The detection of genome polymorphism in Stachys species using RAPD

Molecular genome analysis was for the first time carried out in the genus Stachys. RAPD analysis proved to be suitable for identifying the species-specific markers, studying the interspecific DNA polymorphism, and detecting the genetic changes that arise during in vitro culturing of Stachys sieboldii. In addition, RAPD was used for screening genetic variation in S. sieboldii regenerants obtained at various phytohormone concentrations. High cytokinin concentrations and multiple regeneration were shown to induce genetic changes detectable with RAPD patterns. High DNA polymorphism was demonstrated for two types of S. sieboldii callus cultures and for plants regenerated from a callus culture.     

RAPD and ISSR analyses of species and populations of the genus Stachys

Molecular analysis of the genome was performed for 14 species of the genus Stachys. RAPD and ISSR analyses of the Stachys genome revealed 574 polymorphic fragments, including genus-and species-specific markers. Based on the patterns, UPGMA and the Jacquard coefficient were used to estimate the genetic distances between Stachys species and populations and to construct dendrograms reflecting the phylogenetic relationships among the Stachys species. Molecular analysis of the Stachys genome refined the phylogenetic positions of some species and revealed synonymous species.     

The Detection of Genome Polymorphism in Stachys Species Using RAPD

Molecular genome analysis was for the first time carried out in the genus Stachys. RAPD analysis proved to be suitable for identifying the species-specific markers, studying the interspecific DNA polymorphism, and detecting the genetic changes that arise during in vitro culturing of Stachys sieboldii. RAPD was also used for screening genetic variation in S. sieboldii regenerants obtained at various phytohormone concentrations. High cytokinin concentrations and multiple regeneration were shown to induce genetic changes detectable in RAPD patterns. High DNA polymorphism was detected for two types of S. sieboldii callus cultures and for plants regenerated from a callus culture.     

Cytotoxicity,apoptosis inducing activity and Western blot analysis of tanshinone derivatives from Stachys parviflora on prostate and breast cancer cells

Molecular Biology Reports - Cytotoxic activities of methanolic crude extract of Stachys parviflora (Lamiaceae family) and its sub-fractions were primarily evaluated against human breast...     

Hybridization and introgression between Callicarpa japonica and C. mollis (Verbenaceae) in central Japan, as inferred from nuclear and chloroplast DNA sequences

Callicarpa x shirasawana is a natural hybrid between C. japonica and C. mollis, and has a morphology that is intermediate between those of the parent species. Characterization of natural Callicarpa populations in the Atsumi Peninsula of central Japan, which all three of the above species inhabit sympatrically, revealed hybrids with various morphologies. Molecular analysis revealed a high occurrence of introgression of the C. japonica genome into that of C. mollis. Moreover, all individuals examined with morphology similar to that of C. mollis had genetic traces of hybridization with C. japonica. Molecular analysis of individual C. mollis and C. japonica from five other areas of Japan showed that introgression of C. japonica into C. mollis occurs widely. Molecular data also strongly suggested that the previously recognized C. x shirasawana individuals with intermediate morphology are not F1 hybrids between C. japonica and C. mollis, but instead are progeny of C. x shirasawana backcrossed with C. japonica. Moreover, it was revealed that individuals with F1-type genotypes are indistinguishable morphologically from pure C. mollis. The results of the present study point to the need for re-evaluation of natural populations of C. mollis and C. x shirasawana.     

Circumscription of taxa in the chasmophilous Iranian Stachys species (Lamiaceae: sect. Fragilicaulis, subsect. Fragiles) inferred from isoenzyme variation patterns

Fresh leaves of 150 individuals from 15 populations representing five putative species of Stachys sect. Fragilicaulis, subsect. Fragiles distributed in the Zagros mountains in western Iran were analyzed for isoenzyme variation. Four enzyme systems (peroxidase, esterase, superoxide dismutase and ascorbate peroxidase) have been studied and a total of 32 bands representing seven putative loci have been analyzed by UPGMA using the Euclidean distances. UPGMA analysis resulted in the recognition of three distinct clusters among the considered populations. The average value of Shannon diversity index (H′) estimated for each population ranged from 0.05 to 2.17. The mean number of bands per isoenzyme ranges from 1.60 to 2.50. The value of Euclidean distance ranges from 0.85 to 3.79. The analysis of isoenzyme variation patterns suggests recognizing following species in Stachys sect. Fragilicaulis subsect. Fragiles: Stachys benthamiana (including Stachys megalodonta), Stachys kurdica (including Stachys ballotiformis) and Stachys asterocalyx. These data also suggest paying more attention to geographical distribution of taxa in Stachys for their taxonomic delimitation. This study provides another strong support for application of electrophoretic analysis of isoenzymes in taxonomy at species level.     

Glycosides of tricetin methyl ethers as chemosystematic markers in Stachys subgenus Betonica

Nine species from the genus Stachys L. representing subgenera Stachys and Betonica were surveyed for flavonoid glycosides by means of HPLC coupled to diode-array detection and LC-APCI-MS. Those species belonging to subgenus Betonica were characterised by the presence of glycosides of tricetin methyl ethers, including a new derivative, which was isolated from S. scardica Griseb. and identified as tricetin 3',4',5' -trimethyl ether 7-O-beta-glucopyranoside by spectroscopic methods. This type of flavonoid was absent from species belonging to subgenus Stachys and can be considered as a chemosystematic marker for subgenus Betonica.     

Variation and morphogenetic characteristics of different Stachys species during microclonal propagation

Morphogeneses of Stachys different species introduced in culturing in vitro have been compared. The frequency of altered forms have been demonstrated to be related to the plant genotype. All regenerants of S. sieboldii, which reproduces in vivo only vegetatively, are phenotypically normal, irrespective of the concentrations of plant growth regulators at which they have been obtained. Only changes in isozyme patterns have been observed in the regenerants grown in media containing at least 10 mg/l benzyl aminopurine (BAP); most of these changes are the absence of a particular component of the pattern. The cross-pollinating species Stachys ocymastrum, which typically reproduces by seeds, has yielded morphologically altered forms even in phytohormone-free media; its isozyme patterns often contained a new component. Analysis of the isoperoxidase patterns of regenerants of both Stachys species obtained with the use of high phytohormone concentrations has demonstrated qualitative and quantitative changes suggesting the appearance of somaclonal variants even in the course of plant regeneration directly from nodal segments, bypassing callus formation. Changes have also been found in Stachys plants regenerating from the callus tissue.     

Plants,mycorrhizal fungi and endobacteria: a dialog among cells and genomes

This review focuses on mycorrhizas, which are associations between fungi and the roots of 90% of terrestrial plants. These are the most common symbioses in the world; they involve about 6000 species of fungi distributed through all the fungal phyla and about 240000 species of plants, including forest and crop plants. Thanks to mycorrhizal symbiosis and nutrient exchanges, regulated by complex molecular signals, the plant improves its vegetative growth, while the fungus accomplishes its life cycle. Molecular and cellular analyses demonstrate that during colonization the cellular organization of the two eukaryotes is completely remodeled. For example, in cortical cells, structural modifications involve both the host and the microbiont. Recent studies revealed that in arbuscular mycorrhizas (AM), system complexity is increased by the presence of a third symbiont: a bacterium living inside the fungus. The presence of this resident genome makes the investigation of the molecular dialogues among the symbiotic partners even more complex. Molecular analysis showed that the bacterium has genes involved in the acquisition of mineral nutrients. The experimental data support the current view that mycorrhizal symbioses are often tripartite associations.     

Genome size estimation of brackishwater fishes and penaeid shrimps by flow cytometry

Molecular Biology Reports - Flow cytometry was used for estimating the genome size of five brackishwater finfish and four shrimp species. The genome size for Lutjanus argentimaculatus was...     

Karyological analysis of an interspecific hybrid between the dioecious Silene latifolia and the hermaphroditic Silene viscosa.

The genus Silene is a good model for studying evolution of the sex chromosomes, since it includes species that are hermaphroditic and dioecious, while maintain a basic chromosome number of 2n = 24. For some combinations of Silene species it is possible to construct interspecific hybrids. Here, we present a detailed karyological analysis of a hybrid between the dioecious Silene latifolia as the maternal plant and a related species, hermaphroditic Silene viscosa, used as a pollen partner. Using genomic probes (the genomic in situ hybridization (GISH) technique), we were able to clearly discriminate parental genomes and to show that they are largely separated in distinct nuclear domains. Molecular GISH and fluorescence in situ hybridization (FISH) markers document that the hybrid genome of somatic cells was strictly additive and stable, and that it had 12 chromosomes originating from each parent, including the only X chromosome of S. latifolia. Meiotic analysis revealed that, although related, respective parental chromosomes did not pair or paired only partially, which resulted in frequent chromosome abnormalities such as bridges and irregular non-disjunctions. GISH and FISH markers clearly document that the larger genome of S. latifolia and its largest chromosome component, the X chromosome, were mostly employed in chromosome lagging and misdivision.     

Inheritance and expression patterns of BN28, a low temperature induced gene in Brassica napus, throughout the Brassicaceae.

Molecular genetics is becoming an important tool in the breeding and selection of agronomically important traits. BN28 is a low temperature induced gene in Brassicaceae species. PCR and Southern blot analysis indicate that BN28 is polymorphic in the three diploid genomes: Brassica rapa (AA), Brassica nigra (BB), and Brassica oleracea (CC). Of the allotetraploids, Brassica napus (AACC) is the only species to have inherited homologous genes from both parental genomes. Brassica juncea (AABB) and Brassica carinata (BBCC) have inherited homologues from the AA and CC genomes, respectively, while Sinapsis arvensis (SS) contains a single homologue from the BB genome and Sinapsis alba (dd) appears to be different from all the diploid parents. All species show message induction when exposed to low temperature. However, differences in expression were noticed at the protein level, with silencing occurring in the BB genome at the level of translation. Results suggest that silencing is occurring in diploid species where duplication may not have occurred. Molecular characterization and inheritance of BN28 homologues in the Brassicaceae may play an important role in determining their quantitative function during exposure to low temperature. Key words : Brassicaceae, BN28, inheritance, polymorphism.     

A comparative analysis of the complete mitochondrial genome of the Eurasian otter <Emphasis Type="Italic">Lutra lutra</Emphasis> (Carnivora; Mustelidae)

Otter populations are declining throughout the world and most otter species are considered endangered. Molecular methods are suitable tools for population genetic research on endangered species. In the present study, we analyzed the complete mitochondrial genome (mitogenome) sequence of the Eurasian otter Lutra lutra. The mitochondrial DNA sequence of the Eurasian otter is 16,505 bp in length and consists of 13 protein-coding genes, 22 tRNAs, 2 rRNAs, and a control region (CR). The CR sequence of otters from Europe and Asia showed nearly identical numbers and nucleotide sequences of minisatellites. Phylogenetic analysis of Mustelidae mitogenomes, including individual genes, revealed that Lutrinae and Mustelinae form a clade, and that L. lutra and Enhydra lutris are sister taxa within the Lutrinae. Phylogenetic analyses revealed that of the 13 mitochondrial protein-coding genes, ND5 is the most reliable marker for analysis of phylogenetic relationships within the Mustelidae.     

Molecular cytogenetics of forest trees

The economic and ecological importance of forest trees, as well as their unique biological features, has recently raised the level of interest in studies on their genomes, including sequencing of the entire poplar genome. However, cytogenetic studies have not moved in parallel with developments in genomics. This is especially true for hardwood species characterized by small genomes and relatively high numbers of small chromosomes. Molecular cytogenetic studies have mainly been focused on coniferous species, owing to the larger size of their chromosomes, and have been applied exclusively for chromosome identification and comparative karyotyping in an attempt to understand genome evolution and phylogenetic relationships. In this context, rRNA genes physical mapped by FISH reveal particularly useful chromosomal landmarks with variable distribution patterns between species. Here we present a contribution of DNA markers used for chromosome analysis, which already allowed a deeper characterization and understanding of the processes underlying genome diversity of forest trees. The use of advanced cytogenetic techniques and other potential important methods for genome analysis of forest trees is also discussed.     

Isolation of new Pseudomonas tolaasii bacteriophages and genomic investigation of the lytic phage BF7

Sixteen lytic bacteriophages that infect Pseudomonas tolaasii LMG 2342(T) were isolated from smashed sporocarps of oyster mushroom (Pleurotus ostreatus) showing necrotic symptoms. On the basis of the host range investigation of the phages, they have wide infection abilities against the genus Pseudomonas, mainly in the case of phages Bf3, Bf7, Bf10, and Bf15. Molecular investigations have revealed that they all have dsDNA genomes about 40?kbp in size. Identical restriction patterns resulting from restriction enzyme analysis suggest that the isolates probably belong to the same phage species. However, there was a difference between these phage isolates in their infecting abilities. Phage isolate Bf7 was investigated and characterized more deeply. Morphological characterization of Bf7 by transmission electron microscopy (TEM) has shown that it has a short, noncontractile tail, an icosahedral phage head, and the size is about 60?nm in diameter, suggesting that it belongs to the Podoviridae family. Complete genome sequence analysis of the Bf7 phage isolate revealed a 40?058?bp genome, 58.4% G+C content, 46 open reading frames encoding different proteins showing homology to proteins of the bacteriophage Caulobacter crescentus φCd1 from the Podoviridae family. On the basis of these results and comparative genomic studies, we classified the Bf7 phage to the subfamily of Autographivirinae, φKMV-like phages.     

Origin of the Hawaiian endemic mints within North American Stachys (Lamiaceae)

The Hawaiian endemic mints constitute a major island radiation, displaying a remarkable diversity of floral, fruit, and vegetative features. Haplostachys and Phyllostegia have flowers associated with insect pollination, whereas Stenogyne has flowers typical of bird pollination. The three genera had been thought to be closely related to East Asian members of Lamioideae tribe Prasieae because of the fleshy nutlets borne by Phyllostegia and Stenogyne. We evaluated the origins of the Hawaiian mints using phylogenetic analyses of DNA sequence data from the plastid rbcL and trnL intron loci and the nuclear ribosomal 5S nontranscribed spacer. The Hawaiian genera were found to be monophyletic but deeply nested inside another lamioid genus, Stachys. In particular, they were found to be most closely related to a group of temperate North American Stachys from the Pacific coast, suggesting that the Hawaiian mints derived from a single colonization event from western North America to the Hawaiian Islands. Furthermore, Stachys, which contains amphiatlantic and transberingian clades, was found to be polyphyletic, with some species more closely related to Gomphostemma, Phlomidoschema, Prasium, and Sideritis than to other species of Stachys. Based on chromosomal evidence and our phylogenetic analyses, we hypothesize that the Hawaiian mints may be polyploid hybrids whose reticulate genomes predate the Hawaiian dispersal event and are derived from Stachys lineages with flowers exhibiting insect- vs. bird-pollination characteristics. Thus, the Hawaiian endemic mints may provide yet another insular system for the combined study of polyploidy, hybrid cladogenesis, and adaptive radiation.     

Comparative analysis of chromosome 2A molecular organization in diploid and hexaploid wheat

Molecular Biology Reports - Diploid A genome wheat species harbor immense genetic variability which has been targeted and proven useful in wheat improvement. Development and deployment of...     

Evolution of the Xenopus piggyBac transposon family TxpB: domesticated and untamed strategies of transposon subfamilies

A new family, termed TxpB, of DNA transposons belonging to the piggyBac superfamily was found in 3 Xenopus species (Xenopus tropicalis, Xenopus laevis, and Xenopus borealis). Two TxpB subfamilies of Kobuta and Uribo1 were found in all the 3 species, and another subfamily termed Uribo2 was found in X. tropicalis. Molecular phylogenetic analyses of their open reading frames (ORFs) revealed that TxpB transposons have been maintained for over 100 Myr. Both the Uribo1 and the Uribo2 ORFs were present as multiple copies in each genome, and some of them were framed by terminal inverted repeat sequences. In contrast, all the Kobuta ORFs were present as a single copy in each genome and exhibited high evolutionary conservation, suggesting domestication of Kobuta genes by the host. Genomic insertion polymorphisms of the Uribo1 and Uribo2 transposons (nonautonomous type) were observed in a single species of X. tropicalis, indicating recent transposition events. Transfection experiments in cell culture revealed that an expression vector construct for the intact Uribo2 ORF caused precise excision of a nonautonomous Uribo2 element from the target vector construct but that for the Kobuta ORF did not. The present results support our viewpoint that some Uribo2 members are naturally active autonomous transposons, whereas Kobuta members may be domesticated by hosts.     

Comparative analyses of chloroplast genomes from 13 Lagerstroemia (Lythraceae) species: identification of highly divergent regions and inference of phylogenetic relationships

Plant Molecular Biology - Seven divergence hotspots as plastid markers for DNA barcoding was selected, and the phylogeny of 13 Lagerstroemia species based on the cp genome data was reconstructed...     

Molecular and cytologic analysis of clusters of moderate repeats of bird genomes

Pigeon genome long sequences containing clusters of moderately repeating elements have been cloned. Molecular analysis has shown a dispersed distribution of the repeats in both pigeon and chicken genomes. Within a single cluster, a scrambled distribution of elements belonging to different families of repeats has been shown. Similar repeated sequences have been revealed within clusters. The analysed clusters of repeats are characterized by a limited structural variability in the genomes. In situ hybridization revealed the localization of sequences complementary to the cloned clusters in pigeon and chicken macrochromosomes. Preferential localization has been demonstrated in telomeric and centromeric chromosome regions as well as in the region of R-bands.