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Fig. 3 | BMC Genomics

Fig. 3

From: Construction of anti-codon table of the plant kingdom and evolution of tRNA selenocysteine (tRNASec)

Fig. 3

Phylogenetic tree of tRNASec and other tRNA isotypes. The phylogenetic tree with 21 tRNA isotypes revealed at least 28 major phylogenetic groups where tRNASec (red) was placed with different tRNA isotypes. The phylogenetic tree indicates that tRNA has most likely evolved from multiple common ancestors and has also undergone duplication. The evolutionary history was inferred using the Maximum Likelihood method based on the Kimura 2-parameter model. The tree with the highest log likelihood (− 7466.51) is illustrated. The percentage of the branches in which the associated taxa cluster together is shown next to the branches. Initial tree(s) for the heuristic search were automatically obtained applying the Neighbor-Join and BIONJ algorithms to a matrix of pairwise distances estimated using the Maximum Composite Likelihood (MCL) approach, and then selecting the topology with a superior log likelihood value. A discrete Gamma distribution was used to model evolutionary rate differences among the sites [5 categories (+G, parameter = 2.6875)]. The tree is drawn to scale, with branch lengths representing the number of substitutions per site. The analysis utilized 702 nucleotide sequences. All positions with less than 95% site coverage were eliminated. Fewer than 5% alignment gaps, missing data, and ambiguous bases were allowed at any position. Evolutionary analyses were conducted in MEGA7 [2]

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