Evidence of host-virus co-evolution in tetranucleotide usage patterns of bacteriophages and eukaryotic viruses

Abstract

Background: Virus taxonomy is based on morphologic characteristics, as there are no widely used non-phenotypic measures for comparison among virus families. We examined whether there is phylogenetic signal in virus nucleotide usage patterns that can be used to determine ancestral relationships. The well-studied model of tail morphology in bacteriophage classification was used for comparison with nucleotide usage patterns. Tetranucleotide usage deviation (TUD) patterns were chosen since they have previously been shown to contain phylogenetic signal similar to that of 16S rRNA.

Results: We found that bacteriophages have unique TUD patterns, representing genomic signatures that are relatively conserved among those with similar host range. Analysis of TUD-based phylogeny indicates that host influences are important in bacteriophage evolution, and phylogenies containing both phages and their hosts support their co-evolution. TUD-based phylogeny of eukaryotic viruses indicates that they cluster largely based on nucleic acid type and genome size. Similarities between eukaryotic virus phylogenies based on TUD and gene content substantiate the TUD methodology.

Conclusion: Differences between phenotypic and TUD analysis may provide clues to virus ancestry not previously inferred. As such, TUD analysis provides a complementary approach to morphology-based systems in analysis of virus evolution.

Figure 1

Tetranucleotide difference analysis of representative bacteriophage genomes (H. influenzae phage HP1, B. cepaciae phage 781, and Enterobacteria phage Mu). Tetranucleotide differences were determined with window and step sizes of 5,000 and 1,000, respectively, and Z-scores were determined as described in Materials and Methods. Solid black lines represent Z-scores of ± 3.

Figure 2

Frequency distribution of DNA tetranucleotide usage profiles of selected bacteriophages. The observed/expected TUD was determined for the 256 tetranucleotide combinations for each genome, as described in Materials and Methods. The resulting values were sorted within 0.25 intervals and the ordinate represents the number of tetranucleotide combinations within each interval. Panel A: Blue – All bacteriophages studied. Panel B: Red – Enterobacteria phage HK022 (Siphoviridae), Green – Enterobacteria phage P2 (Myoviridae), Blue – Shigella phage V (Podoviridae). Panel C: Red – Enterobacteria phage HK022, Green – Mycobacterium phage Bxz1 (Myoviridae), Blue – Mycobacterium phage Corndog (Siphoviridae).

Figure 3

Linear regression analysis of DNA tetranucleotide usage profiles among selected genomes. Each of the 256 tetranucleotide combinations were determined for each genome as described in Materials and Methods, and the profiles compared by linear regression analysis. Panels A: Enterobacteria phage HK022 (Siphoviridae) vs. P2 (Myoviridae). Panel B: Enterobacteria phage HK022 vs. Mycobacterium phage Bxz1 (Myoviridae). Panel C: Streptococcus pneumoniae phage EJ1 (Myoviridae) vs. MM1 (Siphoviridae). Panel D: Mycobacterium phage Bxz1 vs. Corndog (Siphoviridae).

Figure 4

Phylogram of 83 selected bacteriophages for which genomic sequences are available. The organisms were grouped by using distance matrices based on the sums of the differences from the other organisms for the 256 tetranucleotide combinations, as described in Materials and Methods. Phylogenies were created by neighbor-joining analysis. Colors indicate Myoviridae (contractile tails; blue), Podoviridae (short tail stubs; green), and Siphoviridae (long tails; red). Bootstrap values >50 based on 100 replicates are represented at each node, and the branch length index is indicated below the phylogeny. Bacteriophage source by host species – gram-positive bacilli, gram-positive cocci, gram-negative enterobacteria, and gram-negative non-enterobacteria are indicated by brackets.

Figure 5

Likelihood analysis of phylogenetic congruence between the bacteriophage TUD phylogeny shown in Figure 4 and random trees. The 99^th percentile of the likelihood differences between the TUD tree and the topologies from 1000 random trees is indicated by the vertical dashed line. The position of the TUD phylogeny (indicated by the arrow) is substantially outside of the null distribution.

Figure 6

Phylogram of 39 selected bacteria and 83 selected bacteriophages for which genomic sequences are available. The organisms were grouped by using distance matrices based on the sums of the differences from the other organisms for the 256 tetranucleotide combinations, as described in Materials and Methods. Phylogenies were created by neighbor-joining analysis. Colors indicate bacteriophages (red), bacteria (green), and bacteriophages that are substantially beyond their presumed distribution (blue). Bootstrap values >50 based on 100 replicates are represented at each node, and branch length index is indicated below the phylogeny. Phages isolated in gram-positive bacilli, gram-positive cocci, gram-negative enterobacteria, and gram-negative non-enterobacteria are indicated by the brackets.

Figure 7

Phylogram of 90 selected viruses for which genomic sequences are available. The organisms were grouped by using distance matrices based on the sums differences from the other organisms for the 256 tetranucleotide combinations, as described in Materials and Methods. Phylogenies were created by neighbor-joining analysis. Colors indicate double stranded DNA viruses (red); single stranded DNA viruses (yellow); retroviruses (green); negative-sense single stranded RNA viruses (blue); positive-sense single stranded RNA viruses (sky blue); and double stranded RNA viruses (black). Bootstrap values >50 based on 100 replicates are represented at each node, and branch length index is indicated below the phylogeny.

Figure 8

Phylograms of 90 selected viruses for which genomic sequences are available. The organisms were grouped according to distance matrices based on the number of shared orthologues between each genome, as described in Materials and Methods. Phylogenies were created by neighbor-joining analysis. Color code as is for Figure 7. The branch length index is indicated below the phylogeny.