Comparative analysis of the retroviral pol and env protein sequences reveal different evolutionary trees

Phylogenetic trees of two different retroviral gene products were constructed by using the progressive alignment method. The reverse transcriptase domain and the amino-terminal region of the transmembrane env protein, including the fusagenic peptide domain of at least one member of each of the established retrovirus subfamilies or groups, were separately aligned. The resulting phylogenetic tree of the reverse transcriptase was compared to that of the transmembrane protein. The similarities and differences are discussed with respect to the genetic events that occurred during the evolution of retroviruses. A segment of the central part of the viral env protein sequence was found to have 22% to 37% homology with some members of the immunoglobulin superfamily.