Widespread horizontal gene transfer from circular single-stranded DNA viruses to eukaryotic genomes

Abstract

Background: In addition to vertical transmission, organisms can also acquire genes from other distantly related species or from their extra-chromosomal elements (plasmids and viruses) via horizontal gene transfer (HGT). It has been suggested that phages represent substantial forces in prokaryotic evolution. In eukaryotes, retroviruses, which can integrate into host genome as an obligate step in their replication strategy, comprise approximately 8% of the human genome. Unlike retroviruses, few members of other virus families are known to transfer genes to host genomes.

Results: Here we performed a systematic search for sequences related to circular single-stranded DNA (ssDNA) viruses in publicly available eukaryotic genome databases followed by comprehensive phylogenetic analysis. We conclude that the replication initiation protein (Rep)-related sequences of geminiviruses, nanoviruses and circoviruses have been frequently transferred to a broad range of eukaryotic species, including plants, fungi, animals and protists. Some of the transferred viral genes were conserved and expressed, suggesting that these genes have been coopted to assume cellular functions in the host genomes. We also identified geminivirus-like and parvovirus-like transposable elements in genomes of fungi and lower animals, respectively, and thereby provide direct evidence that eukaryotic transposons could derive from ssDNA viruses.

Conclusions: Our discovery extends the host range of circular ssDNA viruses and sheds light on the origin and evolution of these viruses. It also suggests that ssDNA viruses act as an unforeseen source of genetic innovation in their hosts.

Figure 1

Integrated plasmid or virus-like genes in Phytophthora sp. (A) and Giardia intestinalis (B). Arrowhead boxes indicate ORFs (orange, Rep-like genes; other colors, unknown genes). Gray sectors connect corresponding homologous regions and the % nucleotide (nt) or amino acid (aa) identity are indicated. The annotated ORF names or accession numbers are indicated. ψ, interrupted ORF.

Figure 2

Circovirus-like sequences in dog and cat genome were validated by PCR amplification and sequencing. PCR products were fractionated by gel electrophoresis on 1% agarose gels and stained with ethidium bromide. Marker, DNA marker DL 2000. The sequences of bands of the expected sizes from lanes: Chr 5, Chr 22, 071, and 274 were deposited under Genbank accession numbers: JF414126-JF414131.

Figure 3

Genomic comparisons showing the endogenous viral sequences inserted into coding regions of host genes. Rectangular boxes with arrowheads indicate genes (Red, viral Rep-like genes; blue, host genes). Gray sectors connect corresponding homologous regions and the % nucleotide (nt) identity scores are indicated.

Figure 4

Phylogeny of geminiviral Rep-like sequences from eukaryotes, known viruses, plasmids and phytoplasma. The phylogenetic tree was built using PhyML-mixtures based on a multiple sequence alignment generated using COBALT with the Constraint E-value parameter setting to 0.1. This tree was rooted with circoviruses and nanoviruses. The topology of blue asterisk marked clade was evaluated independently. Only p-values of the approximate likelihood ratios (SH-test) > 0.5 (50%) are indicated. scale bars correspond to 0.5 amino acid substitutions per site. Sequence accession numbers are given for each sequence.

Figure 5

Genomic organization of ssDNA virus-like transposons in fungi (A) and lower eukaryotes (B). (A) The genomic organization of geminivirus-like transposon in Tuber melanosporum. Arrowhead boxes indicate ORFs (orange, Rep-like gene; blue, transposase gene). The black vertical lines in the arrowhead boxes indicate stop codons. Green rectangular box indicates microsatellite sequence. The sequence of terminal inverted repeat (TIR) is shown at the top to the right. (B) The genomic organization and comparison of parvovirus-like transposon with related exogenous planaria virus. Yellow arrowhead boxes indicate Rep-like ORFs. Swallow tails indicate terminal inverted repeats (TIRs). The annotated ORF names are indicated. Purple rectangular boxes indicate protein domains and the domain family names are shown: Parvo_NS1, Parvovirus non-structural protein NS1 (pfam01057); Parvo_coat_N, Parvovirus coat protein VP1 (pfam08398); PPV_E1_C, Papillomavirus helicase (pfam00519). Gray sectors connect corresponding homologous regions and the % nucleotide (nt) or amino acid (aa) identity are indicated. The Planaria asexual strain-specific virus-like element has not been found to integrate in the host genome.

Figure 6

Organization and transcription maps of endogenous viral Rep-like genes. Blue arrowhead boxes indicate Rep-like ORFs. Similar regions of expressed sequences are identified and the % nt identity with endogenous viral sequences are indicated. Note that the actual endogenous viral sequence extended beyond the ORF in two contigs (AAFB02000406.1 and AAFB02000468.1) of Entamoeba histolytica.

Figure 7

A tree of eukaryotes showing the known distribution of endogenous viral-like sequences and exogenous circo-, nano- and geminivirus like viruses. This tree was drawn base on The Tree of Life Web Project (http://tolweb.org/).