Bursts of transposable elements as an evolutionary driving force.

A burst of transposable elements (TEs) is a massive outbreak that may cause radical genomic rebuilding. This phenomenon has been reported in connection with the formation of taxonomic groups and species and has therefore been associated with major evolutionary events in the past. Over the past few years, several research groups have discovered recent stress-induced bursts of different TEs. The events for which bursts of TEs have been recorded include domestication, polyploidy, changes in mating systems, interspecific and intergeneric hybridization and abiotic stress. Cases involving abiotic stress, particularly bursts of TEs in natural populations driven by environmental change, are of special interest because this phenomenon may underlie micro- and macro-evolutionary events and ultimately support the maintenance and generation of biological diversity. This study reviews the known cases of bursts of TEs and their possible consequences, with particular emphasis on the speciation process.

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.

Heterochromatin differentiation shows the pathways of karyotypic evolution in Israeli mole rats (Spalax, Spalacidae, Rodentia).

C-banding, base-specific fluorochrome staining (CMA3/DA/DAPI), and comparative genomic hybridization (CGH) were used to analyze the constitutive heterochromatin in two Israeli Spalax species, S. galili (2n = 52) and S. judai (2n = 60). It was shown that C-positive centromeric heterochromatin and some telomeric sites comprise GC-rich DNA sequences in both species. Comparative genomic in situ hybridization revealed slight qualitative differences in highly repetitive sequences in the two Spalax species. Eight acrocentric pairs in S. judai that are involved in Robertsonian rearrangements, possessed composite heterochromatin with a preference of S. judai highly repetitive sequences in the proximal region. Heterochromatin of the sex chromosomes, two biarmed homologous pairs (4 and 5) in both species, and acrocentric chromosomes from the group with a variable centromere position in S. judai was entirely species-specific. The high level of homology in the composition of heterochromatin may relate to the recent divergence of Israeli Spalax. Interspecies heterochromatin differences are discussed in the context of possible mechanisms in the Spalax chromosome evolution.

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.

Evolutionary dynamics and chromosomal distribution of repetitive sequences on chromosomes of Aegilops speltoides revealed by genomic in situ hybridization.

Simultaneous genomic in situ hybridization (GISH) with probe preannealing was used to detect the relationship between chromosomal position and sequence conservation on Aegilops speltoides var. aucheri chromosomes. DNA of Secale sylvestre, Hordeum spontaneum, Festuca pratensis, Semiarundinaria fastuosa, Arundo donax and Zea mays that represent several main groups of Poaceae were used as probes. Different GISH-banding patterns that characterize diverse evolutionary trajectories in the repetitive DNA fraction and correlate with evolutionary distance between tested species were observed. Fast-evolving sequences were detected in subterminal telomeric and subtelomeric heterochromatic regions, whereas sequences in pericentromeric regions showed high levels of conservation. GISH experiments revealed extensive conservation in NOR regions on chromosomes 1 and 6 which, in fact, appears to be a complicated mix of rDNA clusters and heterochromatin blocks of different nucleotide composition.

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.

Detection of alien chromosomes from S-genome species in the addition/substitution lines of bread wheat and visualization of A-, B- and D-genomes by GISH.

A modified approach based on the GISH technique for detecting introgressed chromosomes/chromosome arms from closely related S-genome species to wheat genome and for visualization of A-, B- and D-genomes of Triticum aestivum L. (genome AABBDD, 2n = 6x = 42) is presented. For detecting alien chromosomes we investigated two lines of bread wheat, one is an addition line with a pair of chromosome No. 4 short arms from Aegilops searsii (4SsS) and a wheat substitution line with a pair of chromosomes No. 6 from Ae. longissima (6S1). A hybridization mixture consists of two differently labelled DNAs, one from the line used for chromosome spread preparations, and the second from origin species of alien chromosomes. The latter adds different color in the regions of its hybridization showing the presence of alien chromosomes by creating a strong and easily detected combined signal. For discriminating A-, B-, and D-genome chromosomes, the hybridization mixture of differently labelled total DNA from Ae. tauschii--the proposed progenitor of D-genome (detected red) and T. dicoccoides (genome AABB) (detected green) were used. The high temperature of hybridization allows high precision annealing of chromosome/probe sequences and at the same time it sharpens differences between reassociation kinetics of eu- and heterochromatin revealing chromosome substructure. A pre-annealing step increases probe specificity. As a result, we observed brown chromosomes of A-genome, banded green chromosomes of B-genome and red chromosomes of D-genome. Inter genomic invasion of the sequences from A/B-genomes to D-genome has been detected.

Coevolution of A and B genomes in allotetraploid Triticum dicoccoides.

Data is presented on the coevolution of A and B genomes in allotetraploid wheat Triticum dicoccoides (2n = 4x = 28, genome AABB) obtained by genomic in situ hybridization (GISH). Probing chromosomes of T. dicoccoides with DNA from the proposed A/B diploid genome ancestors shows evidence of enriching A-genome with repetitive sequences of B-genome type. Thus, ancestral S-genome sequences have spread throughout the AB polyploid genome to a greater extent than have ancestral A-genome sequences. The substitution of part of the A-genome heterochromatin clusters by satellite DNA of the B genome is detected by using the molecular banding technique. The cause may be interlocus concerted evolution and (or) colonization. We propose that the detected high level of intergenomic invasion in old polyploids might reflect general tendencies in speciation and stabilization of the allopolyploid genome.

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.