Continuous Influx of Genetic Material from Host to Virus Populations

Abstract

Many genes of large double-stranded DNA viruses have a cellular origin, suggesting that host-to-virus horizontal transfer (HT) of DNA is recurrent. Yet, the frequency of these transfers has never been assessed in viral populations. Here we used ultra-deep DNA sequencing of 21 baculovirus populations extracted from two moth species to show that a large diversity of moth DNA sequences (n = 86) can integrate into viral genomes during the course of a viral infection. The majority of the 86 different moth DNA sequences are transposable elements (TEs, n = 69) belonging to 10 superfamilies of DNA transposons and three superfamilies of retrotransposons. The remaining 17 sequences are moth sequences of unknown nature. In addition to bona fide DNA transposition, we uncover microhomology-mediated recombination as a mechanism explaining integration of moth sequences into viral genomes. Many sequences integrated multiple times at multiple positions along the viral genome. We detected a total of 27,504 insertions of moth sequences in the 21 viral populations and we calculate that on average, 4.8% of viruses harbor at least one moth sequence in these populations. Despite this substantial proportion, no insertion of moth DNA was maintained in any viral population after 10 successive infection cycles. Hence, there is a constant turnover of host DNA inserted into viral genomes each time the virus infects a moth. Finally, we found that at least 21 of the moth TEs integrated into viral genomes underwent repeated horizontal transfers between various insect species, including some lepidopterans susceptible to baculoviruses. Our results identify host DNA influx as a potent source of genetic diversity in viral populations. They also support a role for baculoviruses as vectors of DNA HT between insects, and call for an evaluation of possible gene or TE spread when using viruses as biopesticides or gene delivery vectors.

Fig 1. Sequencing depth (number of reads covering a position) along four host TEs found inserted into genomes of AcMNPV populations infecting T. ni or S. exigua moths.

Grey curves represent sequencing depth by reads composed of host TE sequences only. Red curves represent chimeric reads whose right parts are composed of TE sequences (the left part being viral sequences) and green curves represent reads whose left parts are composed of TE sequences. Right and green curves thus respectively represent sequencing depths at junctions involving the left and right ends of a TE. The junctions at each end result from transposition at many viral sites, for which a sequence conservation logo is shown. Conserved bases correspond to known target sites of TE families (which are specified next to the host TE names). Black arrows indicate the locations and orientations of putative transposase genes along TEs. Sequencing depth of other moth contigs and sequence conservation logos of other host-virus junctions are provided in S3 and S4 Figs.

Fig 2. Length distribution of microhomology motifs found at 434 junctions between moth and AcMNPV baculovirus sequences.

The observed distribution is shown in red and the distribution expected by chance is shown in grey. An example of a five base-pair microhomology motif between an integrated moth sequence and the AcMNPV genome is shown at the top right corner of the graph. Negative microhomology lengths correspond to junctions characterized by the presence of 1 to 2 nucleotides that did not originate from either the host or viral genomes.

Fig 3. Patterns of moth DNA sequence integration along the circular AcMNPV baculovirus genome.

A. Distribution of independent moth sequence integrations through transposition (black bars) and microhomology-mediated recombination (red bars) in 500-bp contiguous windows. The blue and grey bar plots respectively illustrate the number of the most frequent transposon target motifs (TTAA, TAA, TTA, TA) and the average sequencing depth in these windows. Beige arrows represent AcMNPV genes. B. Correlation between the numbers of T. ni and S. exigua sequences integrated by transposition in 1500-bp contiguous windows of the AcMNPV genome. Each point on the plot represents a window.

Fig 4. Timetree of various insect species in which we found evidence for horizontal transfer of Spodoptera exigua (A) or/and Trichoplusia ni (B) transposable elements (TEs) found integrated in one or more AcMNPV populations.

Names of contig containing TEs correspond to those in S4 and S5 Tables. Black dots indicate that we have found a Blastn hit aligning with at least 85% nucleotide identity over at least 100 bp to a S. exigua or T. ni TE. For example, the figure shows that the S. exigua contig called Spodo_Contig_23 (which is a piggybac TE according to S4 Table) was horizontally transferred between S. exigua, Danaus plexipus and Glossina fusciceps. Numbers on top of contig names indicate the level (or range) of nucleotide identity between each S. exigua or T. ni TE and their Blastn hit(s) in other species (in percentages). Numbers between brackets at the right of taxa names are the average percent similarities for 11 conserved genes between S. exigua or T. ni and the other species. These percent similarities are derived from synonymous distances (dS) calculated for each gene and are equal to (1 –dS) × 100. All distances are provided in S4 and S5 Tables. Divergence times were taken from refs [–46]. Divergence times between Nymphalidae species are unknown and were set arbitrarily at 50 million years for illustrative purposes. *Species known to be susceptible to AcMNPV [29].