Fig. 1

Diversity of aRNH-containing retrotransposons in oomycetes. a Schematic structural composition of the elements from the identified groups: ORFs are shown as horizontal ovals (ORFs 1 are shaded); PR – protease; gRH – RNH of Ty3/Gypsy LTR-RTs; aRH – aRNH (in red); IN – integrase; CHD – chromodomain (in blue); EN – apurinic/apyrimidinic endonuclease-like endonuclease, RLE – restriction-like endonuclease; CCHC Zn finger motif indicated as vertical gray line; gray arrows, LTRs – long terminal repeats. b Consensus of Maximum-likelihood and Bayesian trees based on the amino acid sequences of RT domain of LTR-RTs. 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. Groups of aRNH-containing retrotransposons of oomycetes and plants are emphasized in bold and highlighted in blue and green, respectively. CHD-containing retrotransposons without aRNH of Chromoviruses (ChromoVir) group are emphasized in bold. On the right from the tree schemes of the consensus structures of the ORF2 of the corresponding groups are shown; cRH – RNH of Tc1/Copia LTR-RTs. The complete Maximum-likelihood and Bayesian phylogenetic trees with accession numbers, the names of the elements, and all the statistical support values are presented in Additional file 2: Figure S1. c Consensus of Maximum-likelihood and Bayesian trees based on the amino acid sequences of RT domain of non-LTR-RTs. 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. On the right of the tree, the schemes of the consensus structures of the corresponding groups are shown; RH – RNH domain of non-LTR-RTs. The complete Maximum-likelihood and Bayesian phylogenetic trees with accession numbers, the names of the elements, and all the statistical support values are presented in Additional file 2: Figure S1