Genetics of Cronartium ribicola. II. Variation in the ribosomal gene cluster

1996 ◽  
Vol 74 (3) ◽  
pp. 461-468 ◽  
Author(s):  
E. E. White ◽  
B. M. Foord ◽  
B. B. Kinloch Jr.
Keyword(s):  
Restriction Site ◽  
Intergenic Spacer ◽  
Fungal Species ◽  
Ribosomal Gene ◽  
Length Variation ◽  
Cronartium Ribicola ◽  
Western North America ◽  
Size Classes ◽  
Restriction Site Variation ◽  
Site Variation

The ribosomal gene repeat in Cronartium ribicola J.C. Fisch is highly variable among spore samples from British Columbia, Canada. Both restriction site variation and length variation occur. Length heterogeneity results from differences in the number of subrepeats in the intergenic spacer (IGS). The number of IGS size classes in haploid cultures is limited but is very large and highly variable in aeciospores from single cankers. The proportions of different size classes vary among cankers on different trees, and among subsamples taken around the periphery of large old cankers. The results are consistent with the fungus having a haploid infective mycelium that produces functional pycnia that result in localized dikaryotic areas following fusion between flexuous hyphae and pycnia. Restriction site variation appears lower than has been reported in range-wide samples of endemic fungal species, consistent with the hypothesis that introduction of C. ribicola to western North America was limited and does not represent the full genetic range of the species. No particular restriction site variants or IGS size classes characterize samples from particular geographic areas. No evidence for geographic races of the fungus was obtained. Keywords: rusts, rust races, ribosomal DNA, intergenic spacer, population structure, RFLP.

Genomic organization of ribosomal RNA genes in Bromus (Poaceae)

Genome ◽  
1996 ◽  
Vol 39 (1) ◽  
pp. 198-205 ◽  
Author(s):  
M. Pillay
Keyword(s):  
Ribosomal Dna ◽  
Restriction Site ◽  
Intergenic Spacer ◽  
Molecular Data ◽  
Length Variation ◽  
Coding Region ◽  
Rdna Genes ◽  
Repeat Units ◽  
Site Mapping ◽  
Site Variation

Restriction site maps of the rDNA genes of nine Bromus species are described. The rDNA repeat units ranged from 8.2 to 11.1 kbp in length. Intraspecific length variation was observed in the BamHI digestions in three of the nine species. Restriction site variation was observed mainly in the intergenic spacer (IGS) but was also detected in the coding region. A unique KpnI site was present in the IGS of Bromus tectorum and Bromus sericeus (subgenus Stenobromus); in addition, B. sericeus contained an extra EcoRI site. An additional DraI site was observed in the IGS of Bromus trinii (subgenus Neobromus). A BstEII site in the IGS, common to seven of the species, was absent in B. tectorum and B. sericeus. In the coding region, a 2.1-kbp BstEII fragment was present in four subgenera represented by Bromus inermis and Bromus erectus (subgenus Festucaria), Bromus marginatus and Bromus carinatus (subgenus Ceratochloa), B. tectorum and B. sericeus (subgenus Stenobromus), and B. trinii (subgenus Neobromus); a similar fragment of only 1.1 kbp was present in Bromus mollis and Bromus arvensis (subgenus Bromus). An additional BamHI site was present in the coding region of B. erectus. Ribosomal DNA data suggested that B. mollis and B. arvensis (subgenus Bromus) are genetically isolated from the other subgenera, which showed a derived relationship. Restriction site mapping of the rDNA genes could provide useful molecular data for species identification and population and evolutionary studies in Bromus. Key words : Bromus, ribosomal DNA, restriction maps, evolutionary relationships.

scholarly journals Hierarchical Analysis of Nucleotide Diversity in Geographically Structured Populations

Genetics ◽  
1996 ◽  
Vol 142 (2) ◽  
pp. 629-639 ◽  
Author(s):  
Kent E Holsinger ◽  
Roberta J Mason-Gamer
Keyword(s):  
Nucleotide Diversity ◽  
Restriction Site ◽  
Rooted Tree ◽  
Structured Populations ◽  
Hierarchical Analysis ◽  
Restriction Site Variation ◽  
Hierarchical Levels ◽  
Site Variation ◽  
The Mean ◽  
Mean Time

Abstract Existing methods for analyzing nucleotide diversity require investigators to identify relevant hierarchical levels before beginning the analysis. We describe a method that partitions diversity into hierarchical components while allowing any structure present in the data to emerge naturally. We present an unbiased version of Nei's nucleotide diversity statistics and show that our modification has the same properties as Wright's  F  ST. We compare its statistical properties with several other F  ST estimators, and we describe how to use these statistics to produce a rooted tree of relationships among the sampled populations in which the mean time to coalescence of haplotypes drawn from populations belonging to the same node is smaller than the mean time to coalescence of haplotypes drawn from populations belonging to different nodes. We illustrate the method by applying it to data from a recent survey of restriction site variation in the chloroplast genome of Coreopsis grandiflora.

More than one origin of hexaploid wheat is indicated by sequence comparison of low-copy DNA

Genome ◽  
1998 ◽  
Vol 41 (3) ◽  
pp. 402-407 ◽  
Author(s):  
L E Talbert ◽  
L Y Smith ◽  
N K Blake
Keyword(s):  
Dna Sequences ◽  
Hexaploid Wheat ◽  
Restriction Site ◽  
Cereal Crop ◽  
Crop Species ◽  
Wheat Evolution ◽  
D Genome ◽  
Restriction Site Variation ◽  
Site Variation ◽  
Copy Dna

Allohexaploid bread wheat is grown on more acreage than any other cereal crop, yet variation at the DNA level seems to be less than that observed in many diploid crop species. A common explanation for the small amount of DNA-level variation is that a severe bottleneck event resulted from the polyploidization events that gave rise to hexaploid wheat, whereby wheat was genetically separated from its progenitors. In this report, we test the extent of the bottleneck separating wheat from its D-genome progenitor, Triticum tauschii, by comparative DNA sequence analysis. Restriction site variation of low-copy DNA sequences amplified by PCR showed an average of 2.9 and 2.4 alleles per primer set in T. tauschii and wheat, respectively. Two different restriction patterns were present in T. tauschii for DNA amplified with a primer set for the A1 locus. Both alleles were also present in wheat. Alleles at the A1 locus were cloned and 527 bp of sequence obtained from 12 and 13 diverse accessions of wheat and T. tauschii, respectively. Average genetic distance among the wheat alleles was similar to that among the T. tauschii alleles (0.0127 and 0.0133, respectively). Nucleotide differences indicated that two distinct alleles existed in T. tauschii, both of which were present in wheat. These data suggest that hexaploid wheat formed at least twice, and that the bottleneck separating wheat from T. tauschii may be less constrictive than previously supposed.Key words: wheat, evolution, DNA.

Phylogenetic Implications of Ribosomal DNA Restriction Site Variation in the Plant Family Onagraceae

1990 ◽  
Vol 77 (3) ◽  
pp. 523 ◽  
Author(s):  
Jorge V. Crisci ◽  
Elizabeth A. Zimmer ◽  
Peter C. Hoch ◽  
George B. Johnson ◽  
Christy Mudd ◽  
...  
Keyword(s):  
Ribosomal Dna ◽  
Restriction Site ◽  
Plant Family ◽  
Restriction Site Variation ◽  
Phylogenetic Implications ◽  
Site Variation ◽  
Dna Restriction

Mitochondrial DNA restriction site variation in Tasmanian populations of Orange Roughy (Hoplostethus atlanticus), a deep-water marine teleost

1989 ◽  
Vol 40 (1) ◽  
pp. 1 ◽  
Author(s):  
JR Ovenden ◽  
AJ Smolenski ◽  
RWG White
Keyword(s):  
Mitochondrial Dna ◽  
West Coast ◽  
East Coast ◽  
Restriction Site ◽  
The West ◽  
Orange Roughy ◽  
Site Change ◽  
Restriction Site Variation ◽  
Site Variation ◽  
Hoplostethus Atlanticus

The orange roughy, Hoplostethus atlanticus, forms the basis of an important trawl fishery in Australia and New Zealand which is currently being over-exploited. To gain information about the stock structure of an Australian orange roughy population, ten restriction enzymes were used to survey the restriction- site variation in the mitochondrial genome of 23 individuals collected from the east coast and 26 individuals collected from the west coast of Tasmania. The mean diversity between all 49 genomes was a low 0.19%. Of the eleven haplotypes identified, only one was present in both the east and west coast samples. Four haplotypes were found only in the east coast sample and six were found only in the west coast sample. Eight haplotypes were related to the haplotype found on both coasts by the gain or loss of one restriction site. One haplotype collected in the east coast sample was related to one other east coast haplotype by one site change. One haplotype collected from the west coast was related to a west coast haplotype by one site change. If this pattern is confirmed by further mitochondrial DNA studies, it could be inferred that gene flow between the orange roughy populations on the east and west coasts of Tasmania is low.

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