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. 2019 Apr 9;10(4):285. doi: 10.3390/genes10040285

Figure 3.

Figure 3

RT phylogenetic tree of Copia and representative members of the Copia lineages. Maximum-likelihood tree with representative RT sequences of each family and the representative members of Copia lineages. In the tree, each family is marked by its name. Representative sequences that were reported in previous studies were selected. Nucleotide sequences of RT of the individual families were aligned by MUSCLE (v.3.8.31). After best-fit models were evaluated by MEGA6, these sequences were used to construct the phylogenetic trees based on the maximum-likelihood method. The entire lineages are shown with different colors: Red, TNT1; Sapphire, TAR; Purple, Angela; Pale purple, Maximus; Black, Ivana; Green, COP21; Orange, TOS17; and Emerald green, Ale. Locus name of representative members of Copia lineages in Repbase (https://www.girinst.org/): ATCopia78_I, TORTL1, ATCopia95_I, RIRE1_I, SHACOP_I_MT, SHACOP3_I_MT, PDR1_I, and COP21_I_MT.