Repeated Sequences and Genome Change

Physical mapping and activity of ribosomal RNA genes in mussel Mytilus galloprovincialis

In bivalve molluscs, NOR analysis was carried out by silver staining, and extensive intra- and interindividual differences in the apparent number of NORs were reported. In this work, we determine the physical mapping of 18S and 28S ribosomal genes of the mussel M. galloprovincialis by fluorescence in situ hybridization (FISH). We also apply silver staining to the same individuals in order to determine if structural changes are involved in the heteromorphism detected by this technique. Our results show that rDNA loci map on the telomeric region of the long arm of two submetacentric-subtelocentric chromosome pairs. In addition to variations in NOR expression, we found some cases of structural variations that affect the number of rDNA loci between individuals and the location of the rDNA locus between the cells of the individual. We suggest that FISH should be applied to other bivalves to assess the variation of rDNA loci and undertake more accurate interspecific comparisons.

The differential expression of ribosomal RNA genes

Ribosomal RNA genes are localized at chromosomal sites termed nucleolus organizers because nucleoli form around transcribed ribosomal RNA genes. The relative activities of arrays of ribosomal RNA genes can be estimated cytologically by comparing the sizes of nucleoli in the same cell. Also, active nucleolus organizers give rise to visible constrictions in metaphase chromosomes whereas inactive nucleolus organizers do not. With these assays the differential expression of nucleolus organizers and ribosomal RNA genes has been observed frequently, especially in interspecies hybrids. Studies on wheat have revealed that differences in gene expression are associated with differences in chromatin structure and cytosine methylation. Active loci have higher proportions of their genes decondensed and accessible to proteins and also higher proportions with a non-methylated cytosine residue at a CCGG site in the region of the promoter. Short, related sequences with dyad symmetry have been noted between —140 and —70 base pairs from where transcription is initiated in a wheat ribosomal RNA gene. Similar sequences are reiterated upstream of the promoter over 2000 base pairs. From comparison of this gene structure with that ofXenopusribosomal RNA genes it can be concluded that these short sequences are likely to act as enhancers of transcription by binding to specific regulatory proteins that function to stimulate the attachment of polymerase I complexes. Differential expression of arrays of ribosomal RNA genes results when genes have different numbers of enhancer repeats or a higher affinity for the regulatory protein(s). This model to explain differential gene expression and the origins of genetic variation affecting ribosomal RNA gene expression are discussed.

Somatic intrachromosomal homologous recombination events in populations of plant siblings

Intrachromosomal homologous recombination in whole tobacco plants was analyzed using beta-glucuronidase as non-selectable marker. We found that recombination frequencies were additive for transgenes in allelic positions and could be enhanced by treatment of plants with DNA-damaging agents. We compared the patterns of distribution of recombination events of different transgenic lines of tobacco and Arabidopsis with the respective Poisson distributions. Some lines showed Poisson-like distributions, indicating that recombination at the transgene locus was occurring in a random fashion in the plant population. In other cases, however, the distributions deviated significantly from Poisson distributions indicating that for specific transgene loci and/or configurations recombination events are not randomly distributed in the population. This was due to overrepresentation of plants with especially many as well as especially few recombination events. Analysis of one tobacco line indicated furthermore that the distribution of recombination events could be influenced by treating the seedlings with external factors. Our results suggest that different plant individuals, or parts of them, might exhibit different transient 'states' of recombination competence. A possible model relating 'recombination silencing' and transcription silencing to heterochromatization of the transgene locus is discussed.

Nuclear DNA content of Vitis species, cultivars, and other genera of the Vitaceae

The nuclear DNA content was analyzed in Vitis species, hybrid cultivars, and genera of the Vitaceae using flow cytometry. Significant variation was found among Vitis species, hybrids, and other genera of the Vitaceae (Ampelopsis and Parthenocissus). DNA content was estimated to range from 0.98 to 1.05 pg/2C within V. labrusca (ns) and 0.86 to 1.00 pg/2C within V. vinifera (ns). Genotypes from Vitis and Parthenocissus were similar in nuclear DNA content (approximately 1.00 pg/2C) whereas they differed significantly from Ampelopsis (1.39 pg/2C). No correlation between DNA content and the center of origin of genotypes of the Vitaceae was noted. Based on the present study, the Vitis genome size is 475 Mbp, 96% of which is non-coding. Knowledge of DNA content is useful in order to understand the complexity of the Vitis genome and to establish a relationship between the genetic and physical map for map-based cloning.

Genetic analyses of rDNA spacer-length variation in barley

The genetic mechanism controlling the inheritance of single and multiple spacer-length variant (slv) phenotypes in barley was investigated in six F2 segregating populations. The results indicated that two independently assorting loci, each with co-dominant alleles, govern genetic variability for rDNA in barley regardless of the number of bands expressed by a given phenotype. The following chromosomal locations are proposed: sl variants 1, 4, 5, 6, and 7 on chromosome 7, and sl variants 7, 8, 9, 12, and 13 on chromosome 6; sl variant 7 is thus located on both of the chromosomes.

Somatic homologous recombination in planta: the recombination frequency is dependent on the allelic state of recombining sequences and may be influenced by genomic position effects

We have previously described a non-selective method for scoring somatic recombination in the genome of whole plants. The recombination substrate consists of a defective partial dimer of Cauliflower Mosaic Virus (CaMV) sequences, which can code for production of viable virus only upon homologous recombination; this leads to disease symptoms on leaves. Brassica napus plants (rapeseed) harbouring the recombination substrate as a transgene were used to examine the time in plant development at which recombination takes place. The analysis of three transgene loci revealed recombination frequencies specific for each locus. Recombination frequencies were increased if more than one transgene locus was present per genome, either in allelic (homozygosity of the transgene locus) or in non-allelic positions. In both cases, the overall recombination frequency was found to be elevated to approximately the sum of the frequencies for the individual transgene loci or slightly higher, suggesting that the respective transgene loci behave largely independently of each other. For all plants tested (single locus, two or multiple loci) maximal recombination frequencies were of the order of 10(-6) events per cell division.

Molecular analysis of highly repeated genome fractions in Solanum and their use as markers for the characterization of species and cultivars

Highly repeated DNA of potato (Solanum sp.) was characterized by cloning various major repeated elements of the nuclear genome. The percentage of the nuclear genome of the specific fractions and the restriction enzyme patterns were determined in order to show the distribution and organization of the respective repeats in the genome of Solanum tuberosum cultivars, dihaploid breeding lines and in wild species of Solanum. Several of the clones obtained were represented in a high copy number but showed no informative RFLP patterns. More information was gained from 'restriction satellite' repeats. The clone pR1T320 was found to contain satellite repeats (360 bp in length) that are proportionally present in the genome of all Solanum species at frequencies, between 0.5% and 2.6% and which are differently organized. This repeat was also found in the genera Lycopersicon, Datura and Nicotiana. With various restriction enzymes characteristic RFLP patterns were detected. A more or less genus-specific element for Solanum was the 183-bp repeat (clone pSA287; between 0.2-0.4% of the nuclear genome) that was present in the majority of the Solanum species analyzed except S. kurtzianum, S. bulbocastanum and S. pinnatisectum. In a few wild species (prominently in S. kurtzianum, S. demissum and S. acaule) a specific repeat type was detected (clone pSDT382; repeat length approximately 370 bp) that could be used to trace the wild species introduced into S. tuberosum cultivars. The repeats analyzed together with the 18S, 5.8S and 25S ribosomal DNA (1.9-5.2%, corresponding to 1800-5500 rDNA copies) comprised approximately 4-7% of the Solanum genome.

Characterization of a plant SINE, p-SINE1, in rice genomes

We have previously found that a short interspersed element (SINE), named p-SINE1, is present in the Waxy gene of Oryza sativa in two copies. Here, we cloned five members of p-SINE1 located at other loci in O. sativa and determined their nucleotide sequences. These sequences had a T-rich pyrimidine tract at their defined 3' end and were flanked by direct repeats of a sequence of mostly 14-15 bp long like p-SINE1s in the Waxy gene. The consensus sequence derived from total seven members of p-SINE1 was 123 bp in length and had an internal promoter region for RNA polymerase III. The 5'-half region of the sequence was partially homologous to the tRNA-related block of rabbit C family, one of SINEs in the animal system. Two of the seven p-SINE1 members were not present in the corresponding loci in African rice, Oryza glaberrima, and may thus be available for classification of some rice strains. Comparison of the nucleotide sequences of the Waxy gene between O. sativa and O. glaberrima showed that base substitutions have frequently occurred in a p-SINE1 member (p-SINE1-r1) and a transposable element Tnr1 also present in the Waxy gene, suggesting that these elements, which appear as repetitive sequences in the rice chromosome, tend to acquire base substitutions at a higher frequency than do unique sequences.

RFLP analysis of Zea mays callus cultures and their regenerated plants

Tissue culture of the Zea mays inbred line A188 resulted in the regeneration of plants having a high level of phenotypic variation compared to seed-grown control plants. To determine how such variation was induced and whether this could be related to specific in vitro culture methods, callus cultures were established and maintained on different, commonly used culture media. Plants were regenerated and the genomic DNA of callus cultures and regenerants analysed for RFLP differences. The results show that regardless of the gene probe used, callus formation resulted in significant deviations from the DNA pattern normally found in seed-grown control plants. Alterations in gene copy number also occurred. As differentiation and organogenesis began, the level of DNA variation fell, and most of the regenerated plants showed a genetic similarity to the controls; those with RFLP differences were the somaclonal variants.

An unusual wheat insertion sequence (WIS1) lies upstream of an alpha-amylase gene in hexaploid wheat, and carries a "minisatellite" array

Comparison of the 5' flanking regions of three alpha-amylase genes from chromosome 6B of hexaploid wheat by heteroduplex and sequence analysis revealed the presence of a 1.6 kb stem-loop insertion sequence (WIS1) in one of them. Polymorphism among hexaploid wheat varieties suggests the relatively recent insertion/excision of this sequence from its present position. The complete sequence of the stem-loop insertion shows that it has many of the features found in transposable elements, including target site duplication and terminal inverted repeats. One unusual feature is a tandem array of direct repeats comprising a wheat "minisatellite" sequence. Both the insertion sequence and the minisatellite are found at multiple locations in the wheat genome, but the functional significance of their association in WIS1 is unknown. The minisatellite arrays share a common core structure, and long arrays are polymorphic between different hexaploid varieties.

Ribosomal RNA genes in plants: variability in copy number and in the intergenic spacer

Ribosomal RNA genes in plants are highly variable both in copy number and in intergenic spacer (IGS) length. This variability exists not only between distantly related species, but among members of the same genus and also among members of the same population of a single species. Analysis of inheritance indicates that copy number change is rapid, occurring even among somatic cells of individual plants, and that up to 90% or more of the gene copies are superfluous. Subrepetitive sequences within the IGS appear to be changing rapidly as well. They are not only variable in sequence from one species to the next, but can vary in number between neighboring gene repeats on the chromosome. In all species examined in detail they are located in the same region of the IGS and contain sequences that can be folded into stem-loop structures flanked by a pyrimidine-rich region. It has been suggested that these subrepeats function in transcriptional enhancement, termination or processing, or in recombination events generating the high multiplicity of ribosomal genes.

Heritable somaclonal variation in wild barley (Hordeum spontaneum)

Progenies of H. spontaneum plants regenerated from immature embryo derived calli were analysed for somaclonal variation on the following traits: (1) organization of the intergenic spacer of the rRNA genes; (2) B and C hordein pattern on SDS-PAGE; (3) genomic organization of the B and C hordein coding sequences; (4) mitochondrial DNA organization assayed by hybridization of Southern blots of total DNA with mitochondrial coding genes; (5) cytology. One out of twelve progeny plants was characterized as variant for two traits: (a) a loss of 1.8 and 2.5 kb Taq I intergenic rDNA spacer fragments and (b) a variant pattern of hordeins on 1-D SDS-PAGE. No numerical or structural chromosome variation was detected among the control plants therefore it is assumed that the variation was caused by the in vitro culture and transmitted, through sexual reproduction, to the analysed progeny.

Nor loci analysis in progenies of plants regenerated from the scutellar callus of bread-wheat : A molecular approach to evaluate somaclonal variation

Progenies of plants regenerated from scutellar callus of bread wheat (Triticum aestivum L.) were analysed for the organization of the intergenic spacer of the rRNA genes, located at the sites of the nucleolar organizer region (Nor loci). Sexual progenies derived from the regenerated plants of three wheat cultivars were subjected to this analysis. The respective DNAs were digested with the restriction endonuclease TaqI, and probed with a specific rDNA fragment by Southern blothybridization. The intergenic rDNA spacer could thus be characterized for each of the three cultivars. Thirty-eight progeny plants of the cultivars 'Chinese Spring' and 'Miriam' were found to be stable in their organisation of the Nor loci: no changes relative to the Nor of control plants from these cultivars were revealed. On the other hand, three progeny plants of 'ND7532' showed reduction in the number of the rDNA spacers. Since no variability in the Nor loci could be revealed among control 'ND7532' plants, this seems to indicate that the changes in the progeny of regenerated plants resulted from the in vitro culture of the scutellar callus. Grain glutenin and gliadin profiles of sexual progenyplants derived from scutellar calli of 'Chinese Spring', of 'Miriam' as well as of 'ND7532' were identical to the respective control plants of these cultivars, indicating low (or no) somaclonal variation in these grain proteins in the analyzed plants.

Different AT-rich satellite DNAs in Cucurbita pepo and Cucurbita maxima

The AT-rich highly repeated satellite DNA of Cucurbita pepo (zucchini) and Cucurbita maxima (pumpkin) were cloned and their DNA structure was investigated. DNA sequencing revealed that the repeat length of satellite DNA in Cucurbita pepo is 349-352 base pairs. The percentage of AT-base pairs is about 61%. This satellite is highly conserved in restriction enzyme pattern and DNA sequence; sequence heterogeneity is about 10%. In contrast, the satellite DNA of Cucurbita maxima has a repeat length of 168-169 base pairs. This satellite is also rich in AT-base pairs (64%), existing in at least three different variants as revealed by restriction enzyme analysis and DNA sequencing. The sequence heterogeneity between these variants is about 15%. The two satellite DNAs showed no cross-hybridization to each other and sequence homology is only limited. Nevertheless, we found in the C. pepo genome a high amount of sequences resembling the satellite of C. maxima. In contrast, the satellite repeat of C. pepo is found in the C. maxima DNA only in a few copies. These observations were discussed with respect to satellite DNA evolution and compared to the data received from monocotyledonous species.

Variation in the ribosomal RNA genes among individuals of Vicia faba

Length heterogeneity in the ribosomal repeat of Vicia faba is due to the presence of variable numbers of a 325 bp subrepetitive element within the nontranscribed spacer region. The distribution of size classes among 88 individuals within a population was investigated by blot-hybridization. We find that individual plants can exhibit more than 20 size classes and that hybridization patterns are highly diverse from individual to individual, more so than for any species so far investigated. In contrast, no such differences are observed in patterns for different tissues from a single plant or from parental to F1 generation. Some changes were observed in the F2 generation. We conclude that unequal recombination can give rise to the diversity that we observe for the V. faba rDNA repeats.

Repetitive DNA and chromosome evolution in plants

Most higher plant genomes contain a high proportion of repeated sequences. Thus repetitive DNA is a major contributor to plant chromosome structure. The variation in total DNA content between species is due mostly to variation in repeated DNA content. Some repeats of the same family are arranged in tandem arrays, at the sites of heterochromatin. Examples from the Secale genus are described. Arrays of the same sequence are often present at many chromosomal sites. Heterochromatin often contains arrays of several unrelated sequences. The evolution of such arrays in populations is discussed. Other repeats are dispersed at many locations in the chromosomes. Many are likely to be or have evolved from transposable elements. The structures of some plant transposable elements, in particular the sequences of the terminal inverted repeats, are described. Some elements in soybean, antirrhinum and maize have the same inverted terminal repeat sequences. Other elements of maize and wheat share terminal homology with elements from yeast, Drosophila, man and mouse. The evolution of transposable elements in plant populations is discussed. The amplification, deletion and transposition of different repeated DNA sequences and the spread of the mutations in populations produces a turnover of repetitive DNA during evolution. This turnover process and the molecular mechanisms involved are discussed and shown to be responsible for divergence of chromosome structure between species. Turnover of repeated genes also occurs. The molecular processes affecting repeats imply that the older a repetitive DNA family the more likely it is to exist in different forms and in many locations within a species. Examples to support this hypothesis are provided from the Secale genus.