title: Use of endogenous retroviral sequences (ERVs) and structural markers for retroviral phylogenetic inference and taxonomy.
abstract: BACKGROUND
  Endogenous retroviral sequences (ERVs) are integral parts of most eukaryotic genomes and vastly outnumber exogenous retroviruses (XRVs). ERVs with a relatively complete structure were retrieved from the genetic archives of humans and chickens, diametrically opposite representatives of vertebrate retroviruses (over 3300 proviruses), and analyzed, using a bioinformatic program, RetroTector, developed by us. This rich source of proviral information, accumulated in a local database, and a collection of XRV sequences from the literature, allowed the reconstruction of a Pol based phylogenetic tree, more extensive than previously possible. The aim was to find traits useful for classification and evolutionary studies of retroviruses. Some of these traits have been used by others, but they are here tested in a wider context than before.
  
  
  RESULTS
  In the ERV collection we found sequences similar to the XRV-based genera: alpha-, beta-, gamma-, epsilon- and spumaretroviruses. However, the occurrence of intermediates between them indicated an evolutionary continuum and suggested that taxonomic changes eventually will be necessary. No delta or lentivirus representatives were found among ERVs. Classification based on Pol similarity is congruent with a number of structural traits. Acquisition of dUTPase occurred three times in retroviral evolution. Loss of one or two NC zinc fingers appears to have occurred several times during evolution. Nucleotide biases have been described earlier for lenti-, delta- and betaretroviruses and were here confirmed in a larger context.
  
  
  CONCLUSIONS
  Pol similarities and other structural traits contribute to a better understanding of retroviral phylogeny. "Global" genomic properties useful in phylogenies are i.) translational strategy, ii.) number of Gag NC zinc finger motifs, iii.) presence of Pro N-terminal dUTPase (dUTPasePro), iv.) presence of Pro C-terminal G-patch and v.) presence of a GPY/F motif in the Pol integrase (IN) C-terminal domain. "Local" retroviral genomic properties useful for delineation of lower level taxa are i.) host species range, ii.) nucleotide compositional bias and iii.) LTR lengths.
authors.affiliation: Department of Medical Sciences, Uppsala University, Uppsala, Sweden. Patric.Jern@medsci.uu.se
authors.forename: Patric
authors.initials: P
authors.lastname: Jern
authors.forename: Göran O
authors.initials: GO
authors.lastname: Sperber
authors.forename: Jonas
authors.initials: J
authors.lastname: Blomberg
mesh_terms: D020077:Endogenous Retroviruses / Q000235:genetics*; D015683:Gene Products, gag / Q000737:chemistry; D015684:Gene Products, pol / Q000737:chemistry; D016679:Genome, Viral; D010802:Phylogeny; D014176:Protein Biosynthesis; D011755:Pyrophosphatases / Q000378:metabolism; D012190:Retroviridae / Q000145:classification*; D020079:Terminal Repeat Sequences; D016335:Zinc Fingers
chemical_list: D015683:Gene Products, gag; D015684:Gene Products, pol; D011755:Pyrophosphatases; C020020:dUTP pyrophosphatase