First record of the spatial organization of the nucleosome-less chromatin of dinoflagellates: The nonrandom distribution of microsatellites and bipolar arrangement of telomeres in the nucleus of Gambierdiscus australes (Dinophyceae)

Dinoflagellates are a group of protists whose exceptionally large genome is organized in permanently condensed nucleosome-less chromosomes. In this study, we examined the potential role of repetitive DNAs in both the structure of dinoflagellate chromosomes and the architecture of the dinoflagellate nucleus. Non-denaturing fluorescent in situ hybridization (ND-FSH) was used to determine the abundance and physical distribution of telomeric DNA and 16 microsatellites (1- to 4-bp repeats) in the nucleus of Gambierdiscus australes. The results showed an increased relative abundance of the different microsatellite motifs with increasing GC content. Two ND-FISH probes, (A)₂₀ and (AAT)₅ , did not yield signals whereas the remainder revealed a dispersed but nonrandom distribution of the microsatellites, mostly in clusters. The bean-shaped interphase nucleus of G. australes contained a region with a high density of trinucleotides. This nuclear compartment was located between the nucleolar organizer region (NOR), located on the concave side of the nucleus, and the convex side. Telomeric DNA was grouped in multiple foci and distributed in two polarized compartments: one associated with the NOR and the other peripherally located along the convex side of the nucleus. Changes in the position of the telomeres during cell division evidenced their dynamic distribution and thus that of the chromosomes during dinomitosis. These insights into the spatial organization of microsatellites and telomeres and thus into the nuclear architecture of G. australes will open up new lines of research into the structure and function of the nucleosome-less chromatin of dinoflagellates.

Chromosomal markers in the genus Karenia: Towards an understanding of the evolution of the chromosomes, life cycle patterns and phylogenetic relationships in dinoflagellates

Dinoflagellates are a group of protists whose genome is unique among eukaryotes in terms of base composition, chromosomal structure and gene expression. Even after decades of research, the structure and behavior of their amazing chromosomes-which without nucleosomes exist in a liquid crystalline state-are still poorly understood. We used flow cytometry and fluorescence in situ hybridization (FISH) to analyze the genome size of three species of the toxic dinoflagellate genus Karenia as well the organization and behavior of the chromosomes in different cell-cycle stages. FISH was also used to study the distribution patterns of ribosomal DNA (45S rDNA), telomeric and microsatellites repeats in order to develop chromosomal markers. The results revealed several novel and important features regarding dinoflagellate chromosomes during mitosis, including their telocentric behavior and radial arrangement along the nuclear envelope. Additionally, using the (AG)10 probe we identified an unusual chromosome in K. selliformis and especially in K. mikimotoi that is characterized by AG repeats along its entire length. This feature was employed to easily differentiate morphologically indistinguishable life-cycle stages. The evolutionary relationship between Karenia species is discussed with respect to differences in both DNA content and the chromosomal distribution patterns of the DNA sequences analyzed.

Sequencing of long stretches of repetitive DNA

Repetitive DNA is widespread in eukaryotic genomes, in some cases making up more than 80% of the total. SSRs are a type of repetitive DNA formed by short motifs repeated in tandem arrays. In some species, SSRs may be organized into long stretches, usually associated with the constitutive heterochromatin. Variation in repeats can alter the expression of genes, and changes in the number of repeats have been linked to certain human diseases. Unfortunately, the molecular characterization of these repeats has been hampered by technical limitations related to cloning and sequencing. Indeed, most sequenced genomes contain gaps owing to repetitive DNA-related assembly difficulties. This paper reports an alternative method for sequencing of long stretches of repetitive DNA based on the combined use of 1) a linear vector to stabilize the cloning process, and 2) the use of exonuclease III for obtaining progressive deletions of SSR-rich fragments. This strategy allowed the sequencing of a fragment containing a stretch of 6.2 kb of continuous SSRs. To demonstrate that this procedure can sequence other kinds of repetitive DNA, it was used to examine a 4.5 kb fragment containing a cluster of 15 repeats of the 5S rRNA gene of barley.

Comparative analysis of gene expression among species of different ploidy

Interspecific comparative studies require that expression data be comparable among species, and when species with different levels of ploidy are contemplated the relative expression per cell should be obtained for accurate comparisons to be made. Quantitative reverse-transcription-PCR is the most popular and sensitive technique for the detection and quantification of mRNA in gene expression analysis. In recent years it has become clear that the choice of reference genes for the normalization of expression data is very important. Several studies have shown that the expression of the traditional housekeeping genes varies under certain situations; their use as reference genes in quantitative PCR assays can therefore lead to errors when interpreting the relative expression of target genes. Normalizing with respect to endogenous genes showing a constant level of expression per cell across species, however, provides an easy way of obtaining comparable expression data for other genes in those species. In this work, the validity of several candidate genes was examined across four diploid and polyploid species of the genera Triticum and Aegilops. Candidate reference genes were chosen among the traditional housekeeping genes used in quantitative PCR analysis, as well as others found to have stable levels of expression under different conditions in other studies. After the analyses, candidate genes were gathered into two groups according to the different levels of expression per cell seen in polyploid species. For the four species studied, two genes suitable for normalization procedures in interspecific studies were identified: cell division control protein and malate dehydrogenase. Both showed a constant number of transcripts per cell, independent of the level of ploidy.

Analysis by PCR-based markers using designed primers to study relationships between species of Hordeum (Poaceae)

An investigation was made into the relationships between six species or subspecies of the genus Hordeum that grow in the Iberian Peninsula and Balearic Islands. Plant material included samples of 19 populations of the annual species H. marinum subsp. marinum, H. marinum subsp. gussoneanum, H. murinum subsp. murinum, and H. murinum subsp. leporinum, and the perennial species H. bulbosum and H. secalinum. Relationships were analysed using PCR-based molecular markers. Thirteen sets of primers were designed and synthesized based on sequences of mapped RFLPs from genomic libraries and conserved regions of structural genes of known function in cultivated species. Primers were used to amplify genomic DNA from all populations. The number of amplified products ranged from 1 to 18 per primer and a total of 168 markers were scored. The markers revealed different degrees of relationships. Hordeum bulbosum was clearly separated from the rest. The populations of both subspecies of H. murinum were closely related. H. marinum subsp. gussoneanum appeared to be closely related to H. secalinum, yet relatively separated from its conspecific subspecies marinum. The use of a large number of DNA markers in this kind of analysis is discussed.Key words: Hordeum, barley, DNA markers, restriction endonucleases, variability, DNA analysis.