Ribosomal RNA Genes of Phaseolus coccineus. IV. Structure and Comparative-analysis of the Intergenic Spacer: Possible Involvement of Some Nucleotides in the Transcription Control of Coding Sequences Sequence of the Intergenic Spacer of Ribosomal Genes

The organization of the nuclear-encoded 18S, 5.8S, and 25S ribosomal RNA genes (ribosomal DNA; rDNA) of 21 New World species from different sections of the genus Solanum, of two Old World Solanum species, and of representatives of other Solanaceae (Nicotiana, Atropa, Datura, Physalis, and Capsicum) was analyzed by restriction enzyme mapping using different rDNA specific hybridization probes. All Solanum species investigated exhibited rDNA repeats between 8.7 and 9.3 kb in length; the only exception was S. neorossii with a repeat length of 10.3 kb. Sequence heterogeneity was observed mostly in the intergenic spacer (IGS) region. Restriction sites for EcoRI and DraI in the spacer sequences were found to be characteristic for the New World species of the genus Solanum and for Lycopersicon esculentum. An additional XbaI site was detected in the spacer region of two nontuber-bearing species, S. brevidens and S. etuberosum (subsection Estolonifera Hawkes; series Etuberosa), as well as in the primitive tuber-bearing species of the series Pinnatisecta and Polyadenia (subsection Potatoe G.Don), thus demonstrating that these Mexican species are separated from the other tuber-bearing species but are closely linked to the nontuber-bearing Estolonifera group. Two EcoRI sites mapped at the 3′end of the 25S rRNA coding region seem to be characteristic for members of the Solanaceae; the first EcoRI site is apparently methylated in approximately 50% of the rDNA repeats. Southern hybridization with an IGS fragment of Solanum tuberosum as hybridization probe and nucleotide sequence analysis of the phylogenetically informative 3′ end of the 25S rDNA support the assumption that the New World species of the genus Solanum are closely related to Lycopersicon (tomato) in contrast with other Solanaceae investigated, Nicotiana, Atropa, Datura, Physalis, and Capsicum. Moreover, the New World potatoes and tomato appear to be more closely related to each other than potatoes and the Old World species Solanum nigrum and Solanum dulcamara.Key words: ribosomal DNA, intergenic spacer, methylation, evolutionary relationship, phylogeny.

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

Plant Molecular Biology ◽

10.1007/bf00015882 ◽

1987 ◽

Vol 9 (5) ◽

pp. 509-520 ◽

Cited By ~ 305

Author(s):

Scott O. Rogers ◽

Arnold J. Bendich

Keyword(s):

Ribosomal Rna ◽

Copy Number ◽

Intergenic Spacer ◽

Ribosomal Rna Genes ◽

Rna Genes

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Electrophoretic mobility anomalies associated with PCR amplification of the intergenic spacer region between 16S and 23S ribosomal RNA genes of Fusobacterium necrophorum

Journal of Microbiological Methods ◽

10.1016/s0167-7012(01)00278-0 ◽

2001 ◽

Vol 46 (2) ◽

pp. 165-169 ◽

Cited By ~ 9

Author(s):

Sanjeev Kumar Narayanan ◽

T.G. Nagaraja ◽

M.M. Chengappa ◽

George C. Stewart

Keyword(s):

Electrophoretic Mobility ◽

Ribosomal Rna ◽

Pcr Amplification ◽

Intergenic Spacer ◽

Fusobacterium Necrophorum ◽

Ribosomal Rna Genes ◽

Intergenic Spacer Region ◽

23S Ribosomal Rna ◽

Rna Genes

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Molecular characterization of intergenic spacer region of 5S ribosomal RNA genes in subgenus Vigna: extensive hybridization among V. unguiculata subspecies

Plant Systematics and Evolution ◽

10.1007/s00606-011-0446-y ◽

2011 ◽

Vol 294 (1-2) ◽

pp. 39-55 ◽

Cited By ~ 4

Author(s):

Archana Vijaykumar ◽

Ajay Saini ◽

Narendra Jawali

Keyword(s):

Molecular Characterization ◽

Ribosomal Rna ◽

Intergenic Spacer ◽

Ribosomal Rna Genes ◽

5S Ribosomal Rna ◽

Intergenic Spacer Region ◽

Rna Genes

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Identification of variability of ribosomal DNA spacer from Pseudomonas soil isolates

Canadian Journal of Microbiology ◽

10.1139/m94-087 ◽

1994 ◽

Vol 40 (7) ◽

pp. 541-547 ◽

Cited By ~ 7

Author(s):

Santokh Gill ◽

Julie Belles-Isles ◽

Gerry Brown ◽

Serge Gagné ◽

Claude Lemieux ◽

...

Keyword(s):

Ribosomal Rna ◽

Ribosomal Dna ◽

Dna Sequences ◽

Intergenic Spacer ◽

Ribosomal Rna Genes ◽

Peat Bog ◽

Variable Segment ◽

Limited Degree ◽

Total Dna ◽

Rna Genes

The polymerase chain reaction was used to amplify the spacer region located between the 16S and 23S ribosomal RNA genes of strains of Pseudomonas fluorescens and Pseudomonas putida isolated from peat bog, canola field, or arctic plants. Some of these amplified spacer regions were used to probe Southern blots of total DNA digests from the various strains of P. fluorescens and P. putida. Differences were observed in the patterns of hybridization of the various bacterial DNAs. The ribosomal DNA spacer region of four of the P. fluorescens strains examined, strains 64-3, 63-28, QP5, and R17-FP2, was about 515 base pairs (bp) in length, and contained the genes for tRNAIle and tRNAAla. The DNA sequences of two strains from canola, 64-3 and 63-28, differed at only two positions. The sequences of the peat bog strains QP5 and R17-FP2 were identical. However, differences were noted between the DNA sequence common to the pair of strains 64-3 and 63-28 and the corresponding common sequence for strains QP5 and R17-FP2. These differences were mainly concentrated in two DNA segments of 10 and 19 bp, respectively. A probe for the 19-bp variable segment that occurs in the ribosomal spacer of strains QP5 and R17-FP2 recognized total DNA from these two strains, but not DNA from other bacteria of different origins. These results suggest the existence of a limited degree of variability within the 16S-23S ribosomal DNA spacer region, and that this variability may be useful to the recognition of particular Pseudomonas strains from environmental samples.Key words: ribosomal RNA genes, intergenic spacer, Pseudomonas soil isolates, specific DNA probe.

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