V. A. Lyubetsky

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We demonstrate the scarcity of conserved bacterial-type promoters in plastids of Streptophyta and report widely conserved promoters only for genes psaA, psbA, psbB, psbE, rbcL. Among the reasonable explanations are: evolutionary changes of sigma subunit paralogs and phage-type RNA polymerases possibly entailing the loss of corresponding nuclear genes, de(More)
A long recognized problem is the inference of the supertree S that amalgamates a given set {G j } of trees G j , with leaves in each G j being assigned homologous elements. We ground on an approach to find the tree S by minimizing the total cost of mappings α j of individual gene trees G j into S. Traditionally, this cost is defined basically as a sum of(More)
The first part of the paper briefly overviews the problem of gene and species trees reconciliation with the focus on defining and algorithmic construction of the evolutionary scenario. Basic ideas are discussed for the aspects of mapping definitions, costs of the mapping and evolutionary scenario, imposing time scales on a scenario, incorporating horizontal(More)
Protein clustering is useful for refining protein annotations and searching for proteins by their phylogenetic profile. We have performed the clustering of proteins encoded in the plastoms of Rhodophyta, as well as other plastid-containing species related to the Rhodophyta branch. The corresponding database and cluster search according to protein(More)
We report the database of plastid protein families from red algae, secondary and tertiary rhodophyte-derived plastids, and Apicomplexa constructed with the novel method to infer orthology. The families contain proteins with maximal sequence similarity and minimal paralogous content. The database contains 6509 protein entries, 513 families and 278(More)
This study considers transcription regulation of plastid genes involved in sulfate transport in the parasites of invertebrate (Helicosporidium sp.) and other species of the Viridiplantae. A one-box conserved motif with the consensus TAAWATGATT is found near promoters upstream the cysT and cysA genes in many species. In certain cases, the motif is repeated(More)
The problem of reconstructing a species supertree from a given set of protein, gene, and regulatorysite trees is the subject of this study. Under the traditional formulation, this problem is proven to be NP-hard. We propose a reformulation: to seek for a supertree, most of the clades of which contribute to the original protein trees. In such a variant, the(More)
BACKGROUND Modeling of a complex biological process can explain the results of experimental studies and help predict its characteristics. Among such processes is transcription in the presence of competing RNA polymerases. This process involves RNA polymerases collision followed by transcription termination. RESULTS A mathematical and computer simulation(More)
A novel algorithm and original software were used to cluster all proteins encoded in plastids of 72 species of the rhodophytic branch. The results are publicly available at http://lab6.iitp.ru/ppc/redline72/ in a database that allows fast identification of clusters (protein families) both by a fragment of an amino acid sequence and by a phylogenetic profile(More)
The study focuses on insertions of perfect direct repeats of words of arbitrary length in plastomes and mitochondriomes. The approach is exemplified using seed plants. Plastomes of close species were analyzed to further develop and refine published evidence for the evolution of non-coding DNA. The results suggest that perfect repeats are common elementary(More)