V. K. Bobrova

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.

Contribution of genosystematics to current concepts of phylogeny and classification of bryophytes

This paper is a survey of the current state of molecular studies on bryophyte phylogeny. Molecular data have greatly contributed to developing a phylogeny and classification of bryophytes. The previous traditional systems of classification based on morphological data are being significantly revised. New data of the authors are presented on phylogeny of Hypnales pleurocarpous mosses inferred from nucleotide sequence data of the nuclear DNA internal transcribed spacers ITS1-2 and the trnL-F region of the chloroplast genome.

Disentangling knots of rapid evolution: origin and diversification of the moss order Hypnales

Abstract The Hypnales are the largest order of mosses comprising approximately 4200 species. Phylogenetic reconstruction within the group has proven to be difficult due to rapid radiation at an early stage of evolution and, consequently, relationships among clades have remained poorly resolved. We compiled data from four sequence regions, namely, nuclear ITS1–5·8S–ITS2, plastid trnL–F and rps4, and mitochondrial nad5, for 122 hypnalean species and 34 species from closely related groups. Tree topologies from both Bayesian and parsimony analyses resolve the order as monophyletic. Although inferences were made from fast-evolving genes, and despite strong phylogenetic signal in the nuclear ITS1–5·8S–ITS2 data, monophyly, as well as backbone nodes within the Hypnales, remains rather poorly supported except under Bayesian inferences. Ancestral distribution based on Bayesian dispersal-vicariance analysis supports a Gondwanan origin of the Hypnales and subsequent geographical radiation in the area of the former Laurasian supercontinent. Reconstruction of historical biogeography is congruent with mainly tropical and Gondwanan distributions in the sister groups Hypnodendrales, Ptychomniales, and Hookeriales, and with the dating for the oldest pleurocarp and hypnalean fossils. We contrast groupings in the phylogenetic tree with recent classifications and other phylogenetic inferences based on molecular data, and summarise current knowledge on the evolutionary history of, and relationships among, the Hypnales.

Novel miR390-Dependent Transacting siRNA Precursors in Plants Revealed by a PCR-Based Experimental Approach and Database Analysis

TAS loci in plant genomes encode transacting small interfering RNAs (ta-siRNAs) that regulate expression of a number of genes. The function of TAS3 precursor in Arabidopsis thaliana is controlled by two miR390 target sites flanking two ta-siARF sequences targeting mRNAs of ARF transcription factors. Cleavage of the 3′-miR390-site initiates ta-siRNAs biogenesis. Here we describe the new method for identification of plant ta-siRNA precursors based on PCR with oligodeoxyribonucleotide primers mimicking miR390. The method was found to be efficient for dicotiledonous plants, cycads, and mosses. Based on sequences of amplified loci and a database analysis, a novel type of miR390-dependent TAS sequences was identified in dicots. These TAS loci are characterized by a smaller distance between miR390 sites compared to TAS3, a single copy of ta-siARF, and a sequence conservation pattern pointing to the possibility that processing of novel TAS-like locus is initiated by cleavage of the 5′-terminal miR390 target site.

RPS4 and NAD5 sequences evidenced of polyphyly of ditrichaceae and parallelisms in the evolution of haplolepidous mosses

Molecular phylogenetic analysis of 66 representatives of haplolepidous mosses showed polyphylia of Ditrichaceae. According to the data obtained, the structure of the peristome, as well as features of the gametophyte on which a family traditionally allocated, arose independently in different groups of haplolepideous mosses. At least six genera (Distichium, Saelania, Eccremidium, Garckea, Rhamphidium, and Wilsoniella) should be excluded from the Ditrichaceae family, while Saelania and Distichium should be assigned even to another order. The loss of the peristome and forming of cleistocarpous capsules also occurs independently in at least two lineages of Ditrichaceae s. str., and in representatives of several lineages of Pottiaceae, a family derived from this group. Ditrichum, the type genus of Ditrichaceae, is also polyphyletic, species of this genus belong to two clades. It was concluded that parallel lines of the morphological variability in this group of mosses occur and its phylogeny need to be resolved based on molecular data.

Structural evolution of the 4/1 genes and proteins in non-vascular and lower vascular plants

The 4/1 protein of unknown function is encoded by a single-copy gene in most higher plants. The 4/1 protein of Nicotiana tabacum (Nt-4/1 protein) has been shown to be alpha-helical and predominantly expressed in conductive tissues. Here, we report the analysis of 4/1 genes and the encoded proteins of lower land plants. Sequences of a number of 4/1 genes from liverworts, lycophytes, ferns and gymnosperms were determined and analyzed together with sequences available in databases. Most of the vascular plants were found to encode Magnoliophyta-like 4/1 proteins exhibiting previously described gene structure and protein properties. Identification of the 4/1-like proteins in hornworts, liverworts and charophyte algae (sister lineage to all land plants) but not in mosses suggests that 4/1 proteins are likely important for plant development but not required for a primary metabolic function of plant cell.

Genetic diversity in pseudomonads associated with cereal cultures infected with basal bacteriosis

The genetic properties of 45 pseudomonad strains isolated from cereal cultures exhibiting symptoms of basal bacteriosis have been investigated. Considerable genetic diversity has been demonstrated using DNA fingerprints obtained by amplification with REP, ERIC, and BOX primers. Restriction analysis of the 16S–23S internal transcribed spacer (ITS1) allowed the strains to be subdivided into two major groups. In a phylogenetic tree, the ITS1s of these groups fell into two clusters, which also included the ITS1 of Pseudomonas syringae (“Syringae” cluster) and the ITS1 of P. fluorescens, P. tolaasii, P. reactans, P. gingeri, and P. agarici (“Fluorescens” cluster) from the GenBank database. Comparison of the ITS1 divergence levels within the “Fluorescens” cluster suggests expediency of treating P. tolaasii, P. reactans, various P. fluorescens groups, and, possibly, P. gingeri and P. agarici as subspecies of one genospecies. The intragenomic heterogeneity of ITS1s was observed in some of the pseudomonad strains studied. The results of amplification with specific primers and subsequent sequencing of the amplificate suggest the possibility of the presence of a functionally active syrB gene involved in syringomycin biosynthesis in the strains studied.