Reduction of nuclear DNA contamination in the analysis of chloroplast DNA with restriction endonucleases

1993 ◽  
Vol 11 (1) ◽  
pp. 48-53 ◽  
Author(s):  
Jian-Wei Liu ◽  
Ray J. Rose
Keyword(s):  
Chloroplast Dna ◽  
Nuclear Dna ◽  
Restriction Endonucleases ◽  
Dna Contamination

scholarly journals Contribution to Globularia phylogeny based on nuclear ribosomal spacer and two chloroplast DNA regions

2017 ◽  
Vol 118 (4) ◽  
Author(s):  
Kroata Hazler Pilepić ◽  
Maja Friščić ◽  
Ahmet Duran ◽  
Semir Maslo ◽  
Rade Garić ◽  
...  
Keyword(s):  
Chloroplast Dna ◽  
Maximum Parsimony ◽  
Nuclear Dna ◽  
Sequence Data ◽  
Leaf Tissue ◽  
Molecular Data ◽  
Rbcl Gene ◽  
Nuclear Its ◽  
Cellular Dna ◽  
Chloroplast Dna Regions

Background and Purpose: Molecular approach has a major impact on phylogenetic studies of plants, considering that it gives useful information about evolutionary events and relations on all taxonomic levels. The sequence data of the nuclear ITS and of two chloroplast regions, trnL-trnF spacer and rbcL gene, obtained from thirteen Globularia L. taxa, including five Anatolian endemics, representing six sections altogether, were analyzed in order to determine the relations between the European and the Anatolian species and get a better insight into the phylogeny of several closely related Globularia taxa.  Materials and Methods: Total cellular DNA was extracted from fresh or frozen leaf tissue of thirteen Globularia samples. The ITS regions of nuclear DNA and two chloroplast DNA regions were amplified and sequenced. Obtained nuclear and combined plastid data matrices were subjected to Maximum Parsimony analyses. Results and Conclusions: Molecular data that were obtained in this study indicate the existence of separate centers of diversification for the European and the Anatolian Globularia. The results provide support for relationships among the studied Anatolian endemic species and indications for a redefinition of affinities of some of the European species. The results presented herein are discussed along with available morphological, karyological, phytogeographical and molecular data. Keywords: Globularia, ITS, trnL-trnF, rbcL, Maximum Parsimony, Quaternary

scholarly journals Chloroplast DNA diversity in wild and cultivated barley: implications for genetic conservation

1984 ◽  
Vol 43 (3) ◽  
pp. 339-343 ◽  
Author(s):  
M. T. Clegg ◽  
A. H. D. Brown ◽  
P. R. Whitfeld
Keyword(s):  
Hordeum Vulgare ◽  
Chloroplast Dna ◽  
Genetic Conservation ◽  
Restriction Endonucleases ◽  
Wild Progenitor ◽  
Dna Diversity ◽  
Cytoplasmic Diversity ◽  
Isozyme Loci ◽  
Cultivated Barley

SUMMARYNine diverse lines of cultivated barley (Hordeum vulgare) and 11 lines of its wild progenitor (H. spontaneum) were assayed for variation in their chloroplast DNA by digestion with ten restriction endonucleases. The cultivated lines exhibited a single cpDNA polymorphism, whereas the wild material exhibited five. The significantly lower level of diversity among the cultivated lines was unexpected because both cultivated and wild lines had been selected for comparable levels of diversity for nuclear encoded isozyme loci. These results suggest that the level of cytoplasmic diversity was markedly restricted during the domestication of cultivated barley.

scholarly journals ContamLD: estimation of ancient nuclear DNA contamination using breakdown of linkage disequilibrium

2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Nathan Nakatsuka ◽  
Éadaoin Harney ◽  
Swapan Mallick ◽  
Matthew Mah ◽  
Nick Patterson ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Nuclear Dna ◽  
Dna Contamination

Tobacco nuclear DNA contains long tracts of homology to chloroplast DNA

1992 ◽  
Vol 85-85 (2-3) ◽  
pp. 229-238 ◽  
Author(s):  
M. A. Ayliffe ◽  
J. N. Timmis
Keyword(s):  
Chloroplast Dna ◽  
Nuclear Dna

Chloroplast deoxyribonucleic acid Isolation: purity achieved without nuclease digestion

1981 ◽  
Vol 59 (11-12) ◽  
pp. 911-915 ◽  
Author(s):  
Patsy R. Rhodes ◽  
S. D. Kung
Keyword(s):  
Chloroplast Dna ◽  
Liquid Nitrogen ◽  
Deoxyribonucleic Acid ◽  
Nuclear Dna ◽  
Buoyant Density ◽  
Silica Sol ◽  
Plant Tissues ◽  
Nuclease Digestion ◽  
Density Analysis ◽  
Digestion Step

Chloroplasts, obtained from plant tissues homogenized in liquid nitrogen, were freed of nuclei on silica sol gradients. Buoyant density analysis of denatured–renatured DNA and the clarity of restriction fragment patterns demonstrate the purity of these preparations. In this manner, chloroplast DNA free of substantial nuclear DNA contamination was obtained from several plant species without the use of a deoxyribonuclease digestion step.

Changes in DNA synthesis during cell growth and chloroplast replication in greening spinach leaf disks

1975 ◽  
Vol 17 (1) ◽  
pp. 27-41 ◽  
Author(s):  
R.J. Rose ◽  
D.G. Cran ◽  
J.V. Possingham
Keyword(s):  
Cell Growth ◽  
Dna Synthesis ◽  
Chloroplast Dna ◽  
Nuclear Dna ◽  
General Relation ◽  
Chloroplast Division ◽  
Mesophyll Cells ◽  
Chloroplast Replication ◽  
Spinach Leaf ◽  
Leaf Disks

Spinach leaf disks grown initially in the dark, show increased cell expansion and chloroplast replication when transferred to the light. These changes are accompanied by increases in the total amount of DNA and the incorporation of [3H]thymidine (3H-TdR). Autoradiography of EDTA-separated cells dried on to glass slides was used to follow changes in 3H-TdR incorporation in both chloroplasts and nuclei. Specificity of incorporation was confirmed by nuclease studies. DNA synthesis occurs in both the chloroplasts and nuclei, and is highest just prior to, and during the period of most rapid cell growth and chloroplast replication which occurs shortly after the transfer to the light. Light, however, appears to have a greater and more immediate effect on nuclear DNA synthesis. Though nuclear and chloroplast DNA syntheses follow similar patterns during disk growth, in a given cell, chloroplast DNA synthesis can be separate in time from nuclear DNA synthesis. The increased nuclear DNA synthesis is possibly required to support the increased population of chloroplasts, while chloroplast DNA synthesis is associated with chloroplast division. If the disks are not transferred to the light but kept in darkness, chloroplast 3H-TdR incorporation remains high, though chloroplast division is reduced. Epidermal cells in light-grown tissue also show 3H-TdR incorporation but low rates of chloroplast division. It would appear that chloroplast DNA synthesis in mesophyll cells from light-grown tissue shows a general relation to chloroplast division, but there does not appear to be an obligatory close coupling between the 2 processes.

scholarly journals Phylogenetic Studies on Prunus Species by DNA Fingerprints

HortScience ◽  
1995 ◽  
Vol 30 (4) ◽  
pp. 762G-763
Author(s):  
Masao Yoshida ◽  
T. Shimada ◽  
M. Yanaguchi
Keyword(s):  
Genetic Diversity ◽  
Chloroplast Dna ◽  
Nuclear Dna ◽  
Restriction Enzymes ◽  
Dna Fingerprints ◽  
Prunus Species ◽  
Random Primers ◽  
Phylogenetic Studies ◽  
Pcr Products ◽  
Template Dna

Twenty-eight Prunus species were examined in order to survey their genetic diversity. Genomic DNA was extracted from 36 varieties and used for the template DNA of PCR. DNA fingerprints were generated by random primers or semi-random primers, some primers consensus to the repeated units as telomers, and three sets of sequence-tagged primers specific to domains of chloroplast DNA (psbA, rbcL-ORF106, atpB-rbcL). PCR products generated from these three domains were digested by 12 restriction enzymes. RFLPs were detected among varieties and subjected to the UPGMA. Thirty-six varieties were classified approximately into two groups: “Plum group” and “Cherry group.” It was inferred that these two groups were divided in old time. P. tomentosa, P. japonica, P. glandurosa, and P. besseyi, which are classified into the cherries, showed the same fingerprint patterns from chloroplast DNA of the plum group; plums and cherries have a large genetic diversity. It was supposed that the diversity of plums depended on nuclear DNA, besides the diversity of cherries on both nuclear and chloroplast DNA.

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