Length variation in the non-transcribed spacer of Calliphora erythrocephala ribosomal DNA is due to a 350 base-pair repeat

Extraordinary ribosomal spacer length heterogeneity in a neotyphodium endophyte hybrid: implications for concerted evolution

An extraordinary level of length heterogeneity was found in the ribosomal DNA (rDNA) of an asexual hybrid Neotyphodium grass endophyte, isolate Lp1. This hybrid Neotyphodium endophyte is an interspecific hybrid between two grass endophytes, Neotyphodium lolii, and a sexual form, Epichlöe typhina, and the length heterogeneity was not found in either of these progenitor species. The length heterogeneity in the hybrid is localized to the intergenic spacer (IGS) and is the result of copy-number variation of a tandemly repeated subrepeat class within the IGS, the 111-/119-bp subrepeats. Copy number variation of this subrepeat class appears to be a consequence of mitotic unequal crossing over that occurs between these subrepeats. This implies that unequal crossing over plays a role in the concerted evolution of the whole rDNA. Changes in the pattern of IGS length variants occurred in just two rounds of single-spore purification. Analysis of the IGS length heterogeneity revealed features that are unexpected in a simple model of unequal crossing over. Potential refinements of the molecular details of unequal crossing over are presented, and we also discuss evidence for a combination of homogenization mechanisms that drive the concerted evolution of the Lp1 rDNA.

Identification of the transcriptional initiation site of ribosomal RNA genes in the crustacean Artemia

The proximal part of the Intergenic Spacer, as well as most of the External Transcribed Spacer of the ribosomal RNA type I genes from the crustacean Artemia have been sequenced. We have identified in the Intergenic Spacer five repeats of around 600 bp in length and, possibly, two imperfect or truncated repeats, derived from the principal ones. These sequences are separated by 485 bp from the 17S rRNA coding sequence. We have also identified the start point of transcription by S1 nuclease analysis. This start point is found 248 bp inside the first repeat. The sequence around the start point shows homology with that described for other members of the same phylum, mostly insects. The most conserved regions are from -1 to +25, and the G residue at position -16. At least the three 600-bp repeats upstream from that containing the promoter also contain the start point sequence, and could therefore act as initiation sites for snPIRNA and/or as enhancer sequences for ribosomal RNA gene transcription.

A stochastic mechanism controls the relative replication of equally competent ribosomal RNA gene sets in individual dipteran polyploid nuclei

The endoreplication of the two nucleolar organizers (NOs) of the diploid genome has been examined in individual polyploid nuclei of the dipteran Calliphora erythrocephala. Crosses between two strains with diagnostic nontranscribed spacer polymorphisms in their rRNA genes were used to provide progeny with distinguishable NOs, and single nuclei of two highly polyploid cell types--salivary gland and nurse cells--were examined from individual F1 animals. Initially the representation of the two NOs in total polyploid tissue DNA was determined. This revealed that, although the NO regions present in one of the strains (Tom) were very similar in spacer composition, they displayed two types of behavior in the hybrids containing the single NO region typical of the second strain (Karla). In TW phenotype F1 progeny, very little replication of the Tom NO relative to the Karla NO occurred, whereas in TS phenotype progeny replication of the Tom and Karla NOs was approximately equivalent. When individual polyploid nuclei of the TS phenotype animals were examined, however, the relative replication of the Tom and Karla NOs was found not to be a fixed genetic property but to vary dramatically from cell to cell. This was true even for the nurse cell nuclei within a single ovarian follicle, which are the products of only four mitotic divisions of a single germ-line cell. These findings indicate that for NOs of similar replicative competence, a stochastic mechanism governs the relative usage of each NO for endoreplication and that the relative activity of the two NOs is not stably determined through the mitotic divisions preceding polyploidization. Stochastic selection after mitotic DNA replication could be a general phenomenon governing the relative usage (transcription) of different, but equally competent, alleles of any gene in individual cells, if the required factors are in short supply.

rDNA in Locusta migratoria is very variable: two introns and extensive restriction site polymorphisms in the spacer

Cloned ribosomal DNA (rDNA) of Locusta migratoria was analyzed by restriction site mapping and SI nuclease experiments. The repeat unit is 18 kb long. The nontranscribed spacer region (NTS) is very large (11 kb) and homogeneous in length, but many of the restriction sites are heterogeneous among the repeat units. Two introns of different length were found at different positions in the 28S gene. They are present in less than 5% of the genes.

The avian malaria Plasmodium lophurae has a small number of heterogeneous ribosomal RNA genes

The structure and number of the ribosomal RNA (rRNA) genes of the avian malaria parasite Plasmodium lophurae has been examined using Southern blot analysis and recombinant DNA techniques. The ribosomal DNA (rDNA) of P. lophurae has been cloned into the plasmid pBR322, beginning with size-selected populations of Cla I- and Hind III-restricted parasite DNA. The structure of two clones (CL-1 and HA-2) is presented in detail. These two clones together probably represent the entire 17s and 25s coding regions of P. lophurae. Analysis of quantitative genomic Southern blots reveals that there are approximately six rRNA genes per haploid genome, and that the rRNA genes may be divided into four distinct classes by restriction analysis. Examination of the flanking regions of these genes indicates that they are not organized into easily recognizable tandem repeats.

Phenotypic reversal in dam mutants of Escherichia coli K-12 by a recombinant plasmid containing the dam+ gene

A recombinant plasmid, pMQ3, carrying the dam gene of Escherichia coli K-12, was constructed and transformed into dam+ and dam- strains. Both dam- and dam+ strains containing pMQ3 showed a wild phenotype for all traits, including mutation rate, except for a 10-fold increase in DNA adenine methylase activity.

Spacer size heterogeneity in ribosomal DNA of Chironomus thummi is due to a 120 bp repeat homologous to a predominantly centromeric repeated sequence

The rDNA of Ch. tepperi is homogeneous in structure with a repeat size of 8.4 kb. This size seems to be typical for the basic repeat unit in Chironomus species. Ch. th. piger rDNA cistrons are slightly increased in length (9.0 kb). In the non-transcribed spacer (NTS) an appr. 0.18 kb segment is additionally present in about 50% of the repeats. Ch. th. thumni DNA contains largely heterogeneous rDNA repeats, mainly between 10 and 16 kb. The heterogeneity is due to varying numbers of 120 bp elements present in the NTS. The different spacer size classes are not randomly distributed. The short repetitive 120 bp elements (Cla I elements) hybridize in situ with the nucleolus and with centromere regions. The Cla I elements are regularly present in the thummi NTS, but are absent in the piger NTS. Only very few piger rDNA cistrons may contain Cla I elements.

The wheat ribosomal DNA spacer region: Its structure and variation in populations and among species

The wheat rDNA clone pTA250 was examined in detail to provide a restriction enzyme map and the nucleotide sequence of two of the eleven, 130 bp repeating units found within the spacer region. The 130 bp units showed some sequence heterogeneity. The sequence difference between the two 130 bp units analysed (130.6 and 130.8) was at 7 positions and could be detected as a 4 °C shift in Tm when heterologous and homologous hybrids were compared. This corresponded to a 1.2% change in nucleotide sequence per ΔTm of 1 °C. The sensitivity of the Tm analysis using cloned sequences facilitated the analysis of small sequence variations in the spacer region of different Triticum aestivum cultivars and natural populations of T. turgidum ssp. dicoccoides (referred to as T. dicoccoides). In addition spacer length variation was assayed by restriction enzyme digestion and hybridization with spacer sequence probes.Extensive polymorphism was observed for the spacer region in various cultivars of T. aestivum, although within each cultivar the rDNA clusters were homogeneous and could be assigned to particular chromosomes. Within natural populations of T. dicoccoides polymorphism was also observed but, once again, within any one individual the rDNA clusters appeared to be homogeneous. The polymorphism, at the sequence level (assayed by Tm analysis), was not so great as to prevent the use of spacer sequence variation as a probe for evolutionary relationships. The length variation as assayed by restriction enzyme digestion did not appear to be as useful in this regard, since its range of variation was extensive even within populations of a species.

Cloning and analysis of ribosomal DNA of Chironomus thummi piger and Chironomus thummi thummi. The nontranscribed spacer of Ch. th. thummi contains a highly repetitive DNA sequence

The ribosomal DNAs from Ch. thummi piger and Ch. th. thummi were cloned and analysed by a variety of restriction endonucleases. Comparison of rDNA clones from the two subspecies revealed a considerable length difference: the length of the analysed rDNA cistrons is approximately 9.0 kb for Ch. th. piger and approximately 14.5 kb for Ch. th. thummi. The nearly 5 kb additional DNA in Ch. th. thummi is clearly located within the non-transcribed spacer region, and consists of AT-rich, repetitive DNA elements. These elements with a basic repeat length of approximately 120 bp, are arranged tandemly in stretches of up to about 50 identical copies, which are characterized by a cleavage site for ClaI restriction endonuclease. They are found only in the Ch. th. thummi rDNA clones and not in the Ch. th. piger clones. Southern hybridizations between cloned ribosomal DNA and "centromeric" highly repetitive DNA have shown that the ribosomal repetitive Cla-elements are closely related to a highly repetitive DNA sequence family, which is present in various chromosomal sites particularly the centromeres. Sequence analysis has revealed more than 90% homology between the ribosomal Cla-elements and the "centromeric" Cla-elements.--Since it is clear from cytological investigations that Ch. th. piger with the small rDNA repeating unit is the phylogenetically older subspecies, we postulate a transposition of Cla-elements into the nucleolar DNA during the evolution of Ch. th. thummi.

Molecular cloning and characterization of ribosomal RNA genes from the brine shrimp

A library of genomic DNA from the brine shrimp, Artemia, has been constructed with the Charon 4A phage vector, utilizing EcoRI passenger fragments. Screening this library with purified Xenopus laevis cloned rDNA genes has resulted in the identification and plaque purification of a recombinant containing a complete Artemia (18 S + 26 S) rDNA repeat unit. A physical map derived from the analysis of restriction endonuclease digests of the repeat unit, which measures 13.9 kilobase pairs, is similar to the map derived from genomic DNA. In common with several other species, the 26 S rRNA gene terminates with a HindIII recognition site.

Rate of turnover of structural variants in the rDNA gene family of Drosophila melanogaster

A high degree of polymorphism for the length and copy number of rDNA spacers, in both the X and Y chromosome clusters, has been found in a wild population of Drosophila melanogaster. The genetic behaviour of rDNA structural variants in separate and mixed populations derived from isofemale lines suggest that they are not subject to strong selection and are stable for over 1,000 generations. The high structural variability suggests an evolutionary rapid process of turnover in the family which could partly explain widespread sequence homogeneity (concerted evolution) of rDNA within a species.

Distribution of spacer length classes and the intervening sequence among different nucleolus organizers in Drosophila hydei

Drosophila hydei rRNA genes from different chromosomes and from different stocks have been studied by restriction enzyme analysis. In DNA from wild-type females, about half of the X chromosomal rRNA genes are interrupted by an intervening sequence within the 28S coding region. In contrast to D. melanogaster, the intervening sequences belong to a single size class of 6.0 kb. Although there are two nucleolus organizers on the Y chromosome, genes containing the intervening sequence seem to be restricted to the X chromosome. -- As shown in four cloned rDNA fragments, the nontranscribed spacers differ in length by having varying numbers of a 242 base pair sequence located in tandem in the right section of the spacer. In genomic rDNA, the spacers also differ in length by a regular 0.25 kb interval. Spacers with between 5 and 15 subrepeats occur frequently within the X and Y chromosomal nucleolus organizers in different D. hydei stocks; shorter and longer spacers are also present but are relatively rare. -- Although each genotype is characterized by different frequencies of some spacer classes, the prominent spacer length heterogeneity pattern is similar among the different nucleolus organizers and, therefore, seems to be conserved during evolution.