title: Phylogenetic analyses of 55 retroelements on the basis of the nucleotide and product amino acid sequences of the pol gene.
abstract: Comparisons of pol gene nucleotide and reverse transcriptase (RT) amino acid sequences of 47 retroviruses, 3 caulimoviruses, and 5 hepadnaviruses showed that approximately one-third of the gene at the 5' end is much more conserved than other pol regions. The most conserved regions on both the nucleotide and amino acid sequences were chosen for construction of phylogenetic trees. The maximum-parsimony and distance-matrix methods were used for analyses of aligned amino acid sequences; these two methods, and the compatibility method, were used to analyze the aligned nucleotide sequences. Essentially identical majority-rule consensus trees were produced by these different methods from both the pol gene nucleotide and RT amino acid sequences, which divided the 55 retroelements into six major groups. The reliability of the phylogenetic trees was probed with the bootstrapping of 100 replicates of the original sequence alignments. The grouping results were shown to be statistically significant by multiple comparisons with the least-significant-difference procedure.
authors.affiliation: Institute of Human Genetics, University of Minnesota, USA.
authors.forename: M D
authors.initials: MD
authors.lastname: Li
authors.forename: D L
authors.initials: DL
authors.lastname: Bronson
authors.forename: T D
authors.initials: TD
authors.lastname: Lemke
authors.forename: A J
authors.initials: AJ
authors.lastname: Faras
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D005075:Biological Evolution; D017796:Caulimovirus / Q000235:genetics; D017124:Conserved Sequence; D015684:Gene Products, pol / Q000737:chemistry* / Q000235:genetics; D015751:Genes, pol; D015613:Hepadnaviridae / Q000235:genetics; D008969:Molecular Sequence Data; D010802:Phylogeny; D012194:RNA-Directed DNA Polymerase / Q000235:genetics; D012190:Retroviridae / Q000145:classification / Q000235:genetics*; D016415:Sequence Alignment; D017386:Sequence Homology, Amino Acid; D012984:Software; D014779:Virus Replication / Q000235:genetics
chemical_list: D015684:Gene Products, pol; D012194:RNA-Directed DNA Polymerase