title: Convergence of retrotransposons in oomycetes and plants.
abstract: BACKGROUND
  Retrotransposons comprise a ubiquitous and abundant class of eukaryotic transposable elements. All members of this class rely on reverse transcriptase activity to produce a DNA copy of the element from the RNA template. However, other activities of the retrotransposon-encoded polyprotein may differ between diverse retrotransposons. The polyprotein domains corresponding to each of these activities may have their own evolutionary history independent from that of the reverse transcriptase, thus underlying the modular view on the evolution of retrotransposons. Furthermore, some transposable elements can independently evolve similar domain architectures by acquiring functionally similar but phylogenetically distinct modules. This convergent evolution of retrotransposons may ultimately suggest similar regulatory pathways underlying the lifecycle of the elements.
  
  
  RESULTS
  Here, we provide new examples of the convergent evolution of retrotransposons of species from two unrelated taxa: green plants and parasitic protozoan oomycetes. In the present study we first analyzed the available genomic sequences of oomycete species and characterized two groups of Ty3/Gypsy long terminal repeat retrotransposons, namely Chronos and Archon, and a subgroup of L1 non-long terminal repeat retrotransposons. The results demonstrated that the retroelements from these three groups each have independently acquired plant-related ribonuclease H domains. This process closely resembles the evolution of retrotransposons in the genomes of green plants. In addition, we showed that Chronos elements captured a chromodomain, mimicking the process of chromodomain acquisition by Chromoviruses, another group of Ty3/Gypsy retrotransposons of plants, fungi, and vertebrates.
  
  
  CONCLUSIONS
  Repeated and strikingly similar acquisitions of ribonuclease H domains and chromodomains by different retrotransposon groups from unrelated taxa indicate similar selection pressure acting on these elements. Thus, there are some major trends in the evolution of the structural composition of retrotransposons, and characterizing these trends may enhance the current understanding of the retrotransposon life cycle.
authors.affiliation: Institute of Cytology and Genetics, Laboratory of Molecular Genetic Systems, Prospekt Lavrentyeva 10, 630090 Novosibirsk, Russia.
authors.forename: Kirill
authors.identifier: 0000-0003-4346-3868
authors.initials: K
authors.lastname: Ustyantsev
authors.affiliation: Institute of Cytology and Genetics, Laboratory of Molecular Genetic Systems, Prospekt Lavrentyeva 10, 630090 Novosibirsk, Russia.
authors.forename: Alexandr
authors.initials: A
authors.lastname: Blinov
authors.affiliation: Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.
authors.forename: Georgy
authors.initials: G
authors.lastname: Smyshlyaev
keywords: Chromodomain; Convergent evolution; Oomycetes; Plants; Retrotransposons; Ribonuclease H