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. 2018 Jul 3;5:180114. doi: 10.1038/sdata.2018.114

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

Kathryn M Kauffman 1,*, Julia M Brown 2,*,‡, Radhey S Sharma 1,§, David VanInsberghe 1, Joseph Elsherbini 1, Martin Polz 1,a,†, Libusha Kelly 2,b,†
PMCID: PMC6029569  PMID: 29969110

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.

Subject terms: Mobile elements, Marine biology, Virology, DNA sequencing

Background & Summary

Viruses influence the structure, function, ecology, and evolution of microbial communities. They represent the richest reservoir of nucleic acid diversity1, and the great abundance of viral particles in the environment1 reflects the expression of these sequences in host cells2. However, understanding the structure of virus-host interaction networks in the wild still poses a major challenge as pair-wise interactions between specific viruses and their hosts cannot be predicted without isolate based studies. Thus, though viruses have been predicted to play a major role in maintaining the extensive fine-scale genomic diversity of environmental microbes, it has not been possible to systematically evaluate the mechanistic or genomic foundations of these interactions, nor their ecological and evolutionary consequences.

Here, we present the annotated viral genomes of the Nahant Collection, a large-scale virus-host model system of cultivated and genome-sequenced bacterial and viral isolates, built on the extensively characterized environmental marine Vibrionaceae model system. By capturing large numbers of closely related host and virus strains, the Nahant Collection allows evaluation of the impact of ecologically relevant fine scale diversity on the interactions between bacteria and lytic viruses. This collection of 251 virus genomes and their associated pairs is a resource for interrogating the determinants of host range and the molecular bases of specific virus-host interactions within one of the most richly contextualized environmental microbial model systems3–7 and time series studies8 available.

Viruses and hosts were isolated from samples collected at three time points within a 93-consecutive-day study of littoral marine microbial communities, the Nahant Time Series8. All viruses were isolated on hosts collected on the same day, and hosts were nearly exclusively Vibrio. The Vibrio are a well-suited host group for the evaluation of the role of ecology and evolution in structuring virus-host interactions – they are ubiquitous in marine systems, ecologically diverse, and are among the most thoroughly characterized model systems for the study of bacterial populations in the wild3–6,9,10. The viruses were recovered using approaches designed to yield representation of diverse viruses, including: isolation from concentrates by plating in agar overlays to allow for more representative recovery of both fast- and slow-growing viruses; use of 2-week incubation times to allow for appearance of plaques by slow plaque-formers; and inclusion of additives to media to improve plaque visualization (glycerol11) and mimic environmental substrates (chitin) that might be necessary to induce expression of host receptors.

To standardize assemblies of purified viral isolate genomes we used an approach informed by predicted differences in packaging strategies among viruses, described in greater detail in the methods. This approach suggests that viruses of the Nahant Collection include members with diverse packaged genome types, including cohesive end overhangs, inverted terminal repeats, headful-packaging type terminal redundancy, and Mu-like host ends. To evaluate whether any of the viruses were prophages derived from the host of isolation, rather than environmentally-derived isolates, sequence-based searches between virus and isolation host genomes were performed; only one case of prophage purification was identified among the virus strains with sequenced host genomes (Supplementary Table 1).

The collection includes highly diverse dsDNA tailed and non-tailed viruses, including the smallest (10,046 bp) and largest (348,911 bp) described Vibrio virus genomes (median 45,072 bp). Using the Virfam12 Caudovirales classifier, we find that the tailed viruses include representatives of all Virfam Types and Clusters previously identified as associated with Proteobacteria, including: Type 1 Clusters 3, 5, 6, 7, 8, 9 (Siphoviridae and Myoviridae); Type 2 (Myoviridae); and Type 3 (Podoviridae), as well as 26 viruses not associated to any previously identified Virfam Types or Clusters. Analyzing portal protein phylogeny revealed groups of closely related viruses as well as extensive collection-wide portal protein diversity (Fig. 1). The non-tailed viruses discovered in the collection are a proposed novel family, the Autolykviridae, and are discussed in greater detail elsewhere13. The overall collection ranges from 37% to 58% GC content, with a median of 43%. Viral genomes in the collection are also notable for their carriage of tRNAs, present in 53 viruses, and the presence of putative CRISPR features, present in 32 viruses (Table 1 (available online only)).

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

Figure 1

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Virfam12 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#.

Table 1. Characteristics of Nahant Collection virus genomes.

Virus Name Isolation host population Coverage Genome Length GC% Coding Sequences tRNA Putative CRISPR features Virfam Morphotype Virfam Type & Cluster Is sub-lineage or replicate?
Vibrio phage 1.003.O._10N.286.48.A2 Vibrio lentus 953 41,891 42.8421 72 0 0 Podo Type-3 no
Vibrio phage 1.004.O._10N.261.54.A2 Vibrio lentus 25957 42,511 44.9837 50 0 0 Sipho Type-1_Cluster-6 no
Vibrio phage 1.005.O._10N.286.48.F2 Vibrio splendidus 14049 50,301 43.9614 69 0 0 Myo Unassigned no
Vibrio phage 1.007.O._10N.261.55.F9 Vibrio cyclitrophicus 13070 49,244 42.8458 80 4 0 Myo Type-1_Cluster-7 no
Vibrio phage 1.008.O._10N.286.54.E5 Vibrio cyclitrophicus 963 10,579 43.3311 21 0 1 . . no
Vibrio phage 1.009.O._10N.261.51.C9 Vibrio lentus 9690 44,443 57.6919 62 0 1 Myo Type-1_Cluster-6 no
Vibrio phage 1.011.O._10N.286.49.B11 Vibrio cyclitrophicus 1461 10,579 43.3595 20 0 1 . . no
Vibrio phage 1.012.O._10N.261.48.C12 Vibrio lentus 8179 59,979 48.6070 98 1 0 Sipho Type-1_Cluster-5 no
Vibrio phage 1.013.O._10N.286.54.F9 Vibrio cyclitrophicus 9139 44,457 43.8626 67 2 0 Sipho Type-1 no
Vibrio phage 1.015.O._10N.222.51.E5 Vibrio breoganii 880 42,586 47.6119 66 0 0 Podo Type-3 no
Vibrio phage 1.016.O._10N.286.46.A11 Vibrio lentus 7686 48,078 43.2880 89 0 0 Myo Type-1_Cluster-7 no
Vibrio phage 1.017.O._10N.286.55.C11 Vibrio sp. F12 3333 51,290 44.2874 73 0 0 Myo Unassigned no
Vibrio phage 1.020.O._10N.222.48.A2 Vibrio tasmaniensis 405 10,636 43.6630 21 0 0 . . no
Vibrio phage 1.021.A._10N.222.51.F9 Vibrio splendidus 617 43,743 46.5172 50 0 0 Podo Type-3 no
Vibrio phage 1.021.B._10N.222.51.F9 Vibrio splendidus 557 43,743 46.5172 50 0 0 Podo Type-3 yes
Vibrio phage 1.021.C._10N.222.51.F9 Vibrio splendidus 625 43,743 46.5149 50 0 0 Podo Type-3 yes
Vibrio phage 1.022.O._10N.286.45.A10 Vibrio splendidus 326 62,440 48.5554 97 1 0 Sipho Type-1 no
Vibrio phage 1.023.O._10N.222.51.B4 Vibrio splendidus 170 59,872 48.6254 91 2 0 Sipho Type-1 no
Vibrio phage 1.024.O._10N.261.45.F8 Vibrio lentus 5579 58,892 49.0610 83 1 1 Sipho Type-1 no
Vibrio phage 1.025.O._10N.222.46.B6 Vibrio splendidus 637 75,797 43.1046 108 1 0 Podo Type-3 no
Vibrio phage 1.026.O._10N.222.49.C7 Vibrio splendidus 200 75,880 43.1023 107 1 0 Podo Type-3 no
Vibrio phage 1.027.O._10N.286.54.B8 Vibrio lentus 447 59,297 48.5927 85 0 0 Sipho Type-1 no
Vibrio phage 1.028.O._10N.286.45.B6 Vibrio sp. 661 31,617 45.9436 50 0 0 Myo Type-1_Cluster-8 no
Vibrio phage 1.029.O._10N.261.55.A7 Vibrio sp. 6525 46,513 42.5537 83 0 0 Myo Type-1_Cluster-7 no
Vibrio phage 1.030.O._10N.222.55.F9 Vibrio sp. F13 776 45,827 43.8933 66 0 0 Myo Unassigned no
Vibrio phage 1.031.O._10N.261.46.F8 Vibrio lentus 247 152,942 43.1588 198 2 0 Myo Unassigned no
Vibrio phage 1.032.O._10N.261.54.F5 Vibrio splendidus 8522 60,399 48.4445 94 1 0 Sipho Type-1 no
Vibrio phage 1.033.O._10N.222.49.B8 Vibrio lentus 7852 61,206 48.3531 89 1 0 Sipho Type-1 no
Vibrio phage 1.034.O._10N.261.46.B7 Vibrio breoganii 795 44,398 48.0224 67 0 1 Podo Type-3 no
Vibrio phage 1.034.X._10N.261.46.B7 Vibrio breoganii 821 44,383 48.0206 68 0 1 Podo Type-3 yes, technical replicate
Vibrio phage 1.036.O._10N.286.45.C3 Vibrio lentus 17026 40,172 42.7985 62 0 0 Podo Type-3 no
Vibrio phage 1.037.O._10N.261.52.F7 Vibrio lentus 563 43,111 44.9676 50 0 0 Sipho Type-1_Cluster-6 no
Vibrio phage 1.038.O._10N.286.51.C2 Vibrio lentus 1537 49,567 43.1678 89 0 0 Myo Type-1_Cluster-7 no
Vibrio phage 1.039.O._10N.286.55.A2 Vibrio lentus 11755 40,972 42.5242 68 0 0 Podo Type-3 no
Vibrio phage 1.040.O._10N.286.45.B9 Vibrio lentus 3323 10,579 43.3217 21 0 1 . . no
Vibrio phage 1.042.O._10N.286.45.B8 Vibrio lentus 399 49,730 43.1751 95 0 0 Myo Type-1_Cluster-7 no
Vibrio phage 1.043.O._10N.261.52.C7 Vibrio lentus 3772 10,272 41.8224 21 0 0 . . no
Vibrio phage 1.044.O._10N.261.51.B8 Vibrio lentus 3311 10,272 41.7932 21 0 0 . . no
Vibrio phage 1.046.O._10N.286.52.E3 Vibrio splendidus 6671 62,503 48.3225 89 2 2 Sipho Type-1 no
Vibrio phage 1.047.O._10N.286.55.F2 Vibrio cyclitrophicus 3221 46,106 43.3002 73 0 1 Sipho Type-1_Cluster-5 no
Vibrio phage 1.048.O._10N.286.46.A10 Vibrio lentus 2562 10,447 41.7249 22 0 0 . . no
Shewanella phage 1.049.O._10N.286.54.B5 Shewanella sp. 1142 45,021 41.5984 60 0 1 Sipho Type-1_Cluster-6 no
Shewanella phage 1.050.O._10N.286.48.A6 Shewanella sp. 467 45,285 41.6407 60 0 1 Sipho Type-1_Cluster-6 no
Enterovibrio phage 1.052.A._10N.286.46.C3 Enterovibrio norvegicus 453 42,889 46.7719 75 0 0 Myo Type-1_Cluster-7 no
Vibrio phage 1.054.O._10N.261.52.A1 Vibrio sp. 771 41,774 42.3182 72 0 0 Myo Type-1_Cluster-7 no
Enterovibrio phage 1.055.O._10N.286.55.E9 Enterovibrio norvegicus 461 47,199 40.9288 66 0 0 Sipho Type-1_Cluster-6 no
Vibrio phage 1.056.O._10N.261.48.C11 Vibrio lentus 260 47,054 44.7571 53 0 0 Sipho Type-1_Cluster-6 no
Vibrio phage 1.057.O._10N.261.46.B12 Vibrio lentus 3223 10,273 41.7794 21 0 0 . . no
Vibrio phage 1.060.A._10N.261.48.B5 Vibrio splendidus 528 41,105 43.2551 65 1 0 Sipho Type-1_Cluster-5 no
Vibrio phage 1.061.O._10N.286.55.C2 Vibrio lentus 465 41,667 43.0749 65 0 0 Podo Type-3 no
Vibrio phage 1.062.O._10N.286.55.C3 Vibrio cyclitrophicus 2774 10,579 43.3311 21 0 1 . . no
Vibrio phage 1.063.O._10N.261.45.C7 Vibrio lentus 166 128,641 37.3357 231 0 0 Myo Type-1_Cluster-7 no
Vibrio phage 1.064.O._10N.261.52.E2 unknown 737 36,584 42.7892 61 0 0 Sipho Type-1_Cluster-5 no
Vibrio phage 1.066.O._10N.286.46.E8 Vibrio lentus 412 47,053 44.7495 53 0 0 Sipho Type-1_Cluster-6 no
Vibrio phage 1.067.O._10N.261.52.C9 Vibrio lentus 401 40,955 42.5418 78 0 0 Podo Type-3 no
Vibrio phage 1.068.O._10N.261.51.F8 Vibrio lentus 997 47,038 44.7596 53 0 0 Sipho Type-1_Cluster-6 no
Vibrio phage 1.069.O._10N.286.49.F11 Vibrio lentus 2906 10,579 43.3311 21 0 1 . . no
Enterovibrio phage 1.070.O._10N.261.45.B2 Enterovibrio norvegicus 709 44,087 49.3955 66 0 0 Podo Type-3 no
Vibrio phage 1.071.A._10N.286.46.A12 Vibrio lentus 753 48,114 43.3096 87 0 0 Myo Type-1_Cluster-7 no
Vibrio phage 1.072.O._10N.286.48.A12 unknown 95 43,788 44.7725 51 0 0 Sipho Type-1_Cluster-6 no
Vibrio phage 1.074.O._10N.222.49.B7 Vibrio breoganii 205 36,922 42.6087 64 0 0 Sipho Type-1_Cluster-5 no
Vibrio phage 1.075.O._10N.286.55.B10 Vibrio sp. F12 435 51,290 44.2893 73 0 0 Myo Unassigned no
Shewanella phage 1.076.O._10N.286.51.B7 Shewanella sp. 119 47,914 42.8434 73 1 0 Sipho Type-1 no
Enterovibrio phage 1.077.O._10N.261.45.A10 Enterovibrio norvegicus 629 44,047 49.3791 66 0 0 Podo Type-3 no
Vibrio phage 1.079.O._10N.286.45.E9 Vibrio lentus 606 42,375 42.7823 72 0 0 Podo Type-3 no
Vibrio phage 1.080.O._10N.286.48.A4 Vibrio lentus 3663 10,046 41.1905 19 0 0 . . no
Shewanella phage 1.081.O._10N.286.52.C2 Shewanella sp. 88 239,318 42.4130 354 23 2 Myo Type-2 no
Vibrio phage 1.082.O._10N.261.49.E4 Vibrio breoganii 275 35,810 42.9964 57 0 0 Sipho Type-1_Cluster-5 no
Shewanella phage 1.083.O._10N.286.52.B9 Shewanella sp. 199 45,120 38.7079 61 0 2 Sipho Type-1_Cluster-6 no
Enterovibrio phage 1.084.O._10N.261.49.F5 Enterovibrio norvegicus 43 141,906 37.1027 244 0 0 Myo Unassigned no
Vibrio phage 1.085.O._10N.222.51.E3 Vibrio breoganii 173 37,820 42.7393 62 2 0 Sipho Type-1_Cluster-5 no
Vibrio phage 1.086.O._10N.222.51.F8 Vibrio splendidus 439 50,835 44.1920 68 0 0 Myo Unassigned no
Vibrio phage 1.087.A._10N.261.45.F9 Vibrio lentus 557 45,674 44.1192 67 0 0 Myo Unassigned no
Vibrio phage 1.088.O._10N.261.46.A1 Vibrio lentus 469 60,385 48.7820 90 1 0 Sipho Type-1_Cluster-5 no
Vibrio phage 1.089.O._10N.261.51.F9 Vibrio lentus 116 59,851 48.5606 97 1 0 Sipho Type-1_Cluster-5 no
Vibrio phage 1.090.B._10N.286.48.F1 Vibrio lentus 1032 41,868 42.5193 68 0 0 Podo Type-3 no
Vibrio phage 1.091.O._10N.286.52.B12 Vibrio lentus 180 43,134 42.7667 75 0 0 Podo Type-3 no
Vibrio phage 1.093.O._10N.286.55.E10 Vibrio sp. F12 287 51,290 44.2874 73 0 0 Myo Unassigned no
Vibrio phage 1.094.O._10N.286.55.E12 Vibrio sp. F12 296 51,290 44.2854 73 0 0 Myo Unassigned no
Vibrio phage 1.095.O._10N.286.46.E10 Vibrio sp. F12 3005 10,436 41.8168 22 0 0 . . no
Vibrio phage 1.097.O._10N.286.49.B3 Vibrio sp. 315 76,918 42.5960 98 0 0 Podo Type-3 no
Vibrio phage 1.098.O._10N.286.51.B9 Vibrio lentus 138 59,851 48.5573 97 1 0 Sipho Type-1_Cluster-5 no
Vibrio phage 1.100.O._10N.261.45.C3 Vibrio lentus 564 51,268 44.4059 70 0 0 Myo Unassigned no
Enterovibrio phage 1.101.O._10N.261.45.C6 Enterovibrio norvegicus 27 130,250 37.3589 224 2 0 Myo Type-1_Cluster-7 no
Vibrio phage 1.102.O._10N.261.45.E3 Vibrio lentus 3460 10,447 41.7249 22 0 0 . . no
Vibrio phage 1.103.O._10N.261.52.F2 Vibrio splendidus 511 61,748 48.6348 93 1 0 Sipho Type-1 no
Vibrio phage 1.104.O._10N.286.49.A12 Vibrio lentus 125 60,990 48.7506 93 0 0 Sipho Type-1 no
Vibrio phage 1.105.O._10N.286.49.B4 Vibrio cyclitrophicus 4312 49,123 42.8089 80 0 0 Myo Type-1_Cluster-7 no
Vibrio phage 1.106.O._10N.286.51.F7 Vibrio cyclitrophicus 174 47,070 42.8001 77 0 0 Myo Type-1_Cluster-7 no
Vibrio phage 1.107.A._10N.286.52.E10 Vibrio lentus 4180 10,447 41.7058 22 0 0 . . no
Vibrio phage 1.107.B._10N.286.52.E10 Vibrio lentus 3583 10,447 41.7058 22 0 0 . . yes
Vibrio phage 1.107.C._10N.286.52.E10 Vibrio lentus 2984 10,447 41.7058 22 0 0 . . yes
Vibrio phage 1.108.O._10N.222.51.A4 Vibrio breoganii 168 36,584 42.7919 62 0 0 Sipho Type-1_Cluster-5 no
Vibrio phage 1.110.O._10N.261.52.C1 Vibrio breoganii 224 37,556 42.9226 66 1 0 Sipho Type-1_Cluster-5 no
Vibrio phage 1.111.A._10N.286.45.E6 Vibrio lentus 730 40,209 43.5748 62 0 0 Myo Type-1_Cluster-6 no
Vibrio phage 1.111.B._10N.286.45.E6 Vibrio lentus 795 40,209 43.5748 62 0 0 Myo Type-1_Cluster-6 yes
Vibrio phage 1.112.O._10N.286.46.B11 Vibrio lentus 643 48,149 43.0829 83 0 0 Myo Type-1_Cluster-7 no
Vibrio phage 1.113.A._10N.286.51.E7 Vibrio splendidus 547 44,150 43.3431 74 0 0 Sipho Type-1_Cluster-5 no
Vibrio phage 1.115.A._10N.222.49.B11 Vibrio breoganii 261 37,416 43.2248 71 0 0 Sipho Type-1_Cluster-5 no
Vibrio phage 1.115.B._10N.222.49.B11 Vibrio breoganii 822 37,416 43.2222 71 0 0 Sipho Type-1_Cluster-5 yes
Vibrio phage 1.116.O._10N.222.52.C10 Vibrio breoganii 245 36,314 42.6833 61 2 0 Sipho Type-1_Cluster-5 no
Vibrio phage 1.117.O._10N.261.45.E9 Vibrio breoganii 459 55,794 49.4713 82 0 0 Sipho Type-1_Cluster-5 no
Vibrio phage 1.118.A._10N.261.49.F6 Vibrio lentus 308 60,458 48.7959 96 1 0 Sipho Type-1_Cluster-5 no
Vibrio phage 1.118.B._10N.261.49.F6 Vibrio lentus 357 60,458 48.7959 96 1 0 Sipho Type-1_Cluster-5 yes
Vibrio phage 1.119.O._10N.261.51.A9 Vibrio lentus 166 44,527 42.1497 76 0 0 Sipho Type-1_Cluster-5 no
Enterovibrio phage 1.121.O._10N.286.46.C4 Enterovibrio norvegicus 36 145,590 39.6861 263 3 0 Myo Type-1_Cluster-7 no
Vibrio phage 1.122.A._10N.286.46.F8 Vibrio cyclitrophicus 418 44,523 43.6246 69 2 0 Sipho Type-1 no
Vibrio phage 1.122.B._10N.286.46.F8 Vibrio cyclitrophicus 450 44,523 43.6291 69 2 0 Sipho Type-1 yes
Enterovibrio phage 1.123.O._10N.286.48.F3 Enterovibrio norvegicus 186 46,071 48.2972 72 0 0 Myo Type-1_Cluster-7 no
Vibrio phage 1.124.O._10N.286.49.B1 Vibrio sp. 220 47,604 43.5216 70 0 1 Myo Unassigned no
Vibrio phage 1.125.O._10N.286.49.F5 Vibrio splendidus 4584 10,578 43.3541 21 0 1 . . no
Vibrio phage 1.127.O._10N.286.52.E12 Vibrio lentus 169 44,915 42.2977 77 0 0 Sipho Type-1_Cluster-5 no
Vibrio phage 1.131.O._10N.222.49.A8 Vibrio breoganii 197 37,933 42.8387 67 0 0 Sipho Type-1_Cluster-5 no
Vibrio phage 1.132.O._10N.222.49.F8 Vibrio breoganii 187 36,926 43.2053 65 0 0 Sipho Type-1_Cluster-5 no
Vibrio phage 1.133.O._10N.222.51.E4 Vibrio breoganii 132 37,087 42.8991 66 0 0 Sipho Type-1_Cluster-5 no
Vibrio phage 1.134.O._10N.222.52.B8 Vibrio breoganii 144 36,379 42.9561 62 2 0 Sipho Type-1_Cluster-5 no
Vibrio phage 1.135.O._10N.222.54.B6 Vibrio sp. F13 411 41,918 42.5450 75 0 0 Sipho Type-1_Cluster-5 no
Vibrio phage 1.136.O._10N.261.45.E11 Vibrio sp. 206 31,617 45.9436 50 0 0 Myo Type-1_Cluster-8 no
Vibrio phage 1.137.O._10N.261.46.B5 Vibrio lentus 523 37,958 42.4100 69 0 0 Sipho Type-1_Cluster-5 no
Vibrio phage 1.138.O._10N.261.48.A1 Vibrio lentus 527 32,510 45.7982 45 0 0 Podo Type-3 no
Vibrio phage 1.139.A._10N.261.48.C6 Vibrio breoganii 96 43,893 47.9553 67 0 1 Podo Type-3 no
Vibrio phage 1.139.B._10N.261.48.C6 Vibrio breoganii 488 44,094 48.0224 68 0 1 Podo Type-3 yes
Vibrio phage 1.141.A._10N.261.49.B3 Vibrio kanaloae 6889 10,047 41.1566 19 0 0 . . no
Vibrio phage 1.142.O._10N.261.49.E11 Vibrio sp. 732 31,617 45.9436 50 0 0 Myo Type-1_Cluster-8 no
Vibrio phage 1.143.O._10N.261.55.C8 Vibrio lentus 194 44,527 42.1475 76 0 0 Sipho Type-1_Cluster-5 no
Vibrio phage 1.144.O._10N.286.45.B3 Vibrio splendidus 153 44,418 42.6336 75 0 0 Sipho Type-1_Cluster-5 no
Vibrio phage 1.147.O._10N.286.49.E9 Vibrio breoganii 165 37,360 42.8132 66 0 0 Sipho Type-1_Cluster-5 no
Vibrio phage 1.148.O._10N.286.54.A10 Vibrio breoganii 537 36,789 42.4475 65 0 0 Sipho Type-1_Cluster-5 no
Vibrio phage 1.149.O._10N.286.55.A12 Vibrio cyclitrophicus 163 48,481 42.7466 79 0 0 Myo Type-1_Cluster-7 no
Vibrio phage 1.150.O._10N.222.46.A6 Vibrio splendidus 127 75,796 43.1065 108 1 0 Podo Type-3 no
Vibrio phage 1.151.O._10N.222.46.B1 Vibrio splendidus 225 44,307 44.3745 64 0 0 Sipho Type-1_Cluster-5 no
Vibrio phage 1.152.O._10N.222.46.E1 Vibrio splendidus 237 75,798 43.1040 108 1 0 Podo Type-3 no
Vibrio phage 1.154.O._10N.222.52.B12 Vibrio sp. 511 37,136 42.2070 60 0 1 Myo Type-1_Cluster-7 no
Vibrio phage 1.155.O._10N.222.55.B3 Vibrio sp. F13 1070 29,029 44.0008 45 0 0 Myo Unassigned no
Vibrio phage 1.156.O._10N.261.45.A6 Vibrio sp. 301 31,617 45.9436 50 0 0 Myo Type-1_Cluster-8 no
Vibrio phage 1.157.O._10N.261.45.B7 Vibrio breoganii 206 35,855 42.9201 59 0 0 Sipho Type-1_Cluster-5 no
Vibrio phage 1.158.O._10N.261.45.E12 Vibrio lentus 110 46,507 44.6191 72 0 0 Myo Unassigned no
Vibrio phage 1.159.O._10N.261.46.F12 Vibrio sp. 997 31,617 45.9468 50 0 0 Myo Type-1_Cluster-8 no
Vibrio phage 1.160.O._10N.261.48.B11 Vibrio lentus 201 60,734 48.6548 93 1 0 Sipho Type-1_Cluster-5 no
Vibrio phage 1.161.O._10N.261.48.C5 Vibrio lentus 71 140,668 37.6802 228 0 1 Myo Type-1_Cluster-7 no
Vibrio phage 1.162.O._10N.261.48.E3 Vibrio breoganii 216 37,360 42.8105 66 0 0 Sipho Type-1_Cluster-5 no
Vibrio phage 1.164.O._10N.261.51.A7 Vibrio sp. F13 677 48,235 44.0282 64 0 1 Myo Unassigned no
Vibrio phage 1.165.O._10N.261.51.B7 Vibrio breoganii 861 37,046 42.9898 61 0 0 Sipho Type-1_Cluster-5 no
Vibrio phage 1.166.O._10N.261.51.C7 Vibrio lentus 214 21,800 45.9679 35 0 0 Myo Unassigned no
Vibrio phage 1.167.O._10N.261.51.F2 Vibrio breoganii 430 35,811 43.0482 66 0 0 Sipho Type-1_Cluster-5 no
Vibrio phage 1.168.O._10N.261.52.A10 Vibrio breoganii 154 37,551 42.5555 66 0 0 Sipho Type-1_Cluster-5 no
Vibrio phage 1.169.O._10N.261.52.B1 Vibrio breoganii 139 72,290 42.9409 85 1 0 Podo Type-3 no
Vibrio phage 1.170.O._10N.261.52.C3 Vibrio sp. 65 133,692 38.6964 214 0 0 Myo Type-1_Cluster-7 no
Vibrio phage 1.171.O._10N.261.52.F12 Vibrio lentus 71 60,216 48.7246 88 0 0 Sipho Type-1 no
Vibrio phage 1.172.O._10N.261.52.F5 Vibrio breoganii 262 36,314 42.6833 61 2 0 Sipho Type-1_Cluster-5 no
Vibrio phage 1.173.O._10N.261.55.A11 Vibrio cyclitrophicus 81 48,063 42.7585 84 0 0 Myo Type-1_Cluster-7 no
Vibrio phage 1.174.O._10N.261.55.A8 Vibrio lentus 145 47,063 43.9496 68 0 0 Myo Unassigned no
Vibrio phage 1.175.O._10N.261.55.B3 Vibrio lentus 593 49,066 44.5135 74 0 0 Myo Unassigned no
Vibrio phage 1.176.O._10N.261.55.F5 Vibrio breoganii 123 36,463 42.9339 63 2 0 Sipho Type-1_Cluster-5 no
Vibrio phage 1.177.O._10N.286.45.E10 Vibrio sp. F12 372 45,439 42.1158 80 0 0 Sipho Type-1_Cluster-5 no
Vibrio phage 1.178.O._10N.286.45.E12 Vibrio cyclitrophicus 449 39,934 41.8491 74 0 0 Sipho Type-1_Cluster-5 no
Vibrio phage 1.179.O._10N.286.45.F12 Vibrio splendidus 1499 31,498 45.6823 45 0 0 Podo Type-3 no
Vibrio phage 1.181.O._10N.286.46.C9 Vibrio splendidus 122 50,228 43.3782 78 0 0 Myo Unassigned no
Vibrio phage 1.182.O._10N.286.46.E1 Vibrio breoganii 829 36,910 42.7283 56 0 0 Podo Type-3 no
Vibrio phage 1.183.O._10N.286.48.B7 Vibrio sp. 91 37,411 44.0165 41 0 1 Podo Type-3 no
Vibrio phage 1.184.A._10N.286.49.A5 Vibrio cyclitrophicus 862 33,272 43.7936 48 0 1 Podo Type-3 no
Vibrio phage 1.185.O._10N.286.49.C2 Vibrio sp. 484 43,397 46.0447 48 0 1 Podo Type-3 no
Vibrio phage 1.186.O._10N.286.49.E3 Vibrio cyclitrophicus 195 48,643 42.7831 78 2 0 Myo Type-1_Cluster-7 no
Vibrio phage 1.187.O._10N.286.49.F1 Vibrio splendidus 370 133,254 37.9268 255 2 0 Myo Type-1_Cluster-7 no
Vibrio phage 1.188.A._10N.286.51.A6 Vibrio breoganii 99 72,305 42.9832 86 1 0 Podo Type-3 no
Vibrio phage 1.188.B._10N.286.51.A6 Vibrio breoganii 300 72,305 42.9832 86 1 0 Podo Type-3 yes
Vibrio phage 1.188.C._10N.286.51.A6 Vibrio breoganii 302 72,305 42.9832 86 1 0 Podo Type-3 yes
Vibrio phage 1.189.B._10N.286.51.B5 Vibrio breoganii 720 36,855 42.7974 66 0 0 Sipho Type-1_Cluster-5 yes
Vibrio phage 1.189.C._10N.286.51.B5 Vibrio breoganii 719 36,855 42.8002 66 0 0 Sipho Type-1_Cluster-5 yes
Vibrio phage 1.189.O._10N.286.51.B5 Vibrio breoganii 469 36,855 42.7974 66 0 0 Sipho Type-1_Cluster-5 no
Vibrio phage 1.190.O._10N.286.51.F12 Vibrio lentus 1810 21,785 45.9353 35 0 0 Myo Unassigned no
Vibrio phage 1.191.O._10N.286.52.B4 Vibrio splendidus 118 48,354 44.1970 72 0 0 Myo Unassigned no
Vibrio phage 1.193.O._10N.286.52.C6 Vibrio splendidus 207 132,560 38.0854 249 4 0 Myo Type-1_Cluster-7 no
Vibrio phage 1.194.O._10N.286.54.B1 Vibrio lentus 110 59,294 48.5800 85 0 0 Sipho Type-1 no
Vibrio phage 1.195.O._10N.286.54.C8 Vibrio lentus 108 59,738 48.6524 88 0 0 Sipho Type-1 no
Vibrio phage 1.196.O._10N.286.54.E12 Vibrio lentus 146 59,414 48.5795 85 0 0 Sipho Type-1 no
Vibrio phage 1.197.A._10N.286.54.F2 Vibrio cyclitrophicus 224 44,587 43.6181 71 0 0 Sipho Type-1_Cluster-5 no
Vibrio phage 1.198.A._10N.286.54.F4 Vibrio cyclitrophicus 576 44,472 41.9050 79 0 0 Sipho Type-1_Cluster-5 no
Vibrio phage 1.198.B._10N.286.54.F4 Vibrio cyclitrophicus 1334 44,343 41.8578 78 0 0 Sipho Type-1_Cluster-5 yes
Vibrio phage 1.199.A._10N.286.55.C10 Vibrio cyclitrophicus 803 48,312 43.0452 77 0 0 Myo Type-1_Cluster-7 no
Vibrio phage 1.199.B._10N.286.55.C10 Vibrio cyclitrophicus 851 48,312 43.0431 77 0 0 Myo Type-1_Cluster-7 yes
Vibrio phage 1.200.O._10N.286.55.E1 Vibrio lentus 513 59,297 48.5927 85 0 0 Sipho Type-1 no
Vibrio phage 1.201.B._10N.286.55.F1 Vibrio cyclitrophicus 730 50,506 44.2918 73 0 0 Myo Unassigned no
Vibrio phage 1.202.O._10N.222.45.E8 Vibrio cyclitrophicus 1174 32,014 44.5586 42 0 0 Myo Type-1_Cluster-9 no
Vibrio phage 1.204.O._10N.222.46.F12 Vibrio cyclitrophicus 658 44,168 43.5157 55 0 0 Podo Type-3 no
Vibrio phage 1.205.O._10N.222.51.A7 Vibrio tasmaniensis 167 57,861 44.9249 70 0 0 Podo Type-3 no
Vibrio phage 1.206.O._10N.222.51.B10 Vibrio breoganii 744 37,551 42.9256 62 0 0 Sipho Type-1_Cluster-5 no
Vibrio phage 1.207.B._10N.222.51.C2 Vibrio breoganii 252 55,793 49.4757 81 0 0 Sipho Type-1_Cluster-5 no
Vibrio phage 1.208.B._10N.222.52.A7 Vibrio splendidus 517 48,927 44.4642 69 2 0 Podo Type-3 no
Vibrio phage 1.209.O._10N.222.52.B2 Vibrio breoganii 508 43,712 48.0005 65 0 1 Podo Type-3 no
Vibrio phage 1.210.O._10N.222.52.C2 Vibrio sp. F13 117 48,224 42.0392 74 1 0 Sipho Type-1 no
Vibrio phage 1.211.A._10N.222.52.F11 Vibrio tasmaniensis 736 37,169 43.7488 40 0 0 Podo Type-3 no
Vibrio phage 1.211.B._10N.222.52.F11 Vibrio tasmaniensis 119 37,169 43.7488 40 0 0 Podo Type-3 yes
Vibrio phage 1.213.O._10N.222.54.F10 Vibrio sp. F13 208 42,443 42.5677 73 0 0 Sipho Type-1_Cluster-5 no
Vibrio phage 1.214.O._10N.222.54.F11 Vibrio cyclitrophicus 173 44,205 43.6285 69 1 0 Sipho Type-1 no
Vibrio phage 1.215.A._10N.222.54.F7 Vibrio splendidus 118 80,834 45.5477 105 0 0 Sipho Type-1_Cluster-9 no
Vibrio phage 1.215.B._10N.222.54.F7 Vibrio splendidus 65 80,834 45.5477 105 0 0 Sipho Type-1_Cluster-9 yes
Vibrio phage 1.216.O._10N.222.55.C12 Vibrio sp. F13 235 41,359 42.6026 69 0 0 Sipho Type-1_Cluster-5 no
Vibrio phage 1.217.O._10N.261.45.A1 Vibrio sp. 334 31,617 45.9436 50 0 0 Myo Type-1_Cluster-8 no
Vibrio phage 1.219.O._10N.261.45.E2 Vibrio sp. 710 31,617 45.9436 50 0 0 Myo Type-1_Cluster-8 no
Vibrio phage 1.223.O._10N.261.48.A9 Vibrio lentus 593 49,535 44.4433 70 0 0 Myo Unassigned no
Vibrio phage 1.224.A._10N.261.48.B1 Vibrio breoganii 95 71,915 43.0633 85 1 0 Podo Type-3 no
Vibrio phage 1.225.O._10N.261.48.B7 Vibrio splendidus 358 52,615 44.2421 75 0 0 Myo Unassigned no
Vibrio phage 1.226.O._10N.261.48.E5 Vibrio breoganii 256 35,655 42.9785 67 0 0 Sipho Type-1_Cluster-5 no
Vibrio phage 1.228.O._10N.261.49.C1 Vibrio breoganii 255 36,667 42.8969 64 0 0 Sipho Type-1_Cluster-5 no
Vibrio phage 1.231.O._10N.261.49.F8 Vibrio lentus 1131 44,527 42.1430 76 0 0 Sipho Type-1_Cluster-5 no
Vibrio phage 1.232.O._10N.261.51.E11 Vibrio tasmaniensis 92 56,736 43.8963 79 0 0 Podo Type-3 no
Vibrio phage 1.233.A._10N.261.51.E6 Vibrio breoganii 789 36,823 43.1144 60 0 0 Sipho Type-1_Cluster-5 no
Vibrio phage 1.233.B._10N.261.51.E6 Vibrio breoganii 657 36,823 43.1144 60 0 0 Sipho Type-1_Cluster-5 yes
Vibrio phage 1.235.O._10N.261.52.B2 Vibrio lentus 2261 47,017 43.0249 59 0 0 Podo Type-3 no
Vibrio phage 1.236.O._10N.261.52.C4 Vibrio cyclitrophicus 482 42,646 42.3252 67 0 0 Sipho Type-1_Cluster-5 no
Vibrio phage 1.237.A._10N.261.52.C5 Vibrio lentus 80 60,097 48.7628 95 1 0 Sipho Type-1_Cluster-5 no
Vibrio phage 1.237.B._10N.261.52.C5 Vibrio lentus 377 60,160 48.7633 95 1 0 Sipho Type-1_Cluster-5 yes
Vibrio phage 1.238.A._10N.261.52.F10 Vibrio breoganii 485 70,494 43.1881 93 0 0 Podo Type-3 no
Vibrio phage 1.238.B._10N.261.52.F10 Vibrio breoganii 86 70,467 43.1890 94 0 0 Podo Type-3 yes
Vibrio phage 1.239.O._10N.261.52.F6 Vibrio breoganii 249 38,618 43.0214 64 0 1 Sipho Type-1_Cluster-5 no
Vibrio phage 1.240.O._10N.261.52.F8 Vibrio breoganii 511 36,710 42.5306 59 1 0 Sipho Type-1_Cluster-5 no
Vibrio phage 1.242.O._10N.261.54.B2 Vibrio breoganii 212 36,910 42.7526 64 1 0 Sipho Type-1_Cluster-5 no
Vibrio phage 1.243.O._10N.261.54.B5 Vibrio cyclitrophicus 163 48,414 42.9401 79 2 0 Myo Type-1_Cluster-7 no
Vibrio phage 1.244.A._10N.261.54.C3 Vibrio sp. F13 219 159,885 44.3350 211 3 1 Myo Type-2 no
Vibrio phage 1.245.O._10N.261.54.C7 Vibrio breoganii 303 71,702 43.1201 94 0 0 Podo Type-3 no
Vibrio phage 1.246.O._10N.261.54.E10 Vibrio sp. F13 361 47,133 44.7606 67 0 0 Myo Unassigned no
Vibrio phage 1.247.A._10N.261.54.E12 Vibrio splendidus 536 43,896 44.0564 70 1 0 Sipho Type-1 no
Vibrio phage 1.247.B._10N.261.54.E12 Vibrio splendidus 673 43,896 44.0541 70 1 0 Sipho Type-1 yes
Vibrio phage 1.248.O._10N.261.54.F1 Vibrio cyclitrophicus 3805 48,301 42.8811 80 0 0 Myo Type-1_Cluster-7 no
Vibrio phage 1.249.A._10N.261.55.B9 Vibrio cyclitrophicus 3423 10,611 46.5555 22 0 0 . . no
Vibrio phage 1.249.B._10N.261.55.B9 Vibrio cyclitrophicus 2160 10,611 46.5555 22 0 0 . . yes
Vibrio phage 1.250.O._10N.261.55.E11 Vibrio splendidus 253 59,981 48.9305 94 1 0 Sipho Type-1 no
Vibrio phage 1.251.O._10N.261.55.E5 Vibrio lentus 298 59,649 48.5658 93 1 0 Sipho Type-1 no
Vibrio phage 1.253.O._10N.286.45.B12 Vibrio cyclitrophicus 611 47,008 43.0182 59 0 0 Podo Type-3 no
Vibrio phage 1.254.O._10N.286.45.C8 Vibrio lentus 676 32,699 45.4662 45 0 0 Podo Type-3 no
Vibrio phage 1.255.O._10N.286.45.F1 Vibrio splendidus 198 159,885 44.3350 211 3 1 Myo Type-2 no
Vibrio phage 1.256.O._10N.286.45.F8 Vibrio cyclitrophicus 123 48,207 42.9668 76 0 0 Myo Type-1_Cluster-7 no
Vibrio phage 1.257.O._10N.286.46.A4 Vibrio splendidus 774 32,371 45.7755 47 0 0 Podo Type-3 no
Vibrio phage 1.259.O._10N.286.48.F4 Vibrio splendidus 371 28,145 43.7733 42 0 0 Myo Unassigned no
Vibrio phage 1.261.O._10N.286.51.A7 Vibrio breoganii 376 71,992 43.1659 82 1 0 Podo Type-3 no
Vibrio phage 1.262.O._10N.286.51.A9 Vibrio breoganii 325 47,635 39.0721 74 4 0 Podo Type-3 no
Vibrio phage 1.263.A._10N.286.51.B1 Vibrio cyclitrophicus 756 49,640 43.0379 76 0 0 Myo Type-1_Cluster-7 no
Vibrio phage 1.263.B._10N.286.51.B1 Vibrio cyclitrophicus 64 49,640 43.0419 76 0 0 Myo Type-1_Cluster-7 yes
Vibrio phage 1.264.O._10N.286.51.F2 Vibrio splendidus 270 47,739 42.7701 67 0 0 Podo Type-3 no
Vibrio phage 1.265.O._10N.286.52.F6 Vibrio cyclitrophicus 405 43,630 42.1797 70 0 0 Sipho Type-1_Cluster-5 no
Vibrio phage 1.266.O._10N.286.52.F9 Vibrio breoganii 257 34,788 43.2620 59 0 0 Sipho Type-1_Cluster-5 no
Vibrio phage 1.267.O._10N.286.54.A1 Vibrio lentus 95 59,414 48.5795 85 0 0 Sipho Type-1 no
Vibrio phage 1.268.A._10N.286.54.A11 Vibrio lentus 435 59,297 48.5876 85 0 0 Sipho Type-1 no
Vibrio phage 1.268.B._10N.286.54.A11 Vibrio lentus 342 59,297 48.5876 85 0 0 Sipho Type-1 yes
Vibrio phage 1.269.O._10N.286.54.A6 Vibrio lentus 85 59,738 48.6524 88 0 0 Sipho Type-1 no
Vibrio phage 1.270.A._10N.286.54.A8 Vibrio lentus 71 59,294 48.5918 85 0 0 Sipho Type-1 no
Vibrio phage 1.270.B._10N.286.54.A8 Vibrio lentus 44 59,294 48.5901 85 0 0 Sipho Type-1 yes
Vibrio phage 1.271.A._10N.286.54.B4 Vibrio lentus 170 59,297 48.5859 85 0 0 Sipho Type-1 no
Vibrio phage 1.271.B._10N.286.54.B4 Vibrio lentus 411 59,297 48.5893 85 0 0 Sipho Type-1 yes
Vibrio phage 1.272.O._10N.286.54.C4 Vibrio lentus 286 59,297 48.5910 85 0 0 Sipho Type-1 no
Vibrio phage 1.273.O._10N.286.54.C7 Vibrio cyclitrophicus 159 48,145 42.8601 78 2 0 Myo Type-1_Cluster-7 no
Vibrio phage 1.274.O._10N.286.54.E1 Vibrio lentus 159 59,409 48.5718 85 0 0 Sipho Type-1 no
Vibrio phage 1.275.O._10N.286.54.E11 Vibrio cyclitrophicus 256 37,915 44.3044 53 1 0 Podo Type-3 no
Vibrio phage 1.276.O._10N.286.54.E4 Vibrio cyclitrophicus 130 44,334 42.1843 72 0 0 Sipho Type-1_Cluster-5 no
Vibrio phage 1.277.A._10N.286.54.E7 Vibrio lentus 337 59,297 48.5876 85 0 0 Sipho Type-1 no
Vibrio phage 1.277.B._10N.286.54.E7 Vibrio lentus 482 59,419 48.6023 85 0 0 Sipho Type-1 yes
Vibrio phage 1.278.O._10N.286.54.E8 Vibrio cyclitrophicus 387 49,282 42.6687 82 0 0 Myo Type-1_Cluster-7 no
Vibrio phage 1.280.O._10N.286.54.F6 Vibrio lentus 373 59,297 48.5910 85 0 0 Sipho Type-1 no
Vibrio phage 1.281.O._10N.286.54.F7 Vibrio lentus 78 59,297 48.5910 85 0 0 Sipho Type-1 no
Vibrio phage 1.282.A._10N.286.54.F8 Vibrio lentus 255 59,359 48.5773 85 0 0 Sipho Type-1 no
Vibrio phage 1.283.A._10N.286.55.A1 Vibrio lentus 532 59,530 48.6209 85 0 0 Sipho Type-1 no
Vibrio phage 1.283.B._10N.286.55.A1 Vibrio lentus 427 59,530 48.6209 85 0 0 Sipho Type-1 yes
Vibrio phage 1.283.C._10N.286.55.A1 Vibrio lentus 370 59,530 48.6192 85 0 0 Sipho Type-1 yes
Vibrio phage 1.284.A._10N.286.55.A5 Vibrio cyclitrophicus 663 45,648 43.4543 71 0 0 Sipho Type-1_Cluster-5 no
Vibrio phage 1.285.O._10N.286.55.C12 Vibrio lentus 809 59,437 48.5522 93 1 0 Sipho Type-1 no
Vibrio phage 1.286.O._10N.286.55.C4 Vibrio cyclitrophicus 575 49,131 42.9932 82 0 0 Myo Type-1_Cluster-7 no
Vibrio phage 1.287.O._10N.286.55.C7 Vibrio cyclitrophicus 720 45,562 43.3344 71 0 0 Sipho Type-1_Cluster-5 no
Vibrio phage 1.289.A._10N.286.55.E8 Vibrio cyclitrophicus 1521 44,529 43.3919 70 0 0 Sipho Type-1_Cluster-5 no
Vibrio phage 1.291.O._10N.286.55.F6 Vibrio cyclitrophicus 759 43,662 42.9687 74 1 0 Sipho Type-1_Cluster-5 no
Vibrio phage 1.293.O._10N.261.52.E1 Vibrio cyclitrophicus 413 48,275 44.1409 76 1 0 Podo Type-3 no
Vibrio phage 2.044.O._10N.261.51.B8 Vibrio lentus 733 45,020 44.8156 53 0 2 Sipho Type-1_Cluster-6 no
Vibrio phage 2.058.O._10N.286.46.B8 Vibrio lentus 322 101,637 41.0648 143 0 0 Sipho Type-1_Cluster-6 no
Vibrio phage 2.092.O._10N.286.52.B7 Vibrio lentus 2518 10,580 43.3176 21 0 1 . . no
Vibrio phage 2.095.A._10N.286.46.E10 Vibrio sp. F12 578 44,649 42.3638 77 0 0 Sipho Type-1_Cluster-5 no
Vibrio phage 2.095.B._10N.286.46.E10 Vibrio sp. F12 607 44,649 42.3593 77 0 0 Sipho Type-1_Cluster-5 yes
Shewanella phage 2.096.O._10N.286.48.B5 Shewanella sp. 611 44,683 38.7843 57 0 2 Sipho Type-1_Cluster-6 no
Vibrio phage 2.117.O._10N.261.45.E9 Vibrio breoganii 438 55,795 49.4704 82 0 0 Sipho Type-1_Cluster-5 no
Vibrio phage 2.130.O._10N.222.46.C2 Vibrio splendidus 411 75,797 43.1099 107 1 0 Podo Type-3 no
Vibrio phage 2.159.A._10N.261.46.F12 Vibrio sp. 1185 31,617 45.9436 50 0 0 Myo Type-1_Cluster-8 no
Vibrio phage 2.159.B._10N.261.46.F12 Vibrio sp. 922 31,617 45.9436 50 0 0 Myo Type-1_Cluster-8 yes
Vibrio phage 2.275.O._10N.286.54.E11 Vibrio cyclitrophicus 51 348,911 38.0928 489 19 1 Myo Type-2 no
Vibrio phage 3.058.O._10N.286.46.B8 Vibrio lentus 295 101,642 41.0677 143 0 0 Sipho Type-1_Cluster-6 no
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The viruses and hosts of the Nahant Collection, the largest available dataset of sequenced co-occurring cultivated virus-host pairs, are embedded within the rich contextualization of the 93-consecutive-day Nahant Time Series study8. The integration of ecological context, sequence-information, and cultivation-based study available for this model system make the Nahant Collection a unique and robust foundation for the study of the role of viruses in the ecology and evolution of their bacterial hosts.

Methods

Environmental sampling

All viruses and their hosts were isolated from water samples collected at three time points within a larger 3-month study8 of coastal marine microbial communities at Canoe Cove, Nahant, MA, USA in 2010 (42° 25’ 10.6”N, 70° 54’ 24.2”W): August 10 (ordinal day 222, water temperature 13.8 °C), September 18 (261, 16.3 °C), and October 13 (286, 14.2 °C). Bacteria were collected using a size-fractionation approach3,4 designed to partition co-occurring strains on the basis of differential associations in the water column. Here, as in previous studies of the Vibrio3,4, bacteria were isolated by dilution series plating of material resuspended from 63 μm, 5 μm, 1 μm, and 0.2 μm size-fractions onto vibrio-selective media (MTCBS) for colony growth and serial purification. We purified 3,456 bacterial isolates comprised of 1,152 strains from each of 3 days, evenly distributed over the size-fractions. Samples collected for isolation of viruses were 0.2 μm-filtered to remove bacteria, flocculated by addition of iron chloride, and the flocs collected on 0.2 μm filters and re-dissolved in oxalate for storage at 4˚C (ref. 14). Using this approach, viable viruses in 1000x-fold concentrated seawater could be preserved for later isolation on bacterial isolates derived from the same time and place.

Agar overlay direct plating of concentrates for isolation of viruses

To isolate viruses on co-occurring hosts we used a quantitative agar-overlay approach that allowed for equal representation of both slow- and fast-growing viruses as follows. Viral concentrates equivalent to 15 ml of seawater (15 μl iron-oxalate concentrate) were mixed with host cultures to form agar-overlays within which discrete plaques could form and from which viruses could be isolated15. In total 1,334 purified bacterial strains were exposed, comprising >400 strains per isolation day and representing all isolation size-fractions; of these, 295 showed plaques. Agar overlays were performed using 150 μl of host overnight culture, 2 ml of molten top agar (52 °C, 0.4% agar, 5% glycerol, in 2216 marine broth [MB]), and bottom agar containing glycerol and chitin (1% agar, 5% glycerol, 125 ml L−1 of chitin supplement [40 g L−1 coarsely ground chitin, autoclaved, 0.2 um filtered] in 2216 MB). Glycerol was added to increase the visibility of plaques11, chitin was added to increase the probability of recovery of viruses dependent on chitin-induced receptors, and low density top agar was used to increase the probability of plaque formation by larger viruses16. Agar overlays were wrapped with plastic to reduce desiccation and held at room temperature for 14-16 days. Virus plaques were harvested at the end of the incubation period and archived by filtration of plaque eluates, as described in (ref. 15). Half of each eluate was stored at 4˚C, and half was preserved with glycerol (to a concentration of 25% glycerol) for storage at −20˚C.

Purification of viral strains

To build a diverse and representative collection of virus-host pairs, at least one randomly selected virus was purified from each bacterial strain for which plaques appeared in the agar overlay plating of environmental concentrate. To achieve this, we serially purified viruses recovered from archived material, prepared small-scale lysates to boost viral titer, and then generated high titer stocks by confluent lysis in agar overlays. Purification resulted in genome sequencing of 283 viral strains (from 251 independent plaques) from 246 hosts, described below. Viral and host strain naming conventions are described in Table 2, using examples of virus 1.008.O_10 N.286.54.E5 and host 10N.286.54.E5.

Table 2. Strain identifier nomenclature, using example virus 1.008.O_10N.286.54.E5 and host 10N.286.54.E5.

Name component Specific Description
1 A unique identifier for each independent plaque isolated from a given host from the initial exposure of a given host to an environmental virus concentrate.
008 A unique working ID for a host strain.
O A lineage generated from a single plaque during viral serial purification, for example due to the emergence of multiple plaque morphologies. Options: Single lineage: O; Sub-lineages: A, B, C, etc….
10N Year & site identifier (2010, Nahant).
286 Ordinal day.
54 A code representing the size-fraction of origin. Options: 0.2um: 45,46,47; 1um: 48,49,50; 5um: 51,52,53; 63um: 54,55,56. Note: Multiple codes within the size-fraction identifier reflect independent water samples for the 63um fraction, and independent water sample fractionation series for the other size classes (water sample A: 45,51,54; sample B: 46, 52, 55; sample C: 47, 53, 56).
E5 Unique storage well identifier.
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Genome sequencing

Viral genomes were prepared from lysates of the host of isolation, as follows. Lysates were concentrated on centrifugal filtration devices (Ultracel 30 K, Amicon Ultra, Millipore, UFC903024), washed with 1:100 2216MB, and concentrates treated with nucleases to digest unencapsidated nucleic acids (18 ml sample brought to 500 μl and amended with DNase I, RNase A, heated for 65 min at 37˚C). Nuclease-treated samples were extracted by addition of 0.1 final volume of SDS mix (0.25 M EDTA; 0.5 M Tris-HCl, pH 9.0; 2.5% sodium dodecyl sulfate), 30 min incubation at 65˚C, addition of 0.125 volumes 8 M potassium acetate, 60 min incubation on ice, addition of 0.5 volumes of phenol-chloroform, and recovery of nucleic acids from aqueous phase by isopropanol and ethanol precipitation. Illumina sequencing libraries of each extract were prepared as follows. Sample DNA (5 μg in 100 μl) was sheared by sonication (6 cycles of 5 min each at an interval of 30 sec on/off on the ‘Low Intensity’ setting of the Biogenode Bioruptor) to enrich for fragment sizes of ~300 bp. Sequencing constructs were prepared by end repair of sheared DNA, 0.72x/0.21x dSPRI size selection to enrich for ~300 bp sized fragments, ligation of Illumina adapters and unique pairs of forward and reverse barcodes for each sample, SPRI bead clean-up, nick translation, and final SPRI bead clean-up17. Constructs were enriched by PCR using paired-end (PE) primers following qPCR-based normalization of template concentrations. Enrichment PCRs were prepared in eight replicate 25 μl volumes, with the recipe: 1 μl Illumina construct template, 5 μl 5x Phusion polymerase buffer, 0.5 μl 10 mM dNTPs, 0.25 μl 40 μm IGA-PCR-PE-F primer, 0.25 μl 40 μm IGA-PCR-PE-R primer, 0.25 μl Phusion polymerase, 17.75 μl PCR-grade water. PCR thermocycling conditions were as follows: initial denaturation at 98 °C for 20 sec; batch dependent number of cycles of 98 °C for 15 sec, 60 °C for 20 sec, 72 °C for 20 sec; final annealing at 72 °C for 5 min; hold at 10 °C. For each sample 8 replicate enrichment PCR reactions were pooled and purified by 0.8x SPRI bead clean-up. Each sample was then checked by Bioanalyzer (2100 expert High Sensitivity DNA Assay) to confirm the presence of a unimodal distribution of fragments with a peak between 350-500 bp. Sequencing of viral genomes was distributed over 4 paired-end sequencing runs as follows: 1 lane on the Illumina HiSeq2000 (18 viral genomes; 100+100 nt paired-end reads; average of 5.1 million reads per genome), 3 lanes on the Illumina MiSeq (92-96 genomes per lane; 150+150 nt paired-end reads; average of 54 K, 208 K, 210 K reads per genome for each lane). Raw paired-end Illumina reads were imported and demultiplexed using CLC Genomics Workbench v.6.5.1 (https://www.qiagenbioinformatics.com/). Sequencing and assembly of genomes of bacterial hosts is described elsewhere13.

Genome assembly and curation

Differences in packaging strategies among viruses yield distinctive and characteristic distributions of packaged physical genomes in progeny virions18. Common examples of such strategies include production of virions with genomes that have: variable termini comprised of host DNA (Mu-like viruses); 5′ or 3′ single strand terminal overhangs (cos-viruses); or different start sequences and terminal redundancies ranging from 10 s to 10,000 s of bases (pac-viruses). To inform final curation of genome sequences, we first performed initial assemblies to group similar genomes and allow identification of the packaging-associated large subunit terminase gene (TerL) where possible. We then evaluated read mapping profiles within groups, considering terminase-predicted packaging strategy, to define final genome start sites. We next used an iterative approach, as described below, to standardize genome assemblies with conserved gene orders and genomic start positions for related viruses, and to place genomic termini at the contig ends.

Initial assembly and viral genome clustering

Initial assembly and clustering of viral genomes identified groups of related viruses (Supplementary Table 2), but also highlighted the need for systematic measures to standardize genome curation. Initial assembly and clustering were performed as follows: viral genomes were assembled using the de novo assembly tool in CLC Genomics WorkBench v.6.5.1 with default parameters following trimming of reads (default parameters except: quality score=0.01, ambiguous nucleotides=0). Open reading frames (ORFs) were identified using Prodigal19 with default parameters, and reciprocal best BLAST hits with ≥75% coverage of the longer sequence and e-value of ≤10−5 were clustered using OrthoMCL20. Viral genomes were clustered into genome groups on the basis of shared protein clusters using the FT algorithm of the ClustnSee21 plug-in in Cytoscape22. Preliminary curation of individual groups to assess synteny between closely related and replicate viruses (see Technical Validation) using LAST23 indicated that assemblies began at different locations, suggesting that virus genome characteristics were confounding consistency in contig start and end sites.

Final assembly and curation

To systematically address the inconsistency in contigs produced by assemblies of closely related viruses, assemblies were repeated and curated based on read mapping patterns and terminase similarities, as described below.

Viral genomes were re-assembled using the command clc_assembler from CLC Assembly Cell (version 4.4.2, https://www.qiagenbioinformatics.com/), using default assembly parameters and an insert size setting of 100 to 300 bp; 154 out of 285 assemblies resulted in one contiguous sequence (contig). For virus assemblies producing more than one contig, the highest coverage contig was extracted and considered the target viral genome contig; lower coverage contigs were considered contamination from host genome or prophages.

Viral genome open reading frames (ORFs) were identified using Prodigal version 2.6.1 with the -p meta flag to identify small ORFs24, and virus terminase protein sequences were identified by UBLAST25 search with a cutoff evalue<0.001 against a database of terminases from public viral genomes with previously described or predicted physical genomic termini18,25. Terminase identity was initially assessed via UBLAST as described above, and then verified via OrthoMCL clustering of terminase ORFs with the same dataset to gauge the fidelity of the BLAST results. To evaluate read coverage patterns in relation to terminases, original reads were mapped back to the contigs using the clc_mapper command with default parameters and per-base coverage was determined using SAMtools26 and BEDtools27. Consistent with previous findings that different terminases are associated with distinct genome packaging strategies18, and thus genome termini, exploratory evaluation of read coverage patterns showed that viruses with close identity to different known phage terminases also generally showed different read coverage patterns (Fig. 2a–d).

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

Figure 2

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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.

To standardize final gene order presentations, start and stop positions for each genome were defined manually, considering three criteria: 1) terminase identity, as identified by UBLAST and OrthoMCL clustering; 2) read coverage; and 3) comparison of contigs between viruses within the genome groups identified in the initial assembly. All members of each group were assigned to a common inferred genome packaging strategy category (see Supplementary Table 2 for details and exceptions) on the basis of overall patterns within the group, and rearranged using the approaches described below. Coverage patterns were determined by visual inspection and by a series of custom R scripts. Where possible, finalized virus genomes were quality checked by comparing the synteny of related phage genomes using command line LAST. A total of 283 virus genomes were assembled, including 251 unique viruses, 31 sub-lineages purified in parallel to the primary unique isolate, and 1 technical replicate (Table 1 (available online only)). We note that though we were guided by group-level coverage patterns, our primary aim was standardization rather than inference of true genome topology, which must be defined by individual genome read coverage patterns and complemented by laboratory studies.

Re-arrangement based on specific ORF

The majority of viral genomes (168/283) in the collection were standardized by circularizing the de novo assembled contigs and re-linearizing them at the start of the ORF upstream of the terminase. As a whole, these viruses showed coverage patterns consistent with a headful, or ‘pac’ site, based genome packaging strategy, wherein up to 110% genome-length monomers are sequentially cleaved from a multigenome-length concatemer, beginning from a conserved ‘pac’ site. Terminase best BLAST matches were dominated by similarity to viruses with headful-like strategies (Sf6, 97 best hits; 933W, 12; and T4, 5), though best hits to short direct terminal repeat (T7, 8) and 5′-cohesive ends (P2, 26) viruses were also identified, along with cases of no similarity to reference virus terminases (20). Read coverage patterns among these viruses were dominated by either a pattern of gradual decreases/shifts (112) consistent with a ‘headful’ or packaging site (‘pac’) – based genome packaging strategy, or even coverage (46); though other patterns of coverage including short peaks (cos pattern, 1; short internal peak, 7) and multiple coverage peaks (2) were also observed. Examination of read coverage following TerL-based rearrangement of contigs (Fig. 2e) often showed coverage maxima localized near the start, consistent with previous observations that headful-packaging viruses commonly have a pac site in or near the small subunit of the terminase gene18, which generally lies upstream of the TerL. Viruses curated using this approach included all the viruses from 7 of the preliminary groups (1, 4, 6, 9, 10, 13, 16), the majority of viruses from group 3, and a single virus from group 7.

Re-arrangement based on peaks or valleys in coverage

The second most commonly applied strategy for standardization (66/283) was circularization of contigs followed by re-linearization by cutting in the middle of a short region of either aberrantly low (36), or high (30), coverage (Fig. 2f,g). As a whole, these viruses showed patterns consistent with the presence of either direct terminal repeats (DTRs) or single-stranded cohesive (‘cos’) ends associated with their genome termini. Genomes with DTRs may yield sharply defined regions of elevated coverage. ‘cos’ genomes may yield regions of either high or low coverage, depending on whether they are 3′ or 5′ overhangs, due to low frequency ligation of ends during library preparation, as well as T4 DNA polymerase 3′ to 5′ exonuclease activity (degradation of 3′ overhangs) and 5′ to 3′ polymerase activity (endfill of 5′ overhangs) of unligated ends. Terminase best BLAST matches were dominated by similarity to viruses with cohesive ends (lambda ‘cos’, 22; HK97 ‘cos’-3′, 7; P2 ‘cos’-5′, 3) and DTRs (N4, 8; T7, 13), though best hits to headful viruses (933W, 4; P22, 1), were also identified, along with cases of no similarity to reference virus terminases (8). Read coverage patterns among these viruses were dominated by either distinctive ‘cos’ (32) or short internal peak (22) patterns, though other patterns of coverage including shifts in coverage (8), multiple coverage peaks (2), even coverage (1), or no pattern (1) were also observed. This approach included all virus genomes in preliminary groups 8, 14, and 18; the majority of viruses in groups 5, 7, 11, and 12; and a minority of viruses in groups 3 and 17.

Scaffolded assembly against reference

If viruses did not follow the patterns described above, but closely related members of the same group (identified as sharing 100% of translated proteins identified via reciprocal UBLAST) did follow a particular pattern, viruses were assembled using closely related strains as a scaffold; this approach was used for genomes in group 5 (3).

Maintenance of original de novo assembly

Singleton viruses with no similar members within the dataset were treated based on closest terminase identity and read coverage pattern, but if no distinct pattern was observed the original assemblies were maintained. This approach was used for 16/283 viruses, including viruses in groups 2 (8), 3 (1), 7 (5), 11 (1), and 12 (1).

Removal of terminal unconserved sequences

A subset of viruses (9/283) were found by BLAST comparison to possess Mu-like terminases, suggesting that they also used a Mu-like replicative transposition headful mechanism that incorporates host DNA upstream and downstream of the site of insertion. Read coverage patterns of initial assemblies of Mu-like viruses exhibited sharp drops in coverage at the termini followed by regions of low coverage (Fig. 2d), these regions of low coverage, representing small pieces of the host genome, were removed in the adjusted assemblies (Fig. 2h). However, closer evaluation of these assemblies revealed several cases of truncated sequences and final Mu-like virus assemblies were performed in CLC Genomics Workbench 8.5.1 as follows. Sequences were trimmed using the NGS Core Tools Trim Sequences tool with trims based on quality scores (limit 0.0001), number of allowable ambiguous nucleotides (max 0), and discard of reads <50 bases. All remaining read pairs and orphans were assembled using the De Novo Assembly tool with a word size of 64 and otherwise default options. The largest contig was extracted from the assembly for each virus and all genomes were aligned using the Geneious 6.0.6 Map to Reference tool to standardize orientation. Genome termini were defined based on the beginning and end of conserved regions at the left and right genome ends, respectively. This yielded 9 independently isolated genomes that were all 100% nucleotide identical and with a length of 31,617 bases, with the exception of virus 1.159.O, which contained a single SNP that was present in both the new and previous assembly versions. Open reading frames for these genomes were called with Prodigal 2.6.3 using the -p meta flag and otherwise default parameters.

Iterative assembly

A subset of the viruses (21/283), described elsewhere as a new family13, had distinctively short (~10 kb) genomes and did not contain predicted terminases. BLAST comparison of ORFs from these genomes showed similarity to the protein-primed DNA polymerase of viruses of the Tectiviridae, which have linear genomes and inverted terminal repeats (ITR), and thus these viruses were also evaluated for ITRs. Final assemblies for this group were performed iteratively, as follows. Following initial assembly, second and third assembly iterations were performed using an increased word size of 64, and the largest contig from the previous assembly was included as one of the “reads” for the successive round of assembly. The longest contigs from each of the three assemblies were then compared and the longest contig that also exhibited ITRs was used, when none of the contigs contained ITRs the longest assembled contig was determined to be the final assembly.

Annotation

Viral genomes were annotated using multiple approaches and tools, as described below. Genomes are available through Genbank (Data Citation 1).

Virfam classification of viral Types and Clusters and morphotypes

Viral proteins were annotated using the Virfam12 classifier, which identifies multiple genes of the head-neck-tail modules of viral genomes and assigns viral genomes to morphotypes within Types and Clusters on the basis of previous characterization of diverse tailed viruses. Annotation was performed individually per genome by submission to the Virfam webserver (http://biodev.cea.fr/virfam/). Output reports for all Virfam annotation runs are available through figshare (Data Citation 2).

Genome content annotation

Phage proteomes were compared to KEGG28, COG29, eggnog30, Pfam31, ACLAME32, CAMERA Viral Proteins (CVP)33 and the OM-RGC collection of sequences34 via UBLAST24. Annotations were determined as the best hit (maximum bit score) to a non-hypothetical protein from EggNOG, KEGG, COG, ACLAME or Pfam (minimum alignment of 75%, minimum percent identity of 35%). Best hits to remaining databases as well as CVP and OM-RGC are reported as notes within the final annotations. Annotations were combined with annotations identified using InterProScan version 5.17-56.0 using the iprlookup, goterms, and pathways options. InterProScan is a program from EMBL-EBI that uses the InterPro database for annotations. The InterPro database contains by default 13 databases, which are listed here: https://github.com/ebi-pf-team/interproscan/wiki/HowToRun#included-analyses. For these annotations, two optional databases were included: TMHMM for predicted transmembrane proteins and SignalP for predicted signal peptide cleavage sites. tRNA sequences were identified using tRNAscan-SE version 1.23 (ref. 35) using the general tRNA model (-G). CRISPR-like elements were identified using CRT36.

Portal protein phylogeny

Portal proteins were identified directly using the Virfam classifier as described above, which provides a portal prediction, as well as by using HMM- and blastp-based searches of all Nahant Collection virus proteins, as follows. The portal protein for the representative virus of each Virfam cluster was downloaded through the Virfam page (http://biodev.cea.fr/virfam/), and an HMM generated by performing 3 iterations of Jackhmmer37 https://www.ebi.ac.uk/Tools/hmmer/search/jackhmmer. Searches of the Nahant Collection virus proteins with this collection of HMMs using the hmmsearch38 tool (hmmer version 3.1b2) identified putative portal proteins in 241 genomes, these 241 together with 6 portal proteins identified directly through the Virfam web page, were used to search the Nahant Collection with blastp39, identifying putative portal proteins in 262 of the 263 Caudovirales (e value <0.0001). In the 2 cases where the predicted portal proteins differed across the two methods (Supplementary Table 3), HHpred as implemented in the MPI bioinformatics Toolkit40 (https://toolkit.tuebingen.mpg.de/#/tools/hhpred) was used to evaluate both predictions and the protein with the longer sequence similarity to a portal protein was selected. The portal protein in virus 1.031.O could only be predicted using the Virfam approach and this protein was included, though HHpred and Phyre2 (ref. 41) based structural similarity based searches did not indicate similarity to known portal proteins. Sequence alignment, trimming, and tree-building were performed using the eggnog41 workflow in the ETE3 (ref. 42) version 3.0.0b36 tree building tool, the tree was visualized using iTOL43, and the figure prepared using Adobe Illustrator.

Data Records

All virus and host-associated sequences and annotations associated with this work have been deposited to the Nahant Collection NCBI BioProject (Data Citation 1), specific accession numbers for each strain are provided in Supplementary Table 1. Viral genome annotation reports generated by the Virfam tool have been deposited with figshare (Data Citation 2).

Technical Validation

Given the known abundance of prophages in bacterial genomes we evaluated whether any viruses in the collection represented induced prophages from the host of isolation. Using megaBLAST in Geneious 6.1.8 we searched all virus genomes against all sequenced hosts, we identified only a single case of a high query cover and high identity match. The virus 1.202.O (32,014 bp) shared a 30,051 bp 100% identity match with its host 10N.222.45.E8; this match region occurred within a larger host contig of 120,557 bp, suggesting that the failure to achieve a full match with the remaining 1,963 bp region of the virus genome contig was not due to incomplete assembly of the associated host region. Full genomes for the host of isolation were not available for 29 viruses and thus this prophage derivation could not be assessed for these strains, information on host sequence availability is provided in Supplementary Table 1.

This dataset contained sets of virus pairs and triplets that served as biological replicates for assembly optimization. Such sets derive from instances of independent purification of viral sub-lineages from a parent plaque due to the occurrence of variable plaque morphology. Though they exhibited sites of polymorphism at the nucleotide level, ranging from 0 to 4 SNPs, and indels of up to 201 bp (Table 3), members of these sets consistently showed identical gene content and are expected to have the same genomic structure and gene order. Methods for rearrangement to maintain synteny were developed around such sets and were verified via alignment of similar/duplicate genomes before and after rearrangement (Supplementary Figures 1–4).

Table 3. Replicate virus genome comparisons.

Phage Query Query Length Subject Subject Length Query Mismatch (bp) Subject Mismatch (bp) ANI SNP (bp) inDEL (bp) Start Variation (bp) Length Variation (bp) MAFFT Alignment # of diffs
1.021 A 43,743 B 43,743 1 1 0.9999771 0 0 0 0 0
1.021 A 43,743 C 43,743 2 2 0.9999543 1 0 0 0 0
1.021 B 43,743 C 43,743 2 2 0.9999543 0 0 0 0 0
1.107 B 10,447 C 10,447 1 0 0.9999521 0 0 0 0 0
1.107 B 10,447 A 10,447 3 2 0.9997607 2 0 0 0 2
1.107 C 10,447 A 10,447 3 2 0.9997607 2 0 0 0 2
1.111 A 40,209 B 40,209 10 9 0.9997637 0 0 9 0 0
1.115 B 37,416 A 37,416 2 3 0.9999332 1 0 1 0 0
1.118 B 60,458 A 60,458 5 5 0.9999173 4 0 0 0 4
1.122 A 44,523 B 44,523 3 4 0.9999214 2 0 1 0 2
1.139 B 44,094 A 43,893 6 1 0.9999204 0 201 48 201 201
1.188 A 72,305 B 72,305 2 3 0.9999654 0 0 2 0 0
1.188 A 72,305 C 72,305 2 3 0.9999654 0 0 2 0 0
1.188 B 72,305 C 72,305 1 1 0.9999862 0 0 0 0 0
1.189 B 36,855 O 36,855 4 3 0.9999050 2 0 1 0 2
1.189 B 36,855 C 36,855 4 4 0.9998915 3 0 0 0 3
1.189 O 36,855 C 36,855 2 3 0.9999322 1 0 1 0 1
1.198 B 44,343 A 44,472 2 43 0.9994933 1 129 0 129 130
1.199 B 48,312 A 48,312 4 4 0.9999172 3 0 0 0 3
1.211 A 37,169 B 37,169 1 1 0.9999731 0 0 0 0 0
1.215 B 80,834 A 80,834 1 2 0.9999814 0 0 1 0 0
1.233 B 36,823 A 36,823 2 1 0.9999593 0 0 1 0 0
1.237 B 60,160 A 60,097 64 3 0.9994429 0 63 1 63 64
1.238 A 70,467 B 70,494 19 20 0.9997233 0 27 19 27 27
1.247 B 43,896 A 43,896 3 2 0.9999430 1 0 1 0 1
1.249 B 10,611 A 10,611 1 0 0.9999529 0 0 0 0 0
1.263 B 49,640 A 49,640 11 12 0.9997683 2 0 9 0 0
1.268 A 59,297 B 59,297 3 3 0.9999494 2 0 0 0 2
1.270 B 59,297 A 59,297 3 2 0.9999578 1 0 1 0 1
1.271 B 59,297 A 59,297 3 3 0.9999494 2 0 0 0 2
1.277 A 59,419 B 59,297 3 21 0.9997978 1 122 1 122 123
1.283 A 59,530 C 59,530 3 2 0.9999580 1 0 0 0 1
1.283 A 59,530 B 59,530 1 1 0.9999832 0 0 0 0 0
1.283 C 59,530 B 59,530 2 3 0.9999580 1 0 0 0 1
2.095 B 44,649 A 44,649 3 4 0.9999216 2 0 1 0 2
2.159 A 31,617 B 31,617 0 0 1.0000000 0 0 0 0 0
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Additional information

How to cite this article: Kauffman, K. M. et al. Viruses of the Nahant Collection, characterization of 251 marine Vibrionaceae viruses. Sci. Data 5:180114 doi: 10.1038/sdata.2018.114 (2018).

Publisher’s note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary Material

sdata2018114-isa1.zip (11.2KB, zip)
Supplementary Information
sdata2018114-s2.pdf (383.2KB, pdf)
Supplementary Table 1
sdata2018114-s3.xls (124KB, xls)
Supplementary Table 2
sdata2018114-s4.xlsx (25.1KB, xlsx)
Supplementary Table 3
sdata2018114-s5.xlsx (57.4KB, xlsx)

Acknowledgments

We thank members of the Polz lab for assistance with sampling and strain isolation, especially Michael Cutler, Tara Soni, Alison Takemura, Gitta Szabo, Hong Xue, Otto Cordero, Nisha Vahora, Aidong Ruan, and Hans Wildschutte, as well as Robert Ratzlaff (ODU). We also thank Simon Labrie (U. Laval) for guidance in viral genome extractions and sequencing library preparation protocols; Raphael Guerois (CEA - IBITECS) for assistance with VirFam; and Will Chang (Einstein) for assistance with genome curation. This work was supported by grants from the National Science Foundation OCE 1435993 and 1435868 to M.P. and L.K., respectively, and the WHOI Ocean Ventures Fund to K.M.K.

Footnotes

The authors declare no competing interests.

Data Citations

  1. 2016. GenBank. MG592390-MG592672
  2. Kauffman K. M., et al. . 2018. figshare. https://dx.doi.org/10.6084/m9.figshare.c.4028239

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Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Data Citations

  1. 2016. GenBank. MG592390-MG592672
  2. Kauffman K. M., et al. . 2018. figshare. https://dx.doi.org/10.6084/m9.figshare.c.4028239

Supplementary Materials

sdata2018114-isa1.zip (11.2KB, zip)
Supplementary Information
sdata2018114-s2.pdf (383.2KB, pdf)
Supplementary Table 1
sdata2018114-s3.xls (124KB, xls)
Supplementary Table 2
sdata2018114-s4.xlsx (25.1KB, xlsx)
Supplementary Table 3
sdata2018114-s5.xlsx (57.4KB, xlsx)

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