LTR retrotransposons phylogenetic tree

Three frame translation of INTERNAL sequences was employed, and hmmsearch (e value ≤10^− 6) was used to search the profile of Gypsy-like RT (PF00078) and Copia-like RT (PF07727). RT domain amino acid sequences longer than 100 aa were retrieved from the translation. We chose one typical RT sequence from each family, and premature stop codons were eliminated from the sequences. Combined with the representatives we collected from the previous studies, Muscle was used to align the RT sequences. MEGA6 [45] (default parameters) was used to construct phylogenetic tree with neighbor-joining method.