Phylogeny:AP LTR retroelements

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Method of phylogenenetic reconstruction

Phylogenetic reconstruction inferred based on the protease protein (AP) -encoded by the pol internal region common to Ty3/Gypsy, Retroviridae, Bel/Pao, Caulimoviridae and Ty1/Copia LTR retroelement families- and on a second non-pol protease-like domain, encoded by the ORF7 of three soymoviruses and by the C-terminus of CSVMV-ORF I Cavemovirus (downstream to the MOV region) (highlighted in red). The tree has been reconstructed using Felsenstein´s protein sequence parsimony method based on (Eck and Dayhoff 1966) and (Fitch 1971) to generate a majority-rule consensus tree (Margush and McMorris 1981). As majority-rule consensus tree usually consists of all groups that occur more than 50% of the time, we take consensus values upper to 50 as an equivalent-bootstrapping reference

 




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Llorens, C., Futami, R., Covelli, L., Dominguez-Escriba, L., Viu, J.M., Tamarit, D., Aguilar-Rodriguez, J. Vicente-Ripolles, M., Fuster, G., Bernet, G.P., Maumus, F., Munoz-Pomer, A., Sempere, J.M., LaTorre, A., Moya, A. (2011) The Gypsy Database (GyDB) of Mobile Genetic Elements: Release 2.0 Nucleic Acids Research (NARESE) 39 (suppl 1): D70-D74 doi: 10.1093/nar/gkq1061

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