Age-Dependent and Tissue-Specific Alterations in the rDNA Clusters of the Panax ginseng C. A. Meyer Cultivated Cell Lines.

Long-term cultivation of Panax ginseng cell lines leads to a decreasing synthesis of the biologically active substances used in traditional medicine. To gain insight into the cellular mechanisms which may influence this process, we analyzed variations within the rDNA cluster of the Oriental ginseng cell lines. The cell lines were cultivated for 6 and 24 years; the number of nucleoli and chromosomes was analyzed. The complete 18S rDNA sequences were cloned and sequenced. The nucleotide polymorphism and phylogenetic relations of the sequences were analyzed, and the secondary structures for separate 18S rRNA regions were modeled. The 18S rDNA accumulated mutations during cell cultivation that correlate well with an increase in the number of chromosomes and nucleoli. The patterns of nucleotide diversity are culture-specific and the increasing polymorphism associates with cytosine methylation sites. The secondary structures of some 18S rRNA regions and their interaction can alter during cultivation. The phylogenetic tree topologies are particular for each cell line.The observed alterations in rDNA clusters are associated with a somaclonal variation, leading to changes in the pattern of intracellular synthesis during cell cultivation. The identified divergent rRNAs could provide additional gene expression regulation in P. ginseng cells by forming heterogeneous ribosomes.

Stephanoprora chasanensis n. sp. (Digenea: Echinochasmidae): Morphology, life cycle, and molecular data.

Echinostomatoidea is a large, globally distributed and heterogeneous group of hermaphroditic digeneans that parasite, as adults, vertebrate hosts of all classes. Species of this group have received attention from researchers as they can cause diseases in wildlife and humans. Here we describe the biological and molecular phylogenetic characteristics of Stephanoprora chasanensis n. sp. (Digenea: Echinochasmidae). The life cycle of this fluke was experimentally completed by the use of hosts, i.e. Stenothyra recondite Lindholm, 1929 snail (the 1st intermediate), Rhynchocypris percnurus mantschuricus (Berg, 1907) freshwater fish (the 2nd intermediate) and Gallus gallus chicken (the definitive host). In the adult worms, vitelline follicles were distributed anteriorly to the mid-level of the ventral sucker in our specimens whereas they did not reach the level of anterior testis in other species of Stephanoprora previously reported. Phylogenetic analysis based on 28S rDNA revealed that Stephanoprora and Echinochasmus with 20-22 collar spines grouped together in a single cluster. In addition, we showed that Stephanoprora chasanensis n. sp. was closely related to Echinochasmus milvi Yamaguti, 1939. Cercariae of these two echinostomes commonly have a long tail.

Variation in the number of nucleoli and incomplete homogenization of 18S ribosomal DNA sequences in leaf cells of the cultivated Oriental ginseng (Panax ginseng Meyer).

BACKGROUND: Wild ginseng, Panax ginseng Meyer, is an endangered species of medicinal plants. In the present study, we analyzed variations within the ribosomal DNA (rDNA) cluster to gain insight into the genetic diversity of the Oriental ginseng, P. ginseng, at artificial plant cultivation. METHODS: The roots of wild P. ginseng plants were sampled from a nonprotected natural population of the Russian Far East. The slides were prepared from leaf tissues using the squash technique for cytogenetic analysis. The 18S rDNA sequences were cloned and sequenced. The distribution of nucleotide diversity, recombination events, and interspecific phylogenies for the total 18S rDNA sequence data set was also examined. RESULTS: In mesophyll cells, mononucleolar nuclei were estimated to be dominant (75.7%), while the remaining nuclei contained two to four nucleoli. Among the analyzed 18S rDNA clones, 20% were identical to the 18S rDNA sequence of P. ginseng from Japan, and other clones differed in one to six substitutions. The nucleotide polymorphism was more expressed at the positions 440-640 bp, and distributed in variable regions, expansion segments, and conservative elements of core structure. The phylogenetic analysis confirmed conspecificity of ginseng plants cultivated in different regions, with two fixed mutations between P. ginseng and other species. CONCLUSION: This study identified the evidences of the intragenomic nucleotide polymorphism in the 18S rDNA sequences of P. ginseng. These data suggest that, in cultivated plants, the observed genome instability may influence the synthesis of biologically active compounds, which are widely used in traditional medicine.

Phylogeny based on two mtDNA genes (Co-1, Cyt-B) among Sculpins (Scorpaeniformes, Cottidae) and some other scorpionfish in the Russian Far East.

The average scores of p-distances at Co-1 and Cyt-b genes revealed a pattern of increased nucleotide diversity for four categories: (1) intraspecies, (2) intragenus, (3) intrafamily, and (4) intraorder. Scores for Co-1 genes were following: (1) 0.24 ± 0.19% (n = 66), (2) 1.54 ± 0.27% (n = 33), (3) 11.57 ± 0.24% (n = 42), and (4) 12.91 ± 0.16% (n = 102); while for Cyt-b genes, those values were (1) 1.92 ± 0.55% (n = 24), (2) 8.19 ± 0.09% (n = 812), (3) 15.42 ± 0.07% (n = 1573), and (4) 23.13 ± 0.19% (n = 211). A concordant increase in the distance score, as the rank of taxa grows, with the minimum at intraspecies level substantiates the concept that speciation in the order Scorpaeniformes mostly follows a geographic mode. Phylogenetic trees for 40 sequences of scorpionfish and four other fishes belonging to Actinopterigii were developed using Co-1 gene and four different analytical approaches: Bayesian, ML, MP, and NJ. Resolution of the Co-1 trees for the three genera that included different species branches was quite distinct in all approaches. Intrafamily branching for Cyt-b in Cottidae was also supported by all four kinds of trees but only for less numerous genera in the research.

Phylogenetic relationships of Paradiclybothrium pacificum and Diclybothrium armatum (Monogenoidea: Diclybothriidae) inferred from 18S rDNA sequence data.

The Diclybothriidae (Monogenoidea: Oligonchoinea) includes specific parasites of fishes assigned to the ancient order Acipenseriformes. Phylogeny of the Diclybothriidae is still unclear despite several systematic studies based on morphological characters. Together with the closely related Hexabothriidae represented by parasites of sharks and ray-fishes, the position of Diclybothriidae in different taxonomical systems has been matter of discussion. Here, we present the first molecular data on Diclybothriidae. The SSU rRNA gene was used to investigate the phylogenetic position of Paradiclybothrium pacificum and Diclybothrium armatum among the other Oligonchoinea. Complete nucleotide sequences of P. pacificum and D. armatum demonstrated high identity (98.53%) with no intraspecific sequence variability. Specimens of D. armatum were obtained from different hosts (Acipenser schrenckii and Huso dauricus); however, variation by host was not detected. The sequence divergence and phylogenetic trees data show that Diclybothriidae and Hexabothriidae are more closely related to each other than with other representatives of Oligonchoinea.