Heterogeneity in cucumber ribosomal DNA

Instability of plastid DNA in the nuclear genome

Functional gene transfer from the plastid (chloroplast) and mitochondrial genomes to the nucleus has been an important driving force in eukaryotic evolution. Non-functional DNA transfer is far more frequent, and the frequency of such transfers from the plastid to the nucleus has been determined experimentally in tobacco using transplastomic lines containing, in their plastid genome, a kanamycin resistance gene (neo) readymade for nuclear expression. Contrary to expectations, non-Mendelian segregation of the kanamycin resistance phenotype is seen in progeny of some lines in which neo has been transferred to the nuclear genome. Here, we provide a detailed analysis of the instability of kanamycin resistance in nine of these lines, and we show that it is due to deletion of neo. Four lines showed instability with variation between progeny derived from different areas of the same plant, suggesting a loss of neo during somatic cell division. One line showed a consistent reduction in the proportion of kanamycin-resistant progeny, suggesting a loss of neo during meiosis, and the remaining four lines were relatively stable. To avoid genomic enlargement, the high frequency of plastid DNA integration into the nuclear genome necessitates a counterbalancing removal process. This is the first demonstration of such loss involving a high proportion of recent nuclear integrants. We propose that insertion, deletion, and rearrangement of plastid sequences in the nuclear genome are important evolutionary processes in the generation of novel nuclear genes. This work is also relevant in the context of transgenic plant research and crop production, because similar processes to those described here may be involved in the loss of plant transgenes.

Molecular evidence for transcription of genes on a B chromosome in Crepis capillaris

Dispensable, supernumerary (B) chromosomes are found in diverse eukaryotic species. The origin and genetic consequences of B chromosomes have been the subjects of speculation for more than a century. Until now, there has been no molecular evidence that B chromosome DNA is transcribed and there is no unequivocal evidence as to their origin. B chromosomes are considered to be genetically inert although they appear to cause a variety of phenotypic effects. We report that members of one of two ribosomal RNA gene families that are confined to the B chromosomes of a plant, Crepis capillaris, are transcribed--thus providing the first molecular evidence of gene activity on B chromosomes. Sequence analysis of part of the A and B chromosome rRNA genes, together with comparisons with related species, indicates that the B chromosome rRNA genes originate from the A chromosome.

Ribosomal RNA genes and the B chromosome of Brachycome dichromosomatica

Fluorescence in situ hybridization (FISH) with biotinylated rDNA revealed the presence of an rRNA gene cluster on both the A and B chromosomes of Brachycome dichromosomatica, an Australian native ephemeral plant of the arid regions of south-eastern Australia. This species contains only two pairs of A chromosomes and up to three B chromosomes. The regular attachment of the B chromosome to a nucleolus suggests that these ribosomal RNA genes are transcribed. Southern hybridization of DNA from 0B and +B plants digested with a variety of restriction enzymes indicates that the rRNA genes on the A and B chromosomes are the same in sequence and methylation status.

Structural analysis of two length variants of the rDNA intergenic spacer from Eruca sativa

Restriction enzyme analysis of the rRNA genes of Eruca sativa indicated the presence of many length variants within a single plant and also between different cultivars which is unusual for most crucifers studied so far. Two length variants of the rDNA intergenic spacer (IGS) from a single individual E. sativa (cv. Itsa) plant were cloned and characterized. The complete nucleotide sequences of both the variants (3 kb and 4 kb) were determined. The intergenic spacer contains three families of tandemly repeated DNA sequences denoted as A, B and C. However, the long (4 kb) variant shows the presence of an additional repeat, denoted as D, which is a duplication of a 224 bp sequence just upstream of the putative transcription initiation site. Repeat units belonging to the three different families (A, B and C) were in the size range of 22 to 30 bp. Such short repeat elements are present in the IGS of most of the crucifers analysed so far. Sequence analysis of the variants (3 kb and 4 kb) revealed that the length heterogeneity of the spacer is located at three different regions and is due to the varying copy numbers of repeat units belonging to families A and B. Length variation of the spacer is also due to the presence of a large duplication (D repeats) in the 4 kb variant which is absent in the 3 kb variant. The putative transcription initiation site was identified by comparisons with the rDNA sequences from other plant species.

Molecular evolution of the intergenic spacer in the nuclear ribosomal RNA genes of cucurbitaceae

The intergenic spacer (IGS) of a 10-kbp repeat (clone pRZ7D) of the nuclear 18S, 5.8S, and 25S ribosomal RNA genes of Cucurbita pepo (zucchini) was sequenced and compared to the IGS sequences of two other Cucurbitaceae, Curcurbita maxima (squash), and Cucumis sativus (cucumber). The nucleotide sequence and the structural organization of the IGS of C. pepo and C. maxima are rather similar (between 75 and 100% sequence similarity depending on the region compared). The IGS are mainly composed of three different repeated elements interspersed into unique sequences: GC-rich clusters, a 422-bp AT-rich element including the transcription initiation site (TIS) for RNA polymerase I, and 260-bp repeats in the 5' external transcribed spacer (D repeats). The TIS is duplicated in the 10-kbp repeat class of C. pepo, as it is also described for the 11.5-kbp rDNA repeat of C. maxima. The IGS of Cucumis sativus is also composed of different repeated elements; however, obvious sequence identity to the Cucurbita species only occurs around the TIS and the preceding AT-rich region. GC-rich clusters with different primary sequences are present in the IGS of all three plants. Remarkably, the repeated elements in the 5'ETS accumulate TpG and TpNpG motifs, whereas CpG and CpNpG motifs less frequently occur. This accumulation might be caused by the transition of methylated cytosines (in mCpG or mCpNpG motifs) into thymidine via deamination in a previously GC-rich ancestor. The following singular region exhibits 50% G + C in C. pepo, 53% G+C in C. maxima, and 63% G + C in C. sativus.(ABSTRACT TRUNCATED AT 250 WORDS)

Molecular and cytological characterization of repetitive DNA sequences in Brassica

We isolated three different repetitive DNA sequences from B. campestris and determined their nucleotide sequences. In order to analyze organization of these repetitive sequences in Brassica, Southern blot hybridization and in situ hybridization with metaphase chromosomes were performed. The sequence cloned in the plasmid pCS1 represented a middle repetitive sequence present only in B. campestris and not detected in closely related B. Oleracea. This sequence was localized at centromeric regions of six specific chromosomes of B. campestris. The second plasmid, pBT4, contained a part of the 25S ribosomal RNA gene, and its copy number was estimated to be 1,590 and 1,300 per haploid genome for B. campestris and B. oleracea, respectively. In situ hybridization with this sequence showed a clear signal at the NOR region found in the second largest chromosome of B. Campestris. The third plasmid, pBT11, contained a 175-bp insert that belongs to a major family of tandem repeats found in all the Brassica species. This sequence was detected at centromeric regions of all the B. campestris chromosomes. Our study indicates that in situ hybridization with various types of repetitive sequences should give important information on the evolution of repetitive DNA in Brassica species.

Length heterogeneity of the rRNA precursor in cucumber (Cucumis sativus)

The length homogeneous part of the intergenic spacer (IGS) of the 18S-25S ribosomal RNA genes of cucumber (Cucumis sativus) was characterized by sequencing 2389 bp preceding the 18S rRNA coding region of a 12.5 kbp repeat type. This part of the IGS is composed of repeated elements and shows a very complex structural organization. Most obvious is a 119 bp element which is repeated seven times. A single transcription initiation site (TIS) was detected by a 'T4 polymerase stop' experiment upstream of these repetitions giving rise to a 2013 bp 5' external transcribed spacer (ETS) for cucumber. Nuclease mapping showed several transcription termination sites (TTS): the first one is located 350 bp downstream of the 25S rRNA coding region, the others are found within the duplications of this region accounting for the length heterogeneity of cucumber rDNA. Therefore, the TTS is repeated two or three times in the IGS depending on the length of the respective repeat classes and the rRNA precursor is heterogeneous in length varying from approx. 8000 to 11000 nts.

Structure of melon rDNA and nucleotide sequence of the 17-25S spacer region

Restriction enzyme and hybridization analysis of melon nuclear DNA suggests a homogenous rDNA population with a repeat unit of 10.2 kb. Several full length Hind III rDNA repeat units were cloned and one of these is described in detail. The regions coding for 25S, 17S and 5.8S rRNAs were located by crossed-contact hybridization and R-loop mapping. Introns were not observed. The nucleotide sequence of the internal transcribed spacer and flanking regions was determined and compared with the corresponding region from rice rDNA by dot matrix analysis. In addition, the extent of gross sequence homology between cloned melon and pea rDNA units was determined by heteroduplex mapping.

Complex structure of the ribosomal DNA spacer of Cucumis sativus (cucumber)

The nuclear 18 S, 5.8 S and 25 S ribosomal RNA genes (rDNA) of Cucumis sativus (cucumber) occur in at least four different repeat types of 10.2, 10.5, 11.5, and 12.5 kb in length. The intergenic spacer of these repeats has been cloned and characterized with respect to sequence organization. The spacer structure is very unusual compared to those of other eukaryotes. Duplicated regions of 197 bp and 311 bp containing part of the 3'end of the 25 S rRNA coding region and approximately 470 bp of 25 S rRNA flanking sequences occur in the intergenic spacer. The data from sequence analysis suggest that these duplications originate from recombination events in which DNA sequences of the original rDNA spacer were paired with sequences of the 25 S rRNA coding region. The duplicated 3'ends of the 25 S rRNA are separated from each other mostly by a tandemly repeated 30 bp element showing a high GC-content of 87.5%. In addition, another tandemly repeated sequence of 90 bp was found downstream of the 3'flanking sequences of the 25 S rRNA coding region. These results suggest that rRNA coding sequences can be involved in the generation of rDNA spacer sequences by unequal crossing over.

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.