Molecular characterization of ribosomal intergenic spacer in the tadpole shrimp Triops cancriformis (Crustacea, Branchiopoda, Notostraca)

Genome ◽  
2006 ◽  
Vol 49 (8) ◽  
pp. 888-893 ◽  
Author(s):  
Andrea Luchetti ◽  
Franca Scanabissi ◽  
Barbara Mantovani
Keyword(s):  
Ribosomal Dna ◽  
Concerted Evolution ◽  
Intergenic Spacer ◽  
Population Level ◽  
Promoter Sequence ◽  
Nuclear Ribosomal Dna ◽  
Rrna Gene ◽  
Living Fossil ◽  
Triops Cancriformis ◽  
External Transcribed Spacer

Nuclear ribosomal DNA constitutes a multigene family, with tandemly arranged units linked by an intergenic spacer (IGS), which contains initiation/termination transcription signals and usually tandemly arranged subrepeats. The structure and variability of the IGS region are analyzed here in hermaphroditic and parthenogenetic populations of the "living fossil" Triops cancriformis (Branchiopoda, Notostraca). The results indicate the presence of concerted evolution at the population level for this G+C-rich IGS region as a whole, with the major amount of genetic variability found outside the subrepeat region. The subrepeats region is composed of 3 complete repeats (a, c, d) intermingled with 3 repeat fragments (b, e, f) and unrelated sequences. The most striking datum is the absolute identity of subrepeats (except type d) occupying the same position in different individuals/populations. A putative promoter sequence is present upstream of the 18S rRNA gene, but not in subrepeats, which is at variance with other arthropod IGSs. The absence of a promoter sequence in the subrepeats and subrepeat sequence conservation suggests that this region acts as an enhancer simply by its repetitive nature, as observed in some vertebrates. The putative external transcribed spacer (840 bp) shows hairpin structures, as in yeasts, protozoans, Drosophila, and vertebrates.Key words: concerted evolution, Crustacea, external transcribed spacer, intergenic spacer, ribosomal DNA, subrepeats, Triops cancriformis.

scholarly journals Ribosomal DNA evolution at the population level: nucleotide variation in intergenic spacer arrays of Daphnia pulex.

Genetics ◽  
1995 ◽  
Vol 141 (4) ◽  
pp. 1327-1337
Author(s):  
T J Crease
Keyword(s):  
Ribosomal Dna ◽  
Consensus Sequence ◽  
Group Analysis ◽  
Daphnia Pulex ◽  
Intergenic Spacer ◽  
Population Level ◽  
Crossing Over ◽  
Nucleotide Variation ◽  
Dna Variation ◽  
Last Glaciation

Abstract Nucleotide variation was surveyed in 21 subrepeat arrays from the ribosomal DNA intergenic spacer of three Daphnia pulex populations. Eighteen of these arrays contained four subrepeats. Contrary to expectations, each of the four positions within the array had a different consensus sequence. However, gene conversion, involving sequences less than the length of a subrepeat, had occurred between subrepeats in different positions. Three arrays had more than four subrepeats and were undoubtedly generated by unequal crossing over between standard-length arrays. The data strongly suggested that most unequal exchanges between arrays are intrachromosomal and that they occur much less frequently than unequal exchanges at the level of the entire rDNA repeat. Strong associations among variants at different positions allowed the recognition of five groups of arrays, two of which were found in more than one population. Five of the seven individuals surveyed had arrays from more than one group. Analysis of the distribution of nucleotide variation suggested that the populations were quite divergent, a result that is concordant with previous surveys of allozyme and mitochondrial DNA variation. It was suggested that some of the subrepeat array types are quite old, at least predating the recolonization of pond habitats in the midwestern United States after the last glaciation.

Interaction between the yeast mitochondrial and nuclear genomes influences the abundance of novel transcripts derived from the spacer region of the nuclear ribosomal DNA repeat

1989 ◽  
Vol 9 (5) ◽  
pp. 1897-1907
Author(s):  
V S Parikh ◽  
H Conrad-Webb ◽  
R Docherty ◽  
R A Butow
Keyword(s):  
Ribosomal Dna ◽  
Transcript Abundance ◽  
Nuclear Ribosomal Dna ◽  
Rrna Synthesis ◽  
Rrna Gene ◽  
Nontranscribed Spacer ◽  
Dna Repeat ◽  
Putative Origin ◽  
Mitochondrial Genotype ◽  
26S Rrna

We have identified stable transcripts from the so-called nontranscribed spacer region (NTS) of the nuclear ribosomal DNA repeat in certain respiration-deficient strains of Saccharomyces cerevisiae. These RNAs, which are transcribed from the same strand as is the 37S rRNA precursor, are 500 to 800 nucleotides long and extend from the 5' end of the 5S rRNA gene to three major termination sites about 1,780, 1,830, and 1,870 nucleotides from the 3' end of the 26S rRNA gene. A survey of various wild-type and respiration-deficient strains showed that NTS transcript abundance depended on the mitochondrial genotype and a single codominant nuclear locus. In strains with that nuclear determinant, NTS transcripts were barely detected in [rho+] cells, were slightly more abundant in various mit- derivatives, and were most abundant in petites. However, in one petite that was hypersuppressive and contained a putative origin of replication (ori5) within its 757-base-pair mitochondrial genome, NTS transcripts were no more abundant than in [rho+] cells. The property of low NTS transcript abundance in the hypersuppressive petite was unstable, and spontaneous segregants that contained NTS transcripts as abundant as in the other petites examined could be obtained. Thus, respiration deficiency per se is not the major factor contributing to the accumulation of these unusual RNAs. Unlike RNA polymerase I transcripts, the abundant NTS RNAs were glucose repressible, fractionated as poly(A)+ RNAs, and were sensitive to inhibition by 10 micrograms of alpha-amanitin per ml, a concentration that had no effect on rRNA synthesis. Abundant NTS RNAs are therefore most likely derived by polymerase II transcription.

scholarly journals Rapid Concerted Evolution of Nuclear Ribosomal DNA in Two Tragopogon Allopolyploids of Recent and Recurrent Origin

Genetics ◽  
2005 ◽  
Vol 169 (2) ◽  
pp. 931-944 ◽  
Author(s):  
A. Kovarik ◽  
J. C. Pires ◽  
A. R. Leitch ◽  
K. Y. Lim ◽  
A. M. Sherwood ◽  
...  
Keyword(s):  
Ribosomal Dna ◽  
Concerted Evolution ◽  
Nuclear Ribosomal Dna

Species and Genus Specificity of the Intergenic Spacer (IGS) in the Ribosomal RNA Genes of Cucurbitaceae

1989 ◽  
Vol 44 (11-12) ◽  
pp. 1029-1034 ◽  
Author(s):  
R. A. Torres ◽  
U. Zentgraf ◽  
V. Hemleben
Keyword(s):  
Cucumis Sativus ◽  
Ribosomal Rna ◽  
Ribosomal Dna ◽  
Cucumis Melo ◽  
Intergenic Spacer ◽  
Specific Pattern ◽  
Cross Hybridization ◽  
Cucumis Species ◽  
External Transcribed Spacer ◽  
Rna Genes

Abstract The use of intergenic spacer (IGS) fragments of plant ribosomal DNA (rDNA) for the differ­ entiation between genera and species is tested by cross-hybridization experiments with different IGS probes of two Cucurbitaceae, Cucurbita pepo (zucchini) and Cucumis sativus (cucum ber). Hybridization with cloned fragments of different parts of the IGS of ribosomal DNA exhibit a different degree of conservation within and between the Cucurbitaceae genera. In general, Cucur­ bita species seem to be closer related to each other than the Cucumis species. A repetitive element of the external transcribed spacer (ETS) shows a more genus-specific pattern, reacting only with the respective genera; the region preceding the ETS is conserved between the Cucurbita species but also cross-hybridizes weakly with the Cucumis species. AGC-rich element of the Cucumis sativus IGS (“Cfo-cluster”) is present in small amounts in Cucumis melo (melon) and even less represented in other genera of the Cucurbitaceae.

Variation in ribosomal DNA among isolates of the mycorrhizal fungus Cenococcum geophilum

1991 ◽  
Vol 69 (11) ◽  
pp. 2331-2343 ◽  
Author(s):  
Katherine F. Lobuglio ◽  
Scott O. Rogers ◽  
C. J. K. Wang
Keyword(s):  
Ribosomal Dna ◽  
Restriction Site ◽  
Mycorrhizal Fungus ◽  
Intergenic Spacer ◽  
Fungal Species ◽  
Nuclear Ribosomal Dna ◽  
Cenococcum Geophilum ◽  
Taxonomic Rank ◽  
Reference Isolate ◽  
Length Polymorphisms

Restriction fragment length polymorphisms in ribosomal DNA were used to assess the degree of variation among 71 Cenococcum geophilum isolates of both geographically distinct and similar origins. Southern hybridizations using cloned C. geophilum ribosomal DNA indicated extensive variation among isolates, greater than has been previously reported to occur within a fungal species. Most of the polymorphisms were located within the region from the intergenic spacer through internal transcribed spacer 1. Restriction-site and length polymorphisms also occurred within the 5.8S through 26S genic region. Sixteen size categories of length mutations, six restriction-site additions, and four restriction-site deletions were observed compared with a reference isolate. HindIII-digested DNAs displayed fewer polymorphisms in the mitochondrial 24S ribosomal RNA gene (and flanking regions) than in nuclear ribosomal DNA. UPGMA cluster analysis of shared nuclear ribosomal DNA patterns indicated 32 unique phenotypes and grouped C. geophilum isolates into a broad range of clusters ranging from 100 to 44% similarity. The amount of ribosomal DNA variation demonstrated in this study indicates that C. geophilum is either an extremely heterogenous species or a fungal complex representing a broader taxonomic rank than presently considered. Key words: Cenococcum geophilum, ribosomal DNA, restriction polymorphisms.

scholarly journals The Evolution of Ribosomal DNA Divergent Paralogues and Phylogenetic Implications

Genetics ◽  
1997 ◽  
Vol 145 (3) ◽  
pp. 821-832 ◽  
Author(s):  
Edward S Buckler ◽  
Anthony Ippolito ◽  
Timothy P Holtsford
Keyword(s):  
Secondary Structure ◽  
Ribosomal Dna ◽  
Concerted Evolution ◽  
Internal Transcribed Spacer ◽  
High Stability ◽  
Nuclear Ribosomal Dna ◽  
Structure Stability ◽  
Phylogenetic Implications ◽  
Ancestral States ◽  
Pcr Conditions

Although nuclear ribosomal DNA (rDNA) repeats evolve together through concerted evolution, some genomes contain a considerable diversity of paralogous rDNA. This diversity includes not only multiple functional loci but also putative pseudogenes and recombinants. We examined the occurrence of divergent paralogues and recombinants in Gossypium, Nicotiana, Tripsacum, Winteraceae, and Zea ribosomal internal transcribed spacer (ITS) sequences. Some of the divergent paralogues are probably rDNA pseudogenes, since they have low predicted secondary structure stability, high substitution rates, and many deamination-driven substitutions at methylation sites. Under standard PCR conditions, the low stability paralogues amplified well, while many high-stability paralogues amplified poorly. Under highly denaturing PCR conditions (i.e., with dimethylsulfoxide), both low- and high-stability paralogues amplified well. We also found recombination between divergent paralogues. For phylogenetics, divergent ribosomal paralogues can aid in reconstructing ancestral states and thus serveas good outgroups. Divergent paralogues can also provide companion rDNA phylogenies. However, phylogeneticists must discriminate among families of divergent paralogues and recombinants or suffer from muddled and inaccurate organismal phylogenies.

The Nuclear Ribosomal DNA Intergenic Spacer as a Target Sequence To Study Intraspecific Diversity of the Ectomycorrhizal Basidiomycete Hebeloma cylindrosporum Directly on Pinus Root Systems

1999 ◽  
Vol 65 (3) ◽  
pp. 903-909 ◽  
Author(s):  
Alice Guidot ◽  
Erica Lumini ◽  
Jean-Claude Debaud ◽  
Roland Marmeisse
Keyword(s):  
Ribosomal Dna ◽  
Sequence Data ◽  
Intergenic Spacer ◽  
Root Systems ◽  
Intraspecific Diversity ◽  
Nuclear Ribosomal Dna ◽  
Restriction Enzyme Digestion ◽  
Target Sequence ◽  
Root Tips ◽  
Hebeloma Cylindrosporum

ABSTRACT Polymorphism of the nuclear ribosomal DNA intergenic spacer (IGS) of the ectomycorrhizal basidiomycete Hebeloma cylindrosporum was studied to evaluate whether this sequence could be used in field studies to estimate the diversity of strains forming mycorrhizas on individual Pinus pinaster root systems. This sequence was amplified by PCR from 125 haploid homokaryotic strains collected in 14 P. pinaster stands along the Atlantic coast of France by using conserved oligonucleotide primers. Restriction enzyme digestion of the amplified 3.4-kbp-long IGS allowed us to characterize 24 alleles whose frequencies differed. Nine of these alleles were found only once, whereas about 60% of the strains contained four of the alleles. Local populations could be almost as diverse as the entire population along a 150-km stretch of coastline that was examined; for example, 13 alleles were found in a single forest stand. The IGS from one strain was partially sequenced, and the sequence data were used to design oligonucleotides which allowed separate PCR amplification of three different segments of the IGS. Most polymorphisms observed among the full-length IGS regions resulted from polymorphisms in an internal ca. 1,500-bp-long sequence characterized by length variations that may have resulted from variable numbers of a T2AG3 motif. This internal polymorphic sequence could not be amplified from the genomes of nine other Hebeloma species. Analysis of this internal sequence amplified from the haploid progenies of 10 fruiting bodies collected in a 70-m2 area resulted in identification of six allelic forms and seven distinct diplotypes out of the 21 possible different combinations. Moreover, optimization of the PCR conditions resulted in amplification of this sequence from more than 80% of the DNA samples extracted from individual H. cylindrosporum infectedP. pinaster mycorrhizal root tips, thus demonstrating the usefulness of this sequence for studying the below-ground diversity of mycorrhizas formed by genets belonging to the same fungal species.

Sign in / Sign up

Export Citation Format

Share Document