Alexander Belyayev

Repetitive DNA and chromosomal rearrangements: speciation-related events in plant genomes

Chromosomal change is one of the more hotly debated potential mechanisms of speciation. It has long been argued over whether – and to what degree – changes in chromosome structure contribute to reproductive isolation and, ultimately, speciation. In this review we do not aim to completely analyze accumulated data about chromosomal speciation but wish to draw attention to several critical points of speciation-related chromosomal change, namely: (a) interrelations between chromosomal rearrangements and repetitive DNA fraction; (b) mobility of ribosomal DNA clusters; and (c) rDNA and transposable elements as perpetual generators of genome instability.

Activity of the En/Spm-like transposons in meiosis as a base for chromosome repatterning in a small, isolated, peripheral population of Aegilops speltoides Tausch.

Chromosomal repatterning is considered to be one of the main mechanisms for plant genome evolution. Here, we report the first cytogenetic evidence for the involvement of En/Spm transposons in ongoing chromosomal repatterning leading to the rise of new fertile genomic forms in a small, isolated, peripheral plant population. Cytogenetical screening of original individual plants of Aegilops speltoides Tausch. with different phenotypes revealed a wide spectrum of chromosomal abnormalities including extra chromosomes, chromosomal rearrangements, and variability in chromosomal position/number of 45S and 5S rDNA sites. Cytogenetic analysis of the dynamics of En/Spm transposons in meiosis indicates that: (i) this type of transposon is active during male gametogenesis; (ii) separately or in conjunction with rDNA they form clusters in the hot spots of large chromosomal rearrangements; (iii) appearance of at least part of the mobile rDNA sites in genome of Ae. speltoides are connected with meiotic activity of En/Spm transposons. PCR screening for the site-selected transposon insertions confirm the presence of combined fragments that consist partly of the sequence of En/Spm transposon and partly of 5S rDNA sequence.

Transposable elements in a marginal plant population: temporal fluctuations provide new insights into genome evolution of wild diploid wheat

BackgroundHow new forms arise in nature has engaged evolutionary biologists since Darwins seminal treatise on the origin of species. Transposable elements (TEs) may be among the most important internal sources for intraspecific variability. Thus, we aimed to explore the temporal dynamics of several TEs in individual genotypes from a small, marginal population of Aegilops speltoides. A diploid cross-pollinated grass species, it is a wild relative of the various wheat species known for their large genome sizes contributed by an extraordinary number of TEs, particularly long terminal repeat (LTR) retrotransposons. The population is characterized by high heteromorphy and possesses a wide spectrum of chromosomal abnormalities including supernumerary chromosomes, heterozygosity for translocations, and variability in the chromosomal position or number of 45S and 5S ribosomal DNA (rDNA) sites. We propose that variability on the morphological and chromosomal levels may be linked to variability at the molecular level and particularly in TE proliferation.ResultsSignificant temporal fluctuation in the copy number of TEs was detected when processes that take place in small, marginal populations were simulated. It is known that under critical external conditions, outcrossing plants very often transit to self-pollination. Thus, three morphologically different genotypes with chromosomal aberrations were taken from a wild population of Ae. speltoides, and the dynamics of the TE complex traced through three rounds of selfing. It was discovered that: (i) various families of TEs vary tremendously in copy number between individuals from the same population and the selfed progenies; (ii) the fluctuations in copy number are TE-family specific; (iii) there is a great difference in TE copy number expansion or contraction between gametophytes and sporophytes; and (iv) a small percentage of TEs that increase in copy number can actually insert at novel locations and could serve as a bona fide mutagen.ConclusionsWe hypothesize that TE dynamics could promote or intensify morphological and karyotypical changes, some of which may be potentially important for the process of microevolution, and allow species with plastic genomes to survive as new forms or even species in times of rapid climatic change.

Chromosomal distribution of reverse transcriptase-containing retroelements in two Triticeae species

A large portion of plant and particularly cereal genomes consist of repetitive DNA families, many of which are likely to be or to have evolved from retroelements. Molecular evidence suggests that repeated DNA sequences, although perhaps originating as innocuous or ‘selfish’ elements, can have dramatic effects on genome organization and function. Knowledge of chromosomal distribution of retroelements is important for understanding plant chromosome structure/functional organization, and could shed light on the dynamics of retroelements and their role in the evolutionary process. In the present study we aim to find a possible correlation between physical location of the regions with species-specific sequences and the distribution of conserved RT domains of the Ty1-copia, Ty3-gypsy and LINE groups of retroelements on the chromosomes of two diploid species that belong to the different branches of the tribe Triticeae, namely Aegilops speltoides Tausch (2n=2x=14) and Hordeum spontaneum L (2n=2x=14). All three groups of retroelements were found in large quantities in the genomes of the tested species. They are cluster-distributed, and the important role of these elements in the formation of terminal heterochromatin is shown. We found that there was a predominance of Ty1-copia and LINE elements in the chromosome regions with preferential content of species-specific sequences.

Variability of the chromosomal distribution of Ty3-gypsy retrotransposons in the populations of two wild Triticeae species

Here, we report data on the population variability of Ty3-gypsy retrotransposons in genomes of Aegilops speltoides (2n = 2x = 14) and Hordeum spontaneum (2n = 2x = 14). Based on the sequence analysis or reverse transcriptase (RT) gene conserved domains, two groups of elements were recognized. Elements of Group I show relatedness to such a known element as RIRE2, and elements of Group II show relatedness to Fatima and Cereba. Cloned and sequenced fragments of Ty3-gypsy RT that show the closest relatedness to known elements (Fatima and RIRE2) were used as probes for fluorescent in situ hybridization (FISH). FISH experiments revealed mini-cluster organization of the Ty3-gypsy element chromosomal distribution in wild Triticeae species. Mini-clusters can be divided into three categories according to their intraspecific stability: (i) stable species-specific clusters that are mainly adjusted to the regions of rRNA genes; (ii) variable clusters that represent 68% of clusters in the genome of Ae. speltoides and 20% in the genome of H. spontaneum; and (iii) population-specific clusters that are mainly insertions into centromeric central domains of different chromosomes and the majority of these insertions were detected in populations with hot, dry environments. Significant interpopulation variability of Ty3-gypsy element chromosomal distribution in the Ae. speltoides genome contrasts with the uniform genome of H. spontaneum and may reflect differences in adaptive strategies between investigated species.

Heterochromatin discrimination in Aegilops speltoides by simultaneous genomic in situ hybridization

Simultaneous genomic in situ hybridization with probe preannealing (SP-GISH) was used for discriminating Aegilops speltoides chromosome regions by their relatedness to DNA of other species. We used a hybridization mixture of two differently labelled DNAs, one from the species used for chromosome spread preparations and a second from species of different and varying affinity, thus creating a two-colour system showing chromosome regions where alien DNA hybridized. Genomic DNA from A. speltoides was labelled with biotin and preannealed with digoxigenin-labelled total genomic DNA from different accessions of Ae. speltoides, Ae. bicornis, Ae. tauschii and Hordeum spontaneum. The probe mixture was hybridized to mitotic chromosmes of Ae. speltoides. Chromosome regions of preferential hybridization of self-DNA were visualized as green, whereas regions of combined hybridization showed orange–yellow fluorescence. We observed GISH banding patterns with a different degree of green fluorescence along Ae. speltoides chromosomes that directly correlated with evolutionary distance. Small green bands were observed in subtelomeric and telomeric heterochromatic regions using DNA of a different accession of Ae. speltoides, whereas when using DNA of H. spontaneum most regions of the chromosomes, except pericentromeric regions, showed mainly green fluorescence. The resolution and application of the approach to the study of heterochromatin differentiation are discussed.

En/Spm-like transposons in Poaceae species: Transposase sequence variability and chromosomal distribution

Belonging to Class II of transposable elements, En/Spm transposons are widespread in a variety of distantly related plant species. Here, we report on the sequence conservation of the transposase region from sequence analyses of En/Spm-like transposons from Poaceae species, namely Zingeria biebersteiniana, Zingeria trichopoda, Triticum monococcum, Triticum urartu, Hordeum spontaneum, and Aegilops speltoides. The transposase region of En/Spm-like transposons was cloned, sequenced, and compared with equivalent regions of Oryza and Arabidopsis from the gene bank database. Southern blot analysis indicated that the En/Spm transposon was present in low (Hordeum spontaneum, Triticum monococcum, Triticum urartu) through medium (Zingeria bieberstiana, Zingeria trichopoda) to relatively high (Aegilops speltoides) copy numbers in Poaceae species. A cytogenetic analysis of the chromosomal distribution of En/Spm transposons revealed the concurence of the chromosomal localization of the En/Spm clusters with mobile clusters of rDNA. An analysis of En/Spm-like transposase amino acid sequences was carried out to investigate sequence divergence between 5 genera — Triticum, Aegilops, Zingeria, Oryza and Arabidopsis. A distance matrix was generated; apparently, En/Spm-like transposase sequences shared the highest sequence homology intra-generically and, as expected, these sequences were significantly diverged from those of O. sativa and A. thaliana. A sequence comparison of En/Spm-like transposase coding regions defined that the intra-genomic complex of En/Spm-like transposons could be viewed as relatively independent, vertically transmitted, and permanently active systems inside higher plant genomes.The sequence data from this article was deposited in the EMBL/GenBank Data Libraries under the accession nos. AY707995-AY707996-AY707997-AY707998-AY707999-AY708000-AY708001-AY708002-AY708003-AY708004-AY708005-AY708005-AY265312.

Diversity of Long Terminal Repeat Retrotransposon Genome Distribution in Natural Populations of the Wild Diploid Wheat Aegilops speltoides

The environment can have a decisive influence on the structure of the genome, changing it in a certain direction. Therefore, the genomic distribution of environmentally sensitive transposable elements may vary measurably across a species area. In the present research, we aimed to detect and evaluate the level of LTR retrotransposon intraspecific variability in Aegilops speltoides (2n = 2x = 14), a wild cross-pollinated relative of cultivated wheat. The interretrotransposon amplified polymorphism (IRAP) protocol was applied to detect and evaluate the level of retrotransposon intraspecific variability in Ae. speltoides and closely related species. IRAP analysis revealed significant diversity in TE distribution. Various genotypes from the 13 explored populations significantly differ with respect to the patterns of the four explored LTR retrotransposons (WIS2, Wilma, Daniela, and Fatima). This diversity points to a constant ongoing process of LTR retrotransposon fraction restructuring in populations of Ae. speltoides throughout the species’ range and within single populations in time. Maximum changes were recorded in genotypes from small stressed populations. Principal component analysis showed that the dynamics of the Fatima element significantly differ from those of WIS2, Wilma, and Daniela. In terms of relationships between Sitopsis species, IRAP analysis revealed a grouping with Ae. sharonensis and Ae. longissima forming a separate unit, Ae. speltoides appearing as a dispersed group, and Ae. bicornis being in an intermediate position. IRAP display data revealed dynamic changes in LTR retrotransposon fractions in the genome of Ae. speltoides. The process is permanent and population specific, ultimately leading to the separation of small stressed populations from the main group.

Tandem repeats on an eco-geographical scale: outcomes from the genome of Aegilops speltoides

The chromosomal pattern of tandem repeat fractions of repetitive DNA is one of the most important characteristics of a species. In the present research, we aimed to detect and evaluate the level of intraspecific variability in the chromosomal distribution of species-specific Spelt 1 and Aegilops-Triticum-specific Spelt 52 tandem repeats in Aegilops speltoides and in closely related diploid and polyploid species. There is a distinct eco-geographical gradient in Spelt 1 and Spelt 52 blocks abundance in Ae. speltoides. In marginal populations, the number of Spelt 1 chromosomal blocks could be 12–14 times lower than in the center of the species distribution. Also, in related diploid species, the abundance of Spelt 52 correlates with evolutionary proximity to Ae. speltoides. Finally, the B- and G-genomes of allopolyploid wheats have Spelt 1 chromosomal distribution patterns similar to those of the types of Ae. speltoides with poor and rich contents of Spelt 1, respectively. The observed changes in numbers of blocks of Spelt 1 and Spelt 52 tandem repeats along the eco-geographical gradient may due to their depletion in the marginal populations as a result of increased recombination frequency under stressful conditions. Alternatively, it may be accumulation of tandem repeats in conducive climatic/edaphic environments in the center of the species’ geographical distribution. Anyway, we observe a bidirectional shift of repetitive DNA genomic patterns on the population level leading to the formation of population-specific chromosomal patterns of tandem repeats. The appearance of a new chromosomal pattern is considered an important factor in promoting the emergence of interbreeding barriers.

Ac-like transposons in populations of wild diploid Triticeae species: comparative analysis of chromosomal distribution

Data are presented on the intra- and interspecific differences/similarities in chromosomal patterns of Ac-like elements (hAT family) in ecologically contrasted populations of three Triticeae species - Aegilops speltoides, Triticum urartu, and Hordeum spontaneum. Application of original computer software made it possible to precisely map transposon clusters and to link them to known chromosomal markers (rDNA sites, centromeres, and heterochromatin regions). From our data we can specify the most visible features of Ac-like elements chromosomal distribution: preferential concentration in chromosomal proximal regions; high percentage of clusters on the border between euchromatin and heterochromatin; complementary chromosomal arrangement towards En/Spm transposons (CACTA); population-specific insertions into centromeres; more differences in total cluster numbers between populations of self-pollinated species than between populations of cross-pollinated species. The application of statistical simulation (Resampling) method to analysis of data indicates that ecology may play a certain role in dynamics of Ac-like elements. Comparison of real Ayala distances, as well as real chromosomal distribution of Ac-like elements in populations of two species with different mating systems with the same but randomly simulated parameters, revealed that non-random population structure in the Mediterranean floral zone suffers and becomes chaotic in the Irano-Turanian zone.