Jiri Macas

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..This slows down the study of nuclear genome and the development of molecular tools to facilitate banana improvement...

..Based on this feature, the Psmar-1 elements are believed to be the most likely candidates for the master elements of the Stowaway MITEs in pea...

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..sativa. The other two V. grandiflora subfamilies showing a considerable divergence from V. sativa sequences were found to be accumulated at subtelomeric regions of V. grandiflora chromosomes...

..k-mer frequencies were also successfully used to identify and characterize smRNAs derived from CentO repeats...

..Thus, the subfamilies may have evolved at these loci following the spreading of the A subrepeats from the IGS to genomic regions outside the rDNA clusters...

..A search for Zaba sequences in EST databases showed that at least some elements are transcribed, most probably due to their association with genic regions...

..In contrast, labeling of VicTR-B repeats in V. sativa resulted in mainly intercalary bands of various intensities and only weak telomeric signals...

..We have also detected an enrichment of satellite DNA sequences for the motif CAAAA that is supposed to be involved in breakage-reunion of repeated sequences...

..Considering this retroelement's constitutive expression and observed high mutual similarity of the element genomic sequences, it is possible to speculate about its recent amplification in the genomes of pea and other legume plants...

..This is one of very few known cases of spliced LTR retrotransposons and the only one where splicing does not involve parts of the element's coding sequences, thus resembling intron splicing found in most cellular genes...

..Another new env-class retrotransposon similar to PIGY was also identified among genomic sequences of Medicago truncatula...

..This fact, together with observed variations in positions and numbers of rDNA loci, suggests considerable divergence between karyotypes of the species studied...

..However, the development of appropriate data mining tools is required in order to fully utilize this sequencing data for repeat characterization...

..While the models including eccDNA are attractive for their potential to explain rapid turnover of satellite DNA, the existence of satellite repeat-derived eccDNA has not yet been systematically studied in a wider range of plant genomes...

..In addition, the protein domain which is otherwise associated with DNA transposons have been detected in part of the Tat-like extra ORFs, pointing to their origin from an insertion event of a mobile element...

..Based on these findings, we propose Pisum as a useful model for investigation of centromere architecture and the still poorly understood role of repetitive DNA in centromere evolution, determination, and function...

..Correlations between the repeat distributions and the current taxonomic classification of these species are discussed...

..abstract:..

..This approach allows the distinguishing of sequences that differ in only a few nucleotides and has proved to be valuable for studies of satellite DNA evolution in plants...

..These experiments enabled assignment of the linkage groups IV and VII to chromosomes 4 and 7, respectively...

..The suitability of the libraries for genome mapping was demonstrated by isolation of clones containing microsatellite motifs...

..Whereas both tandem repeat families are mostly specific to the genus Pisum, many of the dispersed repeats were detected in other legume species, mainly those in the genus Vicia...

..The server allows to analyze several million sequence reads, which typically results in identification of most high and medium copy repeats in higher plant genomes...

..In contrast to VicTR-B, orientation of the PisTR-B clusters with respect to telomeric sequences appeared to be conserved among subtelomeric regions of metacentric chromosomes and of the short arms of acrocentric chromosomes...