Andrey S. Antonov

Molecular Data from the Chloroplast rpoC1 Gene Suggest a Deep and Distinct Dichotomy of Contemporary Spermatophytes into Two Monophyla: Gymnosperms (Including Gnetales) and Angiosperms

Abstract. Partial sequences of the rpoC1 gene from two species of angiosperms and three species of gymnosperms (8330 base pairs) were determined and compared. The data obtained support the hypothesis that angiosperms and gymnosperms are monophyletic and none of the recent groups of the latter is sister to angiosperms.

Sequences of rDNA internal transcribed spacers from the chloroplast DNA of 26 bryophytes: properties and phylogenetic utility

We determined the sequence of the region of the chloroplast DNA inverted repeat spanning from the 3′‐terminus of the 23S rRNA gene to the 5′‐terminus of the tRNAArg(ACG) gene (about 700 bp) from 25 bryophytes and from the charophycean alga Chara australis. Phylogenetic analysis of these sequences using the neighbor‐joining method suggests an early dichotomy of bryophytes and their paraphyly relative to the tracheophyte lineage. A monophyly of liverworts (Marchantiidae plus Jungermanniidae), a deep divergence of Metzgeriales among Jungermanniidae and a close affinity of the two subclasses of mosses, Sphagnidae and Andreaeidae, are evident. The branching pattern observed is consistent with the phylogenetic distribution of several prominent indels observed in the alignment.

Phylogeny of flowering plants by the chloroplast genome sequences: in search of a "lucky gene".

One of the most complicated remaining problems of molecular-phylogenetic analysis is choosing an appropriate genome region. In an ideal case, such a region should have two specific properties: (i) results of analysis using this region should be similar to the results of multigene analysis using the maximal number of regions; (ii) this region should be arranged compactly and be significantly shorter than the multigene set. The second condition is necessary to facilitate sequencing and extension of taxons under analysis, the number of which is also crucial for molecular phylogenetic analysis. Such regions have been revealed for some groups of animals and have been designated as “lucky genes”. We have carried out a computational experiment on analysis of 41 complete chloroplast genomes of flowering plants aimed at searching for a “lucky gene” for reconstruction of their phylogeny. It is shown that the phylogenetic tree inferred from a combination of translated nucleotide sequences of genes encoding subunits of plastid RNA polymerase is closest to the tree constructed using all protein coding sites of the chloroplast genome. The only node for which a contradiction is observed is unstable according to the different type analyses. For all the other genes or their combinations, the coincidence is significantly worse. The RNA polymerase genes are compactly arranged in the genome and are fourfold shorter than the total length of protein coding genes used for phylogenetic analysis. The combination of all necessary features makes this group of genes main candidates for the role of “lucky gene” in studying phylogeny of flowering plants.

Structure and evolution of junctions between inverted repeat and small single copy regions of chloroplast genome in non-core Caryophyllales

The structure of the junction between inverted repeat (IR) and small single copy (SSC) regions of the chloroplast genome in the representatives of non-core Caryophyllales is investigated in this work. It was found that for two families—Polygonaceae and Plumbaginaceae—the extension of inverted region is characteristic. This extension is due to the duplication of the part of the ycf1 gene that is partly located in the small single copy region in plants with typical structure of IR/SSC junctions. Comparison of the position of IR/SSC junctions in different species of Polygonaceae has shown that their exact position is not correlated with the affinity of these species inferred from molecular and morphological data. Possible mechanisms leading to the change in position of IR/SSC junctions observed in this work are discussed.

From birth to christening.

A brief history of comparative studies of nucleic acids for systematic purposes is given. These studies were initiated by a group of Moscow State University scientists headed by A. N. Belozersky. Based mostly on comparative DNA studies, some main dogmas of a new branch of systematics were gradually developed. In Russia, this new branch of systematics is called “genosystematics”. Some of the main results obtained by genosystematics since its birth (1957) and up to its “christening” (1974) are described.

Genosystematics: From E. Chargaff and A.N. Belozersky To the Present

This review considers the history of genosystematics (macromolecular systematics) from early studies of E. Chargaff and A.N. Belozersky up to the present, with emphasis on the most important discoveries in the field. The potential and limitations of genosystematics and possible ways of further development are analyzed using plants as an example. The future of genosystematics depends to a great extent on adequate employment of its methods in studying the problems of phylogeny and taxonomy. Analysis of recent publications shows that this requirement is not always met. It is no less important to design and improve the methods of genosystematics, especially those for comparing complete genomes.

Methods for Studying the Evolution of Macromolecules

Here we shall summarize some of the definitions and concepts characterizing genetic sequences [18, 47] and outline the basic problems of their study in the context of the theory of molecular evolution.

Introduction: Approaches and Problems

The most significant property of individuals in evolution is their capacity for reproduction (inheritance) and hereditary variability. According to modern genetics, this property is largely due to the presence in cells of the so-called non-regular (encoding) polymers: nucleic acids (DNA, RNA) and proteins [18, 33]. In general, the non-regular polymers of a cell together account for other essential properties, such as metabolism, growth, immunity, etc., which form a ‘core’ of the biological organization in individual species.

The Origin and Evolution of the Genetic Coding-System

Proceeding from the well-studied translation system of E. coli and using other evidence, we may describe the basic properties of this system [33, 45, 46, 335].

Theoretical Analysis of the Evolution of Genes and Proteins

In this chapter we shall consider the results of phylogenetic analysis of certain macromolecular families and the problems of devising a unified theory of synonymous molecular macroevolutionary drift.