Tracking of intercalary DNA sequences integrated into tandem repeat arrays in rye Secale vavilovii

The structure of repetitive sequences of the JNK block present in the pericentromeric region of the 2RL chromosome was studied in Secale vavilovii. Amplification of sequences present between the JNK sequences led to the identification of seven abnormal DNA fragments. Two of these fragments showed high similarity to the glutamate 5-kinase gene and putative alcohol dehydrogenase gene of trypanosomatid from the genus Leishmania, whose presence can be explained by horizontal gene transfer (HGT). Other fragments were similar to mitochondrial gene for ribosomal protein S4 in plants and to the glycoprotein (G) gene of the IHNV virus. Presumably, they are pseudogenes inserted into the JNK heterochromatin region. Within this region, also fragments similar to the rye repetitive sequence and chromosome 3B in wheat were found. There is no known mechanism that would explain how foreign sequences were inserted into the block region of tandem repetitive sequences of the JNK family

Tracking of intercalary DNA sequences integrated into tandem repeat arrays in rye Secale vavilovii

The structure of repetitive sequences of the JNK block present in the pericentromeric region of the 2RL chromosome was studied in Secale vavilovii. Amplification of sequences present between the JNK sequences led to the identification of seven abnormal DNA fragments. Two of these fragments showed high similarity to the glutamate 5-kinase gene and putative alcohol dehydrogenase gene of trypanosomatid from the genus Leishmania, whose presence can be explained by horizontal gene transfer (HGT). Other fragments were similar to mitochondrial gene for ribosomal protein S4 in plants and to the glycoprotein (G) gene of the IHNV virus. Presumably, they are pseudogenes inserted into the JNK heterochromatin region. Within this region, also fragments similar to the rye repetitive sequence and chromosome 3B in wheat were found. There is no known mechanism that would explain how foreign sequences were inserted into the block region of tandem repetitive sequences of the JNK family

Genetic diversity of natural psammophilous populations of Hypogymnia physodes (L.) Nyl. on Polish seacoast dunes

Hypogymnia physodes is a lichenized fungus of the family Parmeliaceae. The aim of this study was to compare the level of genetic diversity in eight psammophilous and three epiphytic populations of this species from the Baltic coast in Poland, based on randomly amplified polymorphic DNA (RAPD) markers. In the reactions with nine primers, 153 fragments were obtained, of which 133 were polymorphic. In one reaction, from 0 (for lich2 primer) to 55 (for C02 primer) amplicons were obtained. A Dice’s genetic similarity index matrix was constructed based on the results of RAPD marker polymorphism examination. The values of similarity indices ranged from 0.00 to 0.73. Results of this study confirm the separateness of all three epiphytic populations from those found on sand dunes (100% support, UPGMA/1000 trees)

The distribution pattern of 5-methylcytosine in rye (Secale L.) chromosomes.

The rye (Secale L.) genome is large, and it contains many classes of repetitive sequences. Secale species differ in terms of genome size, heterochromatin content, and global methylation level; however, the organization of individual types of sequences in chromosomes is relatively similar. The content of the abundant subtelomeric heterochromatin fraction in rye do not correlate with the global level of cytosine methylation, hence immunofluorescence detection of 5-methylcytosine (5-mC) distribution in metaphase chromosomes was performed. The distribution patterns of 5-methylcytosine in the chromosomes of Secale species/subspecies were generally similar. 5-methylcytosine signals were dispersed along the entire length of the chromosome arms of all chromosomes, indicating high levels of methylation, especially at retrotransposon sequences. 5-mC signals were absent in the centromeric and telomeric regions, as well as in subtelomeric blocks of constitutive heterochromatin, in each of the taxa studied. Pericentromeric domains were methylated, however, there was a certain level of polymorphism in these areas, as was the case with the nucleolus organizer region. Sequence methylation within the region of the heterochromatin intercalary bands were also demonstrated to be heterogenous. Unexpectedly, there was a lack of methylation in rye subtelomeres, indicating that heterochromatin is a very diverse fraction of chromatin, and its epigenetic regulation or potential influence on adjacent regions can be more complex than has conventionally been thought. Like telomeres and centromeres, subtelomeric heterochromatin can has a specific role, and the absence of 5-mC is required to maintain the heterochromatin state

The DNA methylation level against the background of the genome size and t-heterochromatin content in some species of the genus Secale L

Methylation of cytosine in DNA is one of the most important epigenetic modifications in eukaryotes and plays a crucial role in the regulation of gene activity and the maintenance of genomic integrity. DNA methylation and other epigenetic mechanisms affect the development, differentiation or the response of plants to biotic and abiotic stress. This study compared the level of methylation of cytosines on a global (ELISA) and genomic scale (MSAP) between the species of the genus Secale. We analyzed whether the interspecific variation of cytosine methylation was associated with the size of the genome (C-value) and the content of telomeric heterochromatin. MSAP analysis showed that S. sylvestre was the most distinct species among the studied rye taxa; however, the results clearly indicated that these differences were not statistically significant. The total methylation level of the studied loci was very similar in all taxa and ranged from 60% in S. strictum ssp. africanum to 66% in S. cereale ssp. segetale, which confirmed the lack of significant differences in the sequence methylation pattern between the pairs of rye taxa. The level of global cytosine methylation in the DNA was not significantly associated with the content of t-heterochromatin and did not overlap with the existing taxonomic rye relationships. The highest content of 5-methylcytosine was found in S. cereale ssp. segetale (83%), while very low in S. strictum ssp. strictum (53%), which was significantly different from the methylation state of all taxa, except for S. sylvestre. The other studied taxa of rye had a similar level of methylated cytosine ranging from 66.42% (S. vavilovii) to 74.41% in (S. cereale ssp. afghanicum). The results obtained in this study are evidence that the percentage of methylated cytosine cannot be inferred solely based on the genome size or t-heterochromatin. This is a significantly more complex issue

Comparison of ethylene carbonate and formamide as components of the hybridization mixture in FISH

The protocols for in situ hybridization (ISH) techniques can vary considerably; however, they usually include denaturation and hybridization steps. Denaturing compounds are used to reduce denaturation and hybridization temperature, which keeps the proper morphology of the preparation. Formamide is the most commonly used reagent in in situ hybridization to lower the melting temperature. The substitution of toxic formamide for a non-toxic ethylene carbonate at 20 % and 50 % concentration in the hybridization mixture helped obtain a high quality in situ hybridization result with two sequences characteristic for rye, JNK, and Bilby. The results after hybridization, with a duration of 90 min and 16 h, were identical when formamide or ethylene carbonate were used in the mixture. In addition, the toxic formamide was eliminated from the post-hybridization steps and specific hybridization signals for both probes were still obtained

Mechanisms of genome changes and gene exression in plant hybrid polyploids

Polyploidy is created by multiplication of a single genome or combination of different genomes (allopolyploids). This paper reviews literature data obtained from a study of synthetic plant allopolyploids. The available data shed light on: dynamic and stochastic changes in genome structure and function, genome and sequences elimination, changes in gene control systems and expression, novel activation and gene repression, epigenetic changes, transposons activation and RNA role in gene regulation

Characteristic and applications of SSR and ISSR in study of plant genomes

W badaniach roślin markery DNA stanowią odpowiednie narzędzie pozwalające na szczegółową genetyczną analizę, mapowanie genów oraz określenie genetycznego zróżnicowania. Sekwencje mikrosatelitarne i obszary znajdujące się między nimi okazały się ważnym źródłem markerów DNA i były z powodzeniem stosowane przy badaniach genetycznego zróżnicowania, mapowaniu genomów, selekcji cech pożądanych w rolnictwie oraz przy rozróżnianiu genotypów. Markery SSR (ang simple sequence repeat) i ISSR (ang. inter simple sequence repeat) wykazują wiele zalet w porównaniu do innych markerów stosowanych w badaniach genetycznych. Charakteryzują się one wysokim polimorfizmem i dużą częstością występowania. Niniejszy przegląd przedstawia cechy i zastosowanie markerów SSR i ISSR w badaniach genomów roślinnych.In plant investigations, DNA based markers are suitable tools for detailed genetic analysis, gene mapping and estimation of genetic diversity. Microsatellites and regions between them are important source of DNA markers and have been successfully applied for detection of genetic diversity, genome mapping, marker assisted selection of agronomically important traits and genotype differentiation. Simple sequence repeat (SSR) and inter simple sequence repeat (ISSR) markers have many advantages for genetic studies over other markers. They are highly polymorphic and abundant. This review aimed to characterize and present possible applications of SSR and ISSR in plant genome research

The epigenetic regulation of centromeres and telomeres in plants and animals

The centromere is a chromosomal region where the kinetochore is formed, which is the attachment point of spindle fibers. Thus, it is responsible for the correct chromosome segregation during cell division. Telomeres protect chromosome ends against enzymatic degradation and fusions, and localize chromosomes in the cell nucleus. For this reason, centromeres and telomeres are parts of each linear chromosome that are necessary for their proper functioning. More and more research results show that the identity and functions of these chromosomal regions are epigenetically determined. Telomeres and centromeres are both usually described as highly condensed heterochromatin regions. However, the epigenetic nature of centromeres and telomeres is unique, as epigenetic modifications characteristic of both eu- and heterochromatin have been found in these areas. This specificity allows for the proper functioning of both regions, thereby affecting chromosome homeostasis. This review focuses on demonstrating the role of epigenetic mechanisms in the functioning of centromeres and telomeres in plants and animals