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Fig. 2 | Mobile DNA

Fig. 2

From: Convergence of retrotransposons in oomycetes and plants

Fig. 2

Maximum-likelihood representative tree based on the amino acid sequences of different types of type I RNHs. Approximate likelihood-ratio test (aLRT) statistical support values (unit fractions) are shown at the corresponding nodes of the tree; the values are highlighted in red if the corresponding node was additionally supported by more than 60 of 100 bootstrap replicates. Comparison of Maximum-likelihood and Bayesian reconstructions and bootstrap values are presented in Additional file 4: Figure S3. RNH lineages specific for oomycetes and plants are highlighted in blue and green gradient blocks, respectively. RTV – retroviruses. The names of oomycete non-LTR-RT and LTR-RT RNH sequences identified in the present study correspond to those in Additional file 1: Table S2. Names of RNHs of other LTR-RTs and non-LTR-RTs correspond to those in GyDB [39] and Repbase Update [21], respectively. NCBI accession numbers are indicated to the right of other RNH sequences. Schemes of the secondary structures of three subtypes of RNH with the corresponding active site residues are shown at the right of the tree. The α-helices are depicted as helices, and the β-sheets are shown as arrows. The conserved R/H residue of the active site, which varies between different RNH subtypes, is highlighted in red. *The D-E-D-D catalytic residues are not conserved in the gRNHs of Archon, Chronos and Tat LTR-RTs

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