Variation in the ribosomal DNA repeat unit within single-oospore isolates of the genus Pythium

Genome ◽  
1990 ◽  
Vol 33 (4) ◽  
pp. 585-591 ◽  
Author(s):  
Frank N. Martin
Keyword(s):  
Ribosomal Rna ◽  
Repeat Unit ◽  
Pythium Species ◽  
Coding Region ◽  
Nontranscribed Spacer ◽  
Dna Repeat ◽  
Restriction Sites ◽  
Genus Pythium ◽  
Polymorphic Forms ◽  
Isolate Variation

Restriction analyses of the DNA repeat unit coding for the production of 5.8S, 17S, and 26S ribosomal RNA (rDNA) isolated from several different Pythium species revealed polymorphic forms within a single-oospore isolate. Restriction mapping of cloned rDNA from Pythium paroecandrum indicated that two major forms were present in approximately equal ratios (A and B, 11.6 and 11.9 kb in size, respectively), which differed in the nontranscribed spacer region for numbers and locations of restriction sites for HaeIII, SalI, and KpnI and an insertion–deletion adjacent to the 3′ end of the 26S RNA coding region. The insertion–deletion makes form B 0.27 kb larger than form A. An additional insertion–deletion in both forms of approximately 60 bp in the same region makes a total of four polymorphic types in the isolate investigated. Similar results also were obtained for Pythium spinosum following restriction digestion of purified rDNA. A survey of other Pythium species indicates that the presence of polymorphic forms in the same isolate, variation in the number or polymorphic forms in different isolates of the same species, and insertions–deletions in multiples of approximately 60 bp adjacent to the 3′ end of the 26S coding region are common in the genus.Key words: Pythium spp., rDNA.

Ribosomal DNA repeat unit polymorphism in six Aegilops species

Genome ◽  
1992 ◽  
Vol 35 (3) ◽  
pp. 510-515 ◽  
Author(s):  
W. K. Kim ◽  
R. L. Innes ◽  
E. R. Kerber
Keyword(s):  
Repeat Unit ◽  
Genotypic Diversity ◽  
Type A ◽  
Aegilops Species ◽  
Type B ◽  
Rdna Repeat ◽  
Coding Region ◽  
Repeat Units ◽  
Dna Repeat ◽  
Bamhi Site

Total genomic DNA of 27 accessions representing six Aegilops species was restricted with BamHI, EcoRI, and BamHI plus EcoRI, and the restriction fragments were probed with the ribosomal clones pMF2 containing the ribosomal RNA coding regions. The rDNA repeat lengths varied between 9.0 and 10.8 kb. Intraspecific variation among the 10 accessions of Ae. squarrosa var. strangulata ranged from 9.0 to 9.6 kb, suggesting a diversity of genotypes within as well as between species. These variations were not related to their geographical distributions. Each of 24 accessions had two BamHI sites in the coding region (type A), while three accessions of Ae. squarrosa var. strangulata had four BamHI sites (type B, two sites in the intergenic region). Results for these three accessions of Ae. squarrosa var. strangulata suggest genotypic diversity in this species. In BamHI restriction of each accession, a third DNA fragment, ranging between 9.0 and 10.8 kb in type A and 6.0 kb in type B, resulted from lack of digestion at the 26S BamHI site. In double digestion, all rDNA repeat units were restricted by EcoRI, yielding 3.9-, 0.9-, and 4.8-kb fragments, the last of which arose from the lack of digestion at the 26S BamHI site, estimated to occur in 5–20% of the repeat units, depending on the accession.Key words: Triticum tauschii, RFLP, diversity.

Cerastoderma glaucum 5S ribosomal DNA: characterization of the repeat unit, divergence with respect to Cerastoderma edule, and PCR–RFLPs for the identification of both cockles

Genome ◽  
2005 ◽  
Vol 48 (3) ◽  
pp. 427-442 ◽  
Author(s):  
Ruth Freire ◽  
Ana Insua ◽  
Josefina Méndez
Keyword(s):  
Ribosomal Dna ◽  
Phylogenetic Trees ◽  
Repeat Unit ◽  
5S Rdna ◽  
Restriction Enzymes ◽  
Rrna Gene ◽  
Coding Region ◽  
Cerastoderma Edule ◽  
Cerastoderma Glaucum ◽  
Nontranscribed Spacer

The 5S rDNA repeat unit of the cockle Cerastoderma glaucum from the Mediterranean and Baltic coasts was PCR amplified and sequenced. The length of the units was 539–568 bp, of which 120 bp were assigned to the 5S rRNA gene and 419–448 bp to the spacer region, and the G/C content was 46%–49%, 54%, and 44%–47%, respectively. Two types of units (A and B), differing in the spacer, were distinguished based on the percentage of differences and clustering in phylogenetic trees. A PCR assay with specific primers for each unit type indicated that the occurrence of both units is not restricted to the sequenced individuals. The 5S rDNA units of C. glaucum were compared with new and previously reported sequences of Cerastoderma edule. The degree of variation observed in C. edule was lower than that in C. glaucum and evidence for the existence of units A and B in C. edule was not found. The two cockles have the same coding region but displayed numerous fixed differences in the spacer region and group separately in the phylogenetic trees. Digestion of the 5S rDNA PCR product with the restriction enzymes HaeIII and EcoRV revealed two RFLPs useful for cockle identification.Key words: Cerastoderma, cockle identification, 5S ribosomal DNA, nontranscribed spacer variation, PCR-RFLP.

scholarly journals Development of Resistance to Hymexazol Among Pythium Species in Cucumber Greenhouses in Oman

Plant Disease ◽  
2018 ◽  
Vol 102 (1) ◽  
pp. 202-208 ◽  
Author(s):  
Zainab M. Al-Balushi ◽  
Hesham Agrama ◽  
Issa H. Al-Mahmooli ◽  
Sajeewa S. N. Maharachchikumbura ◽  
Abdullah M. Al-Sadi
Keyword(s):  
Ribosomal Rna ◽  
Management Strategies ◽  
Soil Samples ◽  
Integrated Disease Management ◽  
Pythium Species ◽  
Internal Transcribed Spacer Region ◽  
Development Of Resistance ◽  
The Common ◽  
Cucumber Roots ◽  
Further Development

A study was conducted to characterize the common Pythium spp. in greenhouses in Oman and their level of resistance to hymexazol, a widely used fungicide in the country. Pythium isolates were obtained from soil samples, cocopeat bags, and cucumber roots collected from seven regions in the country. Identification of 80 Pythium isolates to the species level using sequences of the internal transcribed spacer region of the ribosomal RNA showed that they belong to four species: Pythium aphanidermatum (77 isolates), P. spinosum (1 isolate), P. myriotylum (1 isolate), and P. catenulatum (1 isolate). Investigating the aggressiveness of three Pythium spp. on cucumber showed that P. aphanidermatum, P. myriotylum, and P. spinosum are pathogenic. Phylogenetic analysis of P. aphanidermatum isolates showed that most of the isolates obtained from cocopeat clustered separately from isolates obtained from soil and roots. This may indicate a difference in the origin of the cocopeat isolates. Evaluating the resistance of 27 P. aphanidermatum isolates to hymexazol showed that most isolates were sensitive (0.9 to 31.2 mg liter−1) whereas one isolate was resistant (142.9 mg liter−1). This study is the first to report P. myriotylum and P. catenulatum in Oman. It is also the first to report the development of resistance to hymexazol among P. aphanidermatum populations from greenhouses. Growers should use integrated disease management strategies to avoid further development of resistance to hymexazol.

Nosema trichoplusiaeIs a Synonym ofNosema bombycisBased on the Sequence of the Small Subunit Ribosomal RNA Coding Region

1996 ◽  
Vol 67 (3) ◽  
pp. 316-317 ◽  
Author(s):  
Norman J. Pieniazek ◽  
Alexandre J. da Silva ◽  
Susan B. Slemenda ◽  
Govinda S. Visvesvara ◽  
Timothy J. Kurtti ◽  
...  
Keyword(s):  
Ribosomal Rna ◽  
Small Subunit ◽  
Coding Region ◽  
Small Subunit Ribosomal Rna

A physical map of the ribosomal DNA repeat unit of Aspergillus nidulans

Gene ◽  
1982 ◽  
Vol 20 (2) ◽  
pp. 135-137 ◽  
Author(s):  
Robin A. Lockington ◽  
Graham G. Taylor ◽  
Michael Winther ◽  
Claudio Scazzocchio ◽  
R.Wayne Davies
Keyword(s):  
Aspergillus Nidulans ◽  
Ribosomal Dna ◽  
Physical Map ◽  
Repeat Unit ◽  
Dna Repeat

Initiation and termination of DNA replication in human rRNA genes

1993 ◽  
Vol 13 (10) ◽  
pp. 6600-6613
Author(s):  
R D Little ◽  
T H Platt ◽  
C L Schildkraut
Keyword(s):  
Dna Replication ◽  
Ribosomal Dna ◽  
Regulatory Elements ◽  
Transcription Unit ◽  
Replication Initiation ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Replication Forks ◽  
Nontranscribed Spacer ◽  
Dna Repeat

We have used the multicopy human rRNA genes as a model system to study replication initiation and termination in mammalian chromosomes. Enrichment for replicating molecules was achieved by isolating S-phase enriched populations of cells by centrifugal elutriation, purification of DNA associated with the nuclear matrix, and a chromatographic procedure that enriches for molecules containing single-stranded regions, a characteristic of replication forks. Two-dimensional agarose gel electrophoresis techniques were used to demonstrate that replication appears to initiate at multiple sites throughout most of the 31-kb nontranscribed spacer (NTS) of human ribosomal DNA but not within the 13-kb transcription unit or adjacent regulatory elements. Although initiation events were detected throughout the majority of the NTS, some regions may initiate more frequently than others. Termination of replication, the convergence of opposing replication forks, was found throughout the ribosomal DNA repeat units, and, in some repeats, specifically at the junction of the 3' end of the transcription unit and the NTS. This site-specific termination of replication is the result of pausing of replication forks near the sites of transcription termination. The naturally occurring multicopy rRNA gene family offers a unique system to study mammalian DNA replication without the use of chemical synchronization agents.

The complete mitochondrial genomes of four Baikal molluscs from the endemic family Baicaliidae (Caenogastropoda: Truncatelloida)

2020 ◽  
Vol 86 (3) ◽  
pp. 201-209
Author(s):  
T E Peretolchina ◽  
T Ya Sitnikova ◽  
D Yu Sherbakov
Keyword(s):  
Lake Baikal ◽  
Ribosomal Rna ◽  
Rrna Genes ◽  
Trna Genes ◽  
Coding Region ◽  
Base Pairs ◽  
Protein Coding ◽  
Phylogenetic Studies ◽  
Canonical Base ◽  
Complete Mitochondrial Genomes

Abstract Here, we present the complete mitochondrial (mt) genomes of four members of the Baicaliidae Fisher, 1885, a truncatelloidean family that is endemic to Lake Baikal (East Siberia). The mt genomes are those of Korotnewia korotnevi (15,171 bp), Godlewskia godlewskii (15,224 bp), Baicalia turriformis (15,127) and Maackia herderiana (15,154 bp). All these mt genomes contain 13 protein-coding genes, 2 ribosomal RNA (rRNA) genes and 22 transfer RNA (tRNA) genes. We detected non-canonical base pairs in some of the tRNA genes and variable numbers of non-coding spacers; some tRNAs do not have a TψC loop. We found gene order to be highly conserved in these Lake Baikal species and similar to the majority of caenogastropod mt genomes available on GenBank. A position of the putative control region is delimited to the non-coding region between trnF and the cox3 gene. It contains the ‘GAA(A)nT’ motif at the 3′ end and is similar to the replication origin found in most Caenogastropoda studied to date. We also compared the evolutionary rates of different genes to evaluate their use in different kinds of population or phylogenetic studies of this group of gastropods.

scholarly journals Organization of replication of ribosomal DNA in Saccharomyces cerevisiae.

1988 ◽  
Vol 8 (11) ◽  
pp. 4927-4935 ◽  
Author(s):  
M H Linskens ◽  
J A Huberman
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Ribosomal Dna ◽  
Repeat Unit ◽  
Replication Forks ◽  
Sequence Element ◽  
Autonomously Replicating Sequence ◽  
Nontranscribed Spacer ◽  
Precursor Rna ◽  
Mapping Techniques ◽  
Region Ii

Using recently developed replicon mapping techniques, we have analyzed the replication of the ribosomal DNA in Saccharomyces cerevisiae. The results show that (i) the functional origin of replication colocalizes with an autonomously replicating sequence element previously mapped to the nontranscribed spacer region, (ii) only a fraction of the potential origins are utilized in a single S phase, and (iii) the replication forks moving counter to the direction of transcription of the 37S precursor RNA stop at or near the termination site of transcription. Consequently, most ribosomal DNA is replicated unidirectionally by forks moving in the direction of transcription and most replicons are larger than the repeat unit. The significance of this finding for the replication of abundantly transcribed genes is discussed.

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