Retrotransposons represent the most labile fraction for genomic rearrangements in polyploid plant species.

Understanding how increased genome size and diversity within polyploid genomes impacts plant evolution and breeding continues to be challenging. Although historical studies by McClintock suggested the importance of transposable elements mediated by polyploidisation on genomic changes, data from plant crosses remain scarce. Despite the absence of a conclusive proof regarding autonomous retrotransposon movement in synthetic allopolyploids, the transposition of retrotransposons and their ubiquitous dispersion in all plant species might explain the positive correlation between the genome size of plants and the prevalence of retrotransposons. Here, we address polyploidisation-mediated rearrangements of retrotransposon-associated sequences and discuss a tendency for a preferential restructuring of large ancestral genomes after polyploidisation. A comparative analysis of the frequency of modifications of retrotransposon-associated sequences in synthetic polyploids with marked differences in genome sizes is presented. Such analyses suggest the absence of a significant difference in the rates of rearrangements despite vast dissimilarities in the retrotransposon copy number between species, which emphasises the high plasticity of this genomic feature. See also the sister article focusing on animals by Arkhipova and Rodriguez in this themed issue.

Differential effects of high-temperature stress on nuclear topology and transcription of repetitive noncoding and coding rye sequences.

The plant stress response has been extensively characterized at the biochemical and physiological levels. However, knowledge concerning repetitive sequence genome fraction modulation during extreme temperature conditions is scarce. We studied high-temperature effects on subtelomeric repetitive sequences (pSc200) and 45S rDNA in rye seedlings submitted to 40°C during 4 h. Chromatin organization patterns were evaluated through fluorescent in situ hybridization and transcription levels were assessed using quantitative real-time PCR. Additionally, the nucleolar dynamics were evaluated through fibrillarin immunodetection in interphase nuclei. The results obtained clearly demonstrated that the pSc200 sequence organization is not affected by high-temperature stress (HTS) and proved for the first time that this noncoding subtelomeric sequence is stably transcribed. Conversely, it was demonstrated that HTS treatment induces marked rDNA chromatin decondensation along with nucleolar enlargement and a significant increase in ribosomal gene transcription. The role of noncoding and coding repetitive rye sequences in the plant stress response that are suggested by their clearly distinct behaviors is discussed. While the heterochromatic conformation of pSc200 sequences seems to be involved in the stabilization of the interphase chromatin architecture under stress conditions, the dynamic modulation of nucleolar and rDNA topology and transcription suggest their role in plant stress response pathways.

Presence of env-like sequences in Quercus suber retrotransposons.

The main difference between LTR retrotransposons and retroviruses is the presence of the envelope (env) gene in the latter, downstream of the pol gene. The env gene is involved in their infectious capacity. Here we report the presence of env-like sequences in the genome of Quercus suber (cork oak), one of the most economically important Portuguese species. These gene sequences were isolated through DNA amplification between RNaseH conserved motifs and 3' LTR, based on the structure of copia retrotransposons. Phylogenetic analysis revealed that almost all the clones isolated are clustered with Cyclops-2, a Ty3-gypsy element identified in Pisum sativum, except one clustered with gypsy and copia retroelements found in different species. This suggests the existence of a potential ancestral sequence of the env gene, prior to the separation of Ty3-gypsy and Ty1-copia retrotransposons. Additionally, the isolated env-like sequences showed 26-39% of homology with env-like sequences characterized in viruses. The origin of env-like sequences in retrotransposons from host plant taxa is discussed.

Dynamics of functional heterochromatic domains in the plant interphase nucleus.

Biologists have been fascinated for more than 2 centuries about how the nucleus in eukaryotes is organised. Certain of the component parts are well known, but the overall picture is blurred and often confusing. Small genome species have chromosomes in their interphase nuclei disposed in diffuse chromosome territories, without any Rabl arrangement, while in large genomes the chromosomes run string-like through the nucleus with a Rabl orientation following through the cell cycle. What happens in genomes of intermediate size is either a bit of both, depending on the tissue being studied, or still remains to be determined. The centromeres are the most dynamic and least well understood part of the nucleus, subject to rapid evolutionary change and with an epigenetic mark based on a special form of histone CENH3. Nonetheless, the centromere epigenetic mark has been inherited for millions of years by a process that is a complete mystery. Centromeres are involved with the dynamic interactions between chromosomes and other parts of the nuclear environment, such as the nuclear matrix and inner nuclear membrane, and they also engage with the spindle when the order within the nucleus changes during its division. The nucleolus organizer regions have likewise posed tantalising problems about their massive amplification of rDNA sequences, and how they are regulated and expressed. Some of these issues are now becoming clearer with advances in the science and the ongoing development of new molecular tools. These developments are discussed in this contribution, with particular reference to the centromere and the nucleolus organizer.

Distribution patterns of phosphorylated Thr 3 and Thr 32 of histone H3 in plant mitosis and meiosis.

Cell cycle dependent phosphorylation of conserved N-terminal tail residues of histone H3 has been described in both animal and plant cells. Through cytogenetic approaches using different plant species we show a detailed description of distribution patterns of phosphorylated histone H3 at either threonine 3 or threonine 32 in mitosis and meiosis. In meristematic cells of the large genome species Secale cereale, Vicia faba and Hordeum vulgare we have found that phosphorylation of both threonine residues begins in prophase, and dephosphorylation occurs in late anaphase. However, in the small genome species Arabidopsis thaliana dephosphorylation occurs at anaphase. In the first division of meiosis of species with large genomes phosphorylation of histone H3 at either threonine 3 or threonine 32 is seen first in diakinesis and extends to anaphase I, whereas in the second division these post-translational modifications are visible at metaphase II through anaphase II. While in A. thaliana dephosphorylation takes place at anaphase I and II. In all species analysed phosphorylated H3 at either threonine 3 or threonine 32 are distributed along the entire length of chromosomes during mitotic metaphase and metaphase I. In the second meiotic division threonine 3 phosphorylation is restricted to the pericentromeric domain, while phosphorylation of threonine 32 is widespread along chromosome arms of all species analysed.

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.

Colchicine-induced polyploidization depends on tubulin polymerization in c-metaphase cells.

The microtubule cytoskeleton plays a crucial role in the cell cycle and in mitosis. Colchicine is a microtubule-depolymerizing agent that has long been used to induce chromosome individualization in cells arrested at metaphase and also in the induction of polyploid plants. Although attempts have been made to explain the processes and mechanisms underlying polyploidy induction, the role of the cytoskeleton still remains largely unknown. Through immunodetection of alpha-tubulin, different concentrations (0.5 or 5 mM) of colchicine were found to produce opposite effects in the organization of the cytoskeleton in rye (Secale cereale L.). A low concentration (0.5 mM) induced depolymerization of the microtubular cytoskeleton in all phases of the cell cycle. In contrast, a high concentration (5 mM) was found to induce the polymerization of new tubulin-containing structures in c-metaphase cells. Furthermore, both treatments also showed contrasting effects in the induction of polyploid cells. Flow cytometric analysis and quantitative assessments of nucleolus-organizing regions revealed that only the high-concentration colchicine treatment was effective in the formation of polyploid cells. Our studies indicate that spindle disruption alone is insufficient for the induction of polyploid cells. The absence of any tubulin structures in plants treated with colchicine at the low concentration induced cell anomalies, such as the occurrence of nuclei with irregular shape and/or (additional) micronuclei, 12 h after recovery, pointing to a direct effect on cell viability. In contrast, the almost insignificant level of cell anomalies in the high-concentration treatment suggests that the presence of new tubulin-containing structures allows the reconstitution of 4C nuclei and their progression into the cell cycle.

Ribosomal DNA heterochromatin in plants.

The aim of this review is to integrate earlier results and recent findings to present the current state-of-the-art vision concerning the dynamic behavior of the ribosomal DNA (rDNA) fraction in plants. The global organization and behavioral features of rDNA make it a most useful system to analyse the relationship between chromatin topology and gene expression patterns. Correlations between several heterochromatin fractions and rDNA arrays demonstrate the heterochromatic nature of the rDNA and reveal the importance of the genomic environment and of developmental controls in modulating its dynamics.

Different numbers of rye B chromosomes induce identical compaction changes in distinct A chromosome domains.

In rye each B chromosome (B) represents 5.5% of the diploid A genome. Rye Bs have several nuclear to whole plant effects although they seem to bear no genes except for the ones that lead to their maintenance within a population. In this context, and considering that rye Bs are enriched in repetitive non-coding regions that build up heterochromatin (het), we investigated the influence of Bs on the organization of two chromatin fractions, namely the ribosomal DNA (facultative het) and satellite (non-het) domain of rye chromosome 1 by silver staining on root tip metaphase cells. The results show that rye Bs cause condensation both in the NOR and in the chromosome 1 satellite domain. Since the silver staining technique used is indicative of the transcriptional activity of the NORs, the condensation observed at those loci demonstrates that the rRNA gene arrays are down-regulated in the presence of Bs, regardless of their number per individual. Furthermore, the organizational changes of metaphase NORs find parallel with the interphase organization of ribosomal chromatin, since the frequency of cells with intranucleolar condensed rDNA regions increases drastically and nuclear matrix attachment pattern is altered in the presence of the Bs. Our results show an identical effect of the Bs on the organization of two distinct chromosome domains displaying a presence/absence dichotomy.

Physical mapping, expression patterns and interphase organisation of rDNA loci in Portuguese endemic Silene cintrana and Silene rothmaleri.

Double target in situ hybridization to root tip metaphase and interphase cells of Silene cintrana and Silene rothmaleri was used to allocate the position of 18S-5.8S-25S and 5S rRNA genes. In both species, the 18S-5.8S-25S rDNA probe labelled four sites located on the short arms of two submetacentric chromosomes. Only one locus for 5S rDNA was mapped adjacent to 18S-5.8S-25S genes in a subterminal position on the centromere side: in S. rothmaleri the 5S rDNA locus was adjacent to the small 18S-5.8S-25S locus while in S. cintrana it was near the large one. The NOR activity analysed by Ag-staining in metaphase cells revealed proportionality between in situ labelling dimensions and Ag-NORs. In both species all rDNA loci were potentially active, although in S. rothmaleri a tendency for the expression of only one locus was observed. Interphase organisation analysis of rDNA showed some differences between both species that were correlated with NOR activity.

Modification of wheat rDNA loci by rye B chromosomes: a chromatin organization model.

The rDNA loci, and their associated NORs, on chromosomes 1B and 6B of the hexaploid wheat cv. Lindström have been used as a chromatin marker to investigate the functional basis of the phenotype effects of introgressed supernumerary B chromosomes (Bs) of rye. The rye Bs themselves lack genes, other than those which determine their mitotic drive mechanism, and the way in which they can modulate characters determined by the A chromosome background has always been a puzzle. An isogenic line of Lindström plants carrying different numbers of Bs was used as the experimental system to see how different doses of Bs (from 0 to 6) affected the activity of the wheat NORs and the organization of their rDNA loci at interphase. Silver staining on metaphase chromosomes was used to evaluate the previous activity of the NORs, and to reveal variations in their size; and the pTa71 FISH probe from wheat was used to visualize structural modifications to the interphase rDNA loci. A single B had no measurable effect, but, as the B-number increased, there were significant changes in the physical dimensions of the metaphase NORs, reflecting reduced levels of their activity earlier in the cell cycle, and also in the condensation patterns of the interphase rDNA loci. In addition, the higher B-numbers caused a size heteromorphism between the homologous NORs. A model is discussed which interprets the phenotypic effects of Bs generically, in nucleotypic terms, based of their being 'genetically inert' but 'chromosomally active'.

5-Methylcytosine distribution and genome organization in triticale before and after treatment with 5-azacytidine.

Triticale (2n=6x=42) is a hybrid plant including rye (R) and wheat (A and B) genomes. Using genomic in situ hybridization with rye DNA as a probe, we found the chromosomes of the R genome were not intermixed with the wheat chromosomes in 85% of nuclei. After treatment of seedlings with low doses of the drug 5-azacytidine (5-AC), leading to hypomethylation of the DNA, the chromosomes became intermixed in 60% of nuclei; the next generation showed intermediate organization. These results correlate with previous data showing that expression of R-genome rRNA genes, normally suppressed, is activated by 5-AC treatment and remains partially activated in the next generation. The distribution of 5-methylcytosine (5-mC) was studied using an antibody to 5-mC. Methylation was detected along the lengths of all chromosomes; there were some chromosome regions with enhanced and reduced methylation, but these were not located at consistent positions, nor were there differences between R and wheat genome chromosomes. After 5-AC treatment, lower levels of methylation were detected. After 5-AC treatment, in situ hybridization with rye genomic DNA sometimes showed micronuclei of rye origin and multiple translocations between wheat and rye chromosomes. Genomic DNA was analysed using methylation-sensitive restriction enzymes and, as probes, two rDNA sequences, two tandemly organised DNA sequences from rye (pSc200 and pSc250), and copia and the gypsy group retrotransposon fragments from rye and wheat. DNA extracted immediately after 5-AC treatment was cut more by methylation-sensitive restriction enzymes than DNA from untreated seedlings. Each probe gave a characteristic restriction fragment pattern, but rye- and wheat-origin probes behaved similarly, indicating that hypomethylation was induced in both genomes. In DNA samples from leaves taken 13-41 days after treatment, RFLP (Restriction Fragment Length Polymorphism) patterns were indistinguishable from controls and 5-AC treatments with all probes. Surprising differences in hybridization patterns were seen between DNA from root tips and leaves with the copia-fragment probes.

Interphase arrangement of rye B chromosomes in rye and wheat.

Probes for B chromosome-specific sequences in the distal region of the long arm of the rye B have been used to investigate the interphase arrangement of the Bs in rye and in hexaploid wheat. The Lindström strain of wheat carries the rye Bs as additions. The number of in situ signals in nuclei with two, three and four Bs is often less than the maximum B number, and it seems that the Bs may be grouped together in various ways rather than being randomly dispersed throughout the nucleus. The degree of physical association is greater in rye than in the allen wheat background. The results are discussed in relation to the pairing and recombination preferences of the Bs in rye and in Lindström wheat.

Nucleolar dominance in triticales: control by unlinked genes.

Hybrid plants and animals often show suppression of activity of ribosomal genes (rDNA) originating from one of the parental or ancestral species. In the wheat x rye amphiploid triticale, containing 28 chromosomes of wheat origin and 14 from rye, rDNA of rye origin (on chromosome 1R) is not normally expressed, while the 1B- and 6B-origin rDNA from wheat shows strong expression. Expression of rDNA can be accurately assessed by the silver staining method, which stains both interphase nucleoli and metaphase rDNA sites that were actively expressed at the previous interphase. We show here that substitution of another rye chromosome, 2R, by a chromosome from hexaploid wheat, 2D (triticale-2D(2R)), prevents suppression of the rye-origin rDNA, and leads to activity of all six major rDNA loci. These results were found in two different triticales and supported by rDNA behaviour in wheat-rye chromosomal addition lines. Models for chromosomal interactions leading to control of rDNA expression are presented.

Development-dependent inheritance of 5-azacytidine-induced epimutations in triticale: analysis of rDNA expression patterns.

Genomic imprinting of rye origin rDNA sequences in triticale is modulated by DNA methylation responsible for ontogenic expression patterns of those sequences. Considering the dynamic nature of these phenomena, we evaluated the influence of plant development on the inheritance of modified rye rDNA expression patterns. DNA hypomethylation was induced in triticale by 5-azacytidine (5AC) treatments at distinct developmental stages of M1 plants, and expression patterns were analysed in M2. The activity of rye origin rRNA genes in progeny of untreated and 5AC-treated plants was evaluated by silver staining in meristematic root tip cells and in meiocytes at diplotene. In the progeny of 5AC-treated plants, a significant increase in rye rDNA expression was observed, contrasting with the residual activity in untreated plants. Significant differential effects of 5AC treatments were observed in M2 plants and correlated with the M1 plant developmental stage in which DNA hypomethylation was induced. Hypotheses to explain the origin of those differences are discussed here.

Painting rye B chromosomes in wheat: interphase chromatin organization, nuclear disposition and association in plants with two, three or four Bs.

The B chromosomes (Bs) of rye (Secale cereale) have been studied at interphase in terms of their chromatin organization, patterns of nuclear disposition and physical association in plants with two, three, and four Bs. The study was made in the Lindström strain of hexaploid wheat, which carries the rye Bs as an addition line, by in situ hybridization with a B-specific probe and by genomic in situ hybridization (GISH) with rye genomic DNA, enabling whole chromosome painting. Repetitive sequences common to the As and Bs of rye allow for visualization of the rye B at interphase in the wheat background. A B-specific probe enables the orientation of two or more Bs to be determined, and the combination of both probes used together gives information on the disposition of the Bs and on their patterns of physical association within the nucleus. The Bs form linear "strings', and the ends of their long arms, which can be detected by the B-specific probe, are usually located within the hemisphere of the nucleus that has the least condensed chromatin. There is dose-dependent association, and even numbers (2B, 4B) have a greater preference for association than odd ones (3B).

The influence of B chromosomes on rDNA organization in rye interphase nuclei.

Patterns of rye rDNA organization in interphase nuclei were studied through the use of in situ hybridization in spreads of root meristem cells from plants with and without B chromosomes (Bs). In cells from plants without Bs each rDNA locus is organized as a single perinucleolar knob of condensed chromatin with decondensed chromatin inside the nucleolus. In plants with Bs there is a marked modification of the pattern, found in more than 23% of nuclei, which involves several regions of condensed chromatin interspersed with decondensed chromatin inside the nucleolus. This B-induced alteration in rDNA interphase organization suggests a change in expression of the rRNA genes located on the A chromosomes probably related to the reduction in nuclear RNA observed previously in plants with Bs. The influence of the Bs on the expression of A chromosome genes, through rearrangement of interphase chromatin, could provide the basis of an explanation for some of the known phenotypic effects of B chromosomes in rye.

Reprogramming of rye rDNA in triticale during microsporogenesis.

To test the hypothesis that interspecific genomic and chromosome interactions leading to nucleolar dominance could be reprogrammed in meiosis, we compared the expression of distinct nucleolar organizing region (NOR) loci in hexaploid triticale root tip meristematic cells, pollen mother cells and young pollen grains. Interphase and metaphase cells were silver stained to quantify nucleoli and active NOR loci respectively. A marked difference in the ribosomal RNA gene activity of each locus was observed when different types of cells were compared: in somatic and pollen mother cells, rRNA gene activity was mainly restricted to major wheat NORs (1B and 6B) with only a small contribution from rye NORs (1R). In contrast, in young pollen grains, all NORs present, including the 1R NORs, were consistently active. The expression of all NORs just after meiosis is considered to be a consequence of meiotic reprogramming of rye origin rDNA. Gene reprogramming mediated by the resetting of methylation patterns established early in embryogenesis is suggested to be responsible for the differential expression of the NORs of rye origin in distinct developmental stages of triticale.

The developmental stage of inactivation of rye origin rRNA genes in the embryo and endosperm of wheat x rye F1 hybrids.

To identify the developmental stage during which the preferential inactivation of rRNA genes from the rye parent occurs in wheat x rye hybrids, nucleolar activity was evaluated in the embryo and endosperm of developing seeds of the hybrids. The hybrids were obtained from crosses of euploid and aneuploid lines of hexaploid wheat, Triticum aestivum cv. Chinese Spring, with rye, Secale cereale cv. Centeio do Alto. The number of nucleolar organizing regions (NORs) and nucleoli present in the embryo and endosperm cells of wheat, and wheat x rye F1 hybrids, at different times after fertilization was scored by silver staining. The inactivation of rDNA of rye origin in F1 hybrids occurs simultaneously in the embryo and in the endosperm between 4 and 5 days after fertilization, when these have been through six and 10 cell cycles respectively. We conclude that the genomic interactions leading to the inactivation of the rye origin rDNA is a time-dependent process, related to the developmental stage and independent of the number of cell cycles (DNA replication rounds) they have been through.

rRNA gene activity and control of expression mediated by methylation and imprinting during embryo development in wheat x rye hybrids.

Ribosomal RNA genes originating from one parent are often suppressed in interspecific hybrids. We show that treatments during germination with the cytosine analogue 5-azacytidine stably reactivate the expression of the suppressed rRNA genes of rye origin in the wheat x rye amphiploid, triticale, by preventing methylation of sites in the rye rDNA. When 5-azacytidine is applied to embryos of triticale and wheat x rye F1 hybrids nine, or more, days after fertilization, rye rRNA gene expression is stably reactivated in the resulting seedling. Earlier treatments have no effect on rye rRNA gene expression, indicating that undermethylation of DNA early in embryo development is reversible. After 9 days, the methylation status of rRNA genes in maintained throughout development. Since the change in expression follows a methylation change at particular restriction-enzyme sites, the data establish a clear correlation between gene activity and methylation in plants.