Comparative restriction site maps of chloroplast DNA of Piceaabies, Piceaglauca, Piceamariana, and Piceasitchensis

1993 ◽  
Vol 23 (3) ◽  
pp. 427-435 ◽  
Author(s):  
E.E. White ◽  
R.F. Watkins ◽  
D.P. Fowler
Keyword(s):  
Chloroplast Dna ◽  
Chloroplast Genome ◽  
Restriction Fragment ◽  
Gene Order ◽  
Species Differences ◽  
Restriction Site ◽  
Gene Organization ◽  
Physical Maps ◽  
Restriction Site Maps

Physical maps of chloroplast DNA of four species of Picea Diet, were compared. Restriction site differences occur between species. Four restriction site mutations were mapped, and between species differences in three more were inferred from restriction fragment patterns. Differences observed among species were not sufficient to allow phylogenetic interpretations. No differences in gene order among species were observed. Gene organization in the chloroplast genome of Picea is compared with that of Pinus L. and Pseudotsuga Carr. Gene order is colinear with that of Pseudotsuga with the exception of one inversion. Though the genomes of Picea and Pseudotsuga are colinear over a greater length than those of Picea and Pinus, this does not imply that Picea and Pseudotsuga are more closely related to each other than to Pinus, since these three patterns of gene organization could have evolved by inversion events that differed only in the order in which they occurred.

The chloroplast genome of Pinussylvestris; physical map and localization of chloroplast genes

1993 ◽  
Vol 23 (2) ◽  
pp. 234-238 ◽  
Author(s):  
B. Karpinska ◽  
S. Karpinski
Keyword(s):  
16S Rrna ◽  
Chloroplast Dna ◽  
Gene Order ◽  
Restriction Site ◽  
Physical Map ◽  
Genetic Maps ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Chloroplast Genes ◽  
Restriction Fragments

A physical map of Pinussylvestris L. chloroplast DNA for three restriction endonucleases (PstI, SacI, and KpnI) has been prepared by hybridization of isolated or cloned restriction fragments. Pinussylvestris chloroplast DNA is about 120 kilobases. Ten chloroplast genes have been localized by hybridization with heterologous chloroplast DNA probes. The genome contains single copies of the 23S and 16S rRNA genes and lacks any large repeated sequences. The restriction site arrangement and gene order have been compared with other known chloroplast DNA genetic maps of pine species.

CHLOROPLAST DNA VARIATION AND EVOLUTION IN PISUM: PATTERNS OF CHANGE AND PHYLOGENETIC ANALYSIS

Genetics ◽  
1985 ◽  
Vol 109 (1) ◽  
pp. 195-213
Author(s):  
Jeffrey D Palmer ◽  
Richard A Jorgensen ◽  
William F Thompson
Keyword(s):  
Chloroplast Dna ◽  
Chloroplast Genome ◽  
Restriction Site ◽  
Garden Pea ◽  
Dna Variation ◽  
Mitochondrial Dnas ◽  
Chloroplast Dna Variation ◽  
Dna Restriction ◽  
Chloroplast Dnas ◽  
High Degree

ABSTRACT Variation in 30 chloroplast DNAs, representing 22 wild and cultivated accessions in the genus Pisum, was analyzed by comparing fragment patterns produced by 16 restriction endonucleases. Three types of mutations were detected. First, an inversion of between 2.2 kilobase pairs (kb) and 5.2 kb distinguished a population of P. humile from all other Pisum accessions examined. Second, deletions and insertions of between 50 and 1200 base pairs produced small restriction fragment length variations in four regions of the 120-kb chloroplast genome. Two of these regions—one of which is located within the sequence that is inverted in P. humile—showed a high degree of size polymorphism, to the extent that size differences were detected between individuals from the same accession. Finally, a total of only 11 restriction site mutations were detected among the 165 restriction sites sampled in the 30 DNAs. Based on these results and previous data, we conclude that the chloroplast genome is evolving very slowly relative to nuclear and mitochondrial DNAs. The Pisum chloroplast DNA restriction site mutations define two major lineages: One includes all tested accessions of P. fulvum, which is known to be cytogenetically quite distinct from all other Pisum taxa. The second includes 12 of 13 cultivated lines of the garden pea (P. sativum) and a wild population of P. humile from northern Israel. These observations strongly reinforce an earlier conclusion that the cultivated pea was domesticated primarily from northern populations of P. humile. A 13th P. sativum cultivar has a chloroplast genome that is significantly different from those of the aforementioned lines and somewhat more similar to those of P. elatius and southern populations of P. humile. This observation indicates that secondary hybridization may have occurred during the domestication of the garden pea.

scholarly journals Comparison of Restriction Fragment Length Polymorphisms in Chloroplast DNA of Five Leafy Spurge (Euphorbiaspp.) Accessions

Weed Science ◽  
1992 ◽  
Vol 40 (1) ◽  
pp. 63-67 ◽  
Author(s):  
Scott J. Nissen ◽  
Robert A. Masters ◽  
Donald J. Lee ◽  
Martha L. Rowe
Keyword(s):  
Chloroplast Dna ◽  
Chloroplast Genome ◽  
Genome Size ◽  
Restriction Fragment ◽  
Fragment Length ◽  
Mung Bean ◽  
Leafy Spurge ◽  
Restriction Fragment Length Polymorphisms ◽  
Length Polymorphisms ◽  
Restriction Fragment Length

Chloroplast DNA (cpDNA) restriction fragment length polymorphisms (RFLPs) were analyzed to assess genetic variation and relatedness among selections of North American and Eurasian leafy spurge. Leafy spurge accessions from Nebraska, Montana, Russia, Italy, and Austria were evaluated. Total DNA was extracted from young leaves and digested with the restriction endonuclease,EcoRI. CpDNA fragment patterns were determined by Southern blot analysis using mung bean cpDNA probes. Colinearity between the mung bean and leafy spurge chloroplast genomes was indicated by the observation that common fragments were hybridized by adjacent probes. Minimum estimates of chloroplast genome size for the five leafy spurge accessions, which ranged in kilobase size from 130 to 132, were within the size range of most terrestrial plants. Structural collinearity and reasonable estimates of chloroplast genome size provided evidence that the mung bean cpDNA library was suitable for characterizing leafy spurge cpDNA. Seven of the 13 mung bean probes hybridized to polymorphic leafy spurge cpDNA fragments. Based on number of polymorphisms unique to each Eurasian accession, the Austrian accession appeared to be most divergent followed by the Italian and Russian. The North American accessions seem to be most closely related to each other and to the Russian leafy spurge accession.

Phylogenetic relationships and patterns of character change in the tribe Lactuceae (Asteraceae) based on chloroplast DNA restriction site variation

1995 ◽  
Vol 73 (7) ◽  
pp. 1058-1073 ◽  
Author(s):  
Jeannette Whitton ◽  
Robert S. Wallace ◽  
Robert K. Jansen
Keyword(s):  
Phylogenetic Tree ◽  
Chloroplast Dna ◽  
Key Words ◽  
Chloroplast Genome ◽  
Phylogenetic Relationships ◽  
Restriction Site ◽  
Restriction Site Variation ◽  
Site Variation ◽  
Dna Restriction ◽  
Rapid Diversification

The Lactuceae is perhaps the most easily recognizable tribe in the Asteraceae, distinguished by the presence of milky latex and of ligulate florets in the inflorescence. Three existing taxonomic treatments of the tribe establish subtribal classifications but fail to resolve relationships among major lineages. Our study of chloroplast DNA restriction site variation sampled 60 Lactuceae taxa. We detected 1268 mutations, 612 of which are phylogenetically informative. Despite the large amount of variation detected, little resolution of relationships among major lineages was obtained from parsimony analyses, although the monophyly of many groups is strongly supported. These results, when considered along with data from morphological analyses of other workers, suggest that rapid diversification played an important role in early stages of the tribe's evolution. Our examination of character change further reveals that as noted by other workers, restriction site variation is not evenly distributed across the chloroplast genome and that regions with higher levels of variation do not necessarily have higher amounts of homoplasy. This is somewhat surprising, since we found that amounts of homoplasy along terminal branches of our phylogenetic tree are related to levels of divergence. Key words: Asteraceae, chloroplast DNA, homoplasy, Lactuceae, phylogeny, restriction site variation.

Restriction Fragment Length Polymorphisms in Chloroplast DNA From Six Species of Eucalyptus

1991 ◽  
Vol 39 (5) ◽  
pp. 399 ◽  
Author(s):  
DA Steane ◽  
AK West ◽  
BM Potts ◽  
JR Ovenden ◽  
JB Reid
Keyword(s):  
Chloroplast Dna ◽  
Chloroplast Genome ◽  
Restriction Fragment ◽  
Fragment Length ◽  
Restriction Enzymes ◽  
Restriction Fragment Length Polymorphisms ◽  
Taxonomic Distance ◽  
Length Polymorphisms ◽  
Well Differentiated ◽  
Restriction Fragment Length

Chloroplast DNA was extracted from six species of Eucalyptus (E. perriniana, E. nitens, E. ovata, E. regnans, E. amygdalina and E. risdonii). Digests with four restriction enzymes (Hind III, Xho I, Nco I and Eco RV) revealed restriction fragment length polymorphisms (RFLPs) between subgenera, between species and within species. However, no variation in fragment pattern was detected with Sac II or Pst I. The subgenera Monocalyptus and Symphyomyrtus were clearly differentiated by their RFLP patterns where, with the exception of one outlying specimen of E. amygdalina, 45% of all polymorphic fragments were specific to one or other subgenus. While species from different subgenera and series were well differentiated, it was more difficult to differentiate species within series with the low sample sizes used. However, the average net divergence between species increased with increasing taxonomic distance between species, from 0.02% within series and 0.20% between species from different series within subgenera, to 0.99% of nucleotides per nucleotide site for species from different subgenera. Based on Eco RV digests, the eucalypt chloroplast genome was estimated at 143 kb.

scholarly journals Chloroplast DNA Restriction Fragment Variation among Strawberry (Fragaria spp.) Taxa

1997 ◽  
Vol 122 (1) ◽  
pp. 63-68 ◽  
Author(s):  
Richard E. Harrison ◽  
James J. Luby ◽  
Glenn R. Furnier
Keyword(s):  
Nicotiana Tabacum ◽  
Chloroplast Dna ◽  
Chloroplast Genome ◽  
Restriction Fragment ◽  
Restriction Enzymes ◽  
Closely Related Species ◽  
Length Polymorphisms ◽  
Phylogenetic Resolution ◽  
Dna Restriction ◽  
Restriction Fragment Length

Restriction fragment-length polymorphisms (RFLPs) of chloroplast DNA (cpDNA) were used to study phylogenetic relationships among twenty-six Fragaria taxa and two closely related species, Potentilla fruticosa L. and Duchesnea indica (Andrews) Focke. Sixteen restriction enzymes and probes of the entire Nicotiana tabacum L. chloroplast genome revealed a very low level of variation among the Fragaria taxa, limiting phylogenetic resolution. However, Fragaria appears to be more closely related to Potentilla than Duchesnea. The diploid taxa, F. iinumae Makino, F. nilgerrensis Schlect. and F. vesca L. were the most divergent Fragaria taxa and F. iinumae appears to be the most ancestral taxon. Little variation was revealed within the economically important octoploid group of taxa, which gave rise to the cultivated strawberry, and no progenitor taxa to the octoploid group could be identified. The lack of variation in the chloroplast genome suggests that these Fragaria species may be of relatively recent evolutionary origin.

Chloroplast DNA Restriction Site Phylogeny of the Genus Androcymbium (Colchicaceae)

1999 ◽  
Vol 24 (4) ◽  
pp. 581 ◽  
Author(s):  
Juli Caujape-Castells ◽  
Robert K. Jansen ◽  
Joan Pedrola-Monfort ◽  
Nuria Membrives
Keyword(s):  
Chloroplast Dna ◽  
Restriction Site ◽  
Dna Restriction
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