title: 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.
authors.affiliation: State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, Hubei Province, P R China.
authors.forename: Huiquan
authors.initials: H
authors.lastname: Liu
authors.forename: Yanping
authors.initials: Y
authors.lastname: Fu
authors.forename: Bo
authors.initials: B
authors.lastname: Li
authors.forename: Xiao
authors.initials: X
authors.lastname: Yu
authors.forename: Jiatao
authors.initials: J
authors.lastname: Xie
authors.forename: Jiasen
authors.initials: J
authors.lastname: Cheng
authors.forename: Said A
authors.initials: SA
authors.lastname: Ghabrial
authors.forename: Guoqing
authors.initials: G
authors.lastname: Li
authors.forename: Xianhong
authors.initials: X
authors.lastname: Yi
authors.forename: Daohong
authors.initials: D
authors.lastname: Jiang
mesh_terms: D001483:Base Sequence; D016000:Cluster Analysis; D019295:Computational Biology; D004267:DNA Viruses / Q000235:genetics*; D004277:DNA, Single-Stranded / Q000235:genetics*; D004279:DNA, Viral / Q000235:genetics*; D030541:Databases, Genetic; D056890:Eukaryota / Q000235:genetics* / Q000821:virology; D019143:Evolution, Molecular; D022761:Gene Transfer, Horizontal / Q000235:genetics*; D008957:Models, Genetic; D008969:Molecular Sequence Data; D010802:Phylogeny; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA
chemical_list: D004277:DNA, Single-Stranded; D004279:DNA, Viral