diversity. Using the ubiquitous and ecologically diverse marine Vibrionaceae as a host platform, we isolate and sequence 251 dsDNA viruses and their hosts from three time points within a 93-day time-series study. The virus collection includes representatives of the three Caudovirales tailed virus morphotypes, a novel family of nontailed viruses, and the smallest (10,046 bp) and largest (348,911 bp) Vibrio virus genomes described. We provide general characterization and annotation of the viruses and describe read-mapping protocols to standardize genome presentation. The rich ecological and genomic contextualization of hosts and viruses make the Nahant Collection a unique platform for high-resolution studies of environmental virus-host infection networks.

Figure 1. Overview of the diversity of Nahant Collection tailed viruses, organized by portal protein phylogeny.

Virfam classifier annotation of the Nahant Collection Caudovirales viruses reveals a diverse collection of myo-, sipho-, and podoviruses (indicated by color of leaf lable) representing all Types and Clusters (indicated in first attribute ring, and see Discussion for cluster identifiers) previously known to infect Proteobacteria, as well as many genomes unassignable to previously described groups. All 262 Caudovirales genome sequences are presented, including 28 replicate sub-lineage genomes. Genome %GC is provided in the second attribute ring and genome size is indicated by bars. The portal protein tree is unrooted and based on trimmed alignments; red circles indicate aLRT-supports ≥0.9. Associated data provided in Table 1, portal protein sequences in provided in Supplementary Table 3, interactive tree available at http://itol.embl.de/tree/181897146181191519509155#.

Figure 2. Examples of read recruitment by contig assemblies before and after adjustment for virus genomes with differing read mapping patterns.

Coverage mapping onto contigs of viruses with: Headful-like read mapping before (a) and after contig adjustment (e); Terminal repeat-like read mapping before (b) and after (f) contig adjustment; Single-stranded cos-end-like read mapping before (c) and after (g) contig adjustment; Mu-like read mapping before (d) and after (h) contig adjustment. Note that, as indicated in the methods, though read mapping patterns were evaluated for each virus, final adjustment strategy for each virus (Supplementary Table 2) was not determined solely based on read mapping pattern and the majority of virus contigs were defined as starting one open reading frame upstream of the large subunit of the terminase (TerL) regardless of the read mapping pattern.