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Topic: CpDNA

In the News (Fri 17 Feb 12)

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	Campbell, Christopher S.*, Rodger C. Evans, Matthew P. Arsenault, and Timothy A. Dickinson.
		For outgroups we used Kageneckia, Lindleya, and Vauquelinia, the closest relatives of the traditionally circumscribed, pome-fruited subfamily.
		CpDNA supports (Chamaemespilus, Torminalis) at a 100% bootstrap (BS) level and (Aria, Cormus) at 71% BS in a larger, weakly supported clade that also includes Sorbus s.s.
		This lack of resolution is at least partly the result of low sequence divergence (about 0.5-2.0% in cpDNA data), which is remarkable in that several maloid genera are known as fossils from the Middle Eocene.
	www.botany2002.org /sympos13/abstracts/6.shtml (350 words)

	Haplotype variation of cpDNA in the agamic grass complex Pennisetum section Brevivalvula (Poaceae)
		Moreover, because cpDNA is maternally inherited in most angiosperms, the use of that marker may be particularly informative for clarifying genetic relationships between the taxa of a predominantly agamic polyploid complex such as Brevivalvula, in which pollen has little influence on gene exchange.
		It is an easy-to-use method which has the main advantage of providing an estimate of cpDNA variation in the whole molecule and not only in a part of it, as is the case with methods using complementary probes intended for hybridization or specific primers for PCR amplification.
		In those species, the average proportion of cpDNA diversity attributable to differentiation between populations reached 85% and was attributed to both low seed dispersal and, more importantly, to the occurrence of substantial interspecific hybridization and cytoplasmic introgression (Dumoulin-Lapègue et al., 1997).
	www.nature.com /hdy/journal/v86/n5/full/6888540a.html (4208 words)

	Plant Methods \| Full text \| A high-throughput method for detection of DNA in chloroplasts using flow cytometry
		During the cell expansion phase that follows cell division in the meristem, the amount of cpDNA is diluted by chloroplast division without compensatory DNA synthesis [7,8], accompanied by cpDNA degradation in barley [9] and rice [10].
		Whether the loss of cpDNA is a general feature of development among all chloroplast-containing organisms remains to be assessed, in part because the assay for DNA content of individual chloroplasts is quite laborious.
		DAPI fluorescence did not accurately reflect cpDNA content, as chloroplasts treated with DNase showed a distribution of fluorescence values that was similar to (Figure 1A) and sometimes exceeded (Figure 1B) untreated chloroplasts.
	www.plantmethods.com /content/3/1/5 (5528 words)

	BioMed Central \| Full text \| The complete chloroplast DNA sequence of the green alga Oltmannsiellopsis viridisreveals a ...
		Investigations of chloroplast DNA (cpDNA) from green algae representing each of the five recognized classes have revealed that the genomes of the charophyte Chaetosphaeridium globosum [13] and the prasinophytes Mesostigma [7] and Nephroselmis olivacea [14] are highly similar to those of land plants.
		In the context of the debate concerning the branching order of the UTC lineages, the predicted architecture of the chloroplast genome of the earliest members of the Ulvophyceae strengthens the notion that this lineage is sister to the Chlorophyceae [5,6].
		Fragmented ancestral gene clusters in the cpDNAs of UTC algae.
	www.biomedcentral.com /1741-7007/4/3 (5620 words)

	BioMed Central \| Full text \| The complete chloroplast DNA sequences of the charophycean green algae Staurastrum and ...
		Clearly, loss of the IR appears to be a major event that shaped the architecture of the chloroplast genome in the Zygnematales, an event that apparently occurred early during the evolution of this group of charophycean green algae.
		Considering that this ancestor occupies a basal position in the tree describing the relationships among zygnematalean green algae [21,22], then most, if not all, of the algae belonging to the Zygnematales are expected to lack an IR in their chloroplast genome.
		Staurastrum cpDNA lacks seven of the 13 introns that are present in Zygnema cpDNA, whereas the latter cpDNA lacks five of the eight introns found in the former genome.
	www.biomedcentral.com /1741-7007/3/22 (5212 words)

	CpDNA and mtDNA primers
		The conservation of the arrangement of the genes in cpDNA has lead to the design of numerous 'consensus' or 'universal' chloroplast primers which facilitate phylogenetic or population genetic studies.
		Such straightforward, efficient and rapid PCR approaches seem extremely attractive by comparison to the more traditional RFLP studies where cpDNA is transferred on a membrane and hybridized with a labelled heterologous probe before autoradiography, and are likely to become the standard way to obtain chloroplast or mitochondrial genetic markers.
		Table 1 list the names of the genes where the primers are anchored, followed in brackets by the name given to the primers by the authors which have described them (if different from the name of the gene).
	www.pierroton.inra.fr /genetics/labo/cpdna.html (1707 words)

	Chloroplast DNA methylation and inheritance in Chlamydomonas -- Umen and Goodenough 15 (19): 2585 -- Genes and ...
		cpDNA is not replicated in gametes or maturing zygotes.
		(E) cpDNA signals from A and C were normalized to the nuclear signal and plotted on a logarithmic scale against the same time course of zygote maturation and germination.
		The patterns of cpDNA replication were as anticipated from Figure 6.
	www.genesdev.org /cgi/content/full/15/19/2585 (6710 words)

	Reversible DNA Compaction by Sulfite Reductase Regulates Transcriptional Activity of Chloroplast Nucleoids -- Sekine et ...
		Fluorescence intensity of cpDNA (A) and chloroplast nucleoids (B) after staining with DAPI was monitored with a fluorescence spectrophotometer.
		A, before monitoring, three aliquots of identical amounts of isolated cpDNA were incubated in the absence (filled diamonds) or the presence of 150 µg/ml (open circles) and 300 µg/ml (filled triangles) SiR for 2 h on ice.
		of cpDNA was affected indirectly by the exogenous SiR.
	www.jbc.org /cgi/content/full/277/27/24399 (3452 words)

	Phylogeny of the genus Pistacia as determined from analysis of the chloroplast genome -- Parfitt and Badenes 94 (15): ...
		Variation at the DNA level in the chloroplast genome has been used since the early 1980s to study species relationships (5).
		Chloroplast DNA (cpDNA) is ideal for this purpose because it is
		Pistacia polymorphic cpDNA restriction fragments from 3.2-kb amplified region in a 2% agarose gel.
	www.pnas.org /cgi/content/full/94/15/7987 (3278 words)

	* Parham Jabbarzadeh :: PhD Research Proposal in Department of Botany * (Site not responding. Last check: 2007-10-26)
		For example, transpositions in Rubiaceae cpDNA have not been demonstrated, although they have been suggested in a few cases.
		Both gene sequences and genomic rearrangements will be used to resolve several very controversial issues in plant phylogeny, including relationships among the basal land plant lineages, among spore bearing plants, among seed plant lineages, and among basal angiosperms groups.
		Total cpDNA will be isolated from leaves of either seedlings or fully mature plants.
	www.pj-lab.com /PHD.html (1409 words)

	Directory of open access journals
		The five complete chloroplast DNA (cpDNA) sequences currently available for representatives of these classes display considerable variability in overall structure, gene content, gene density, intron content and gene order.
		It is clearly more compact than the four UTC algal cpDNAs that have been examined so far, displays the lowest proportion of short repeats among these algae and shows a stronger bias in clustering of genes on the same DNA strand compared to
		The two chlorophycean genomes share 11 gene clusters that are not found in previously sequenced trebouxiophyte and ulvophyte cpDNAs as well as a few genes that have an unusual structure; however, their single-copy regions differ considerably in gene content.
	www.doaj.org /doaj?func=abstract&id=173077&recNo=37&toc=1 (345 words)

	ZÜRICH ABSTRACTS
		Circumpolar phylogeography of Vaccinium uliginosum inferred from cpDNA sequences.
		Samples have so far been analyzed from most main geographic regions (AFLP: 100 plants from 43 populations; cpDNA: 274 plants from 71 populations), but there is still a major gap in the central Siberian Arctic and the Central Asian mountains.
		In this project, we use cpDNA data to infer the phylogeography of Vaccinium uliginosum L., of which three subspecies have been described: the circumpolar diploid ssp.
	www.toyen.uio.no /botanisk/brochmann/zurich.htm (1107 words)

	Plant Genome Organization and Structure : Mitochondrial Genome Organization
		They next mapped the clone and compared it to the map of the corn cpDNA and found that the clone map was almost congruent with that of the the cpDNA 16S RNA region.
		Kemble et al (1983) demonstrated that mitochondrial DNA sequences are located in the nucleus of corn.
		Scott and Timmis (1984) showed that cpDNA sequences are found in the nuclear DNA.
	www.ndsu.nodak.edu /instruct/mcclean/plsc731/genome/genome8.htm (513 words)

	Association Between Chloroplast DNA and Mitochondrial DNA Haplotypes in Prunus spinosa L. (Rosaceae) Populations across ...
		Minimum-length spanning tree of 33 cpDNA haplotypes of Prunus spinosa with the mtDNA haplotypes plotted on it.
		The length of segments joining the circles is proportional to the number of mutations between haplotypes.
		The dissociations are in the cpDNA haplotypes C9 and
	aob.oxfordjournals.org /cgi/content/full/92/6/749 (2848 words)

	Seed Orchard Management Utilizing DNA Markers \| Vizon SciTec Inc. (Site not responding. Last check: 2007-10-26)
		Chloroplasts are paternally inherited in many conifers and the ability to differentiate unique cpDNAs, using polymorphic DNA markers, provides a means to track pollen contribution in fertilized seed.
		Although cpDNA haplotypes are not all unique, they provide sufficient discrimination for a wide variety of applications and are more robust and easily interpreted than other marker systems (isozymes, nuclear microsatellites, RAPDs, AFLPs etc).
		Seeds are dissected to separate the maternally inherited megagametophyte cpDNA from the paternally inherited embryo cpDNA.
	www.bcresearch.com /ourservices/biotechnology/seedorchard.htm (590 words)

	Elymus cpDNA (Site not responding. Last check: 2007-10-26)
		We analyze new and previously published chloroplast DNA data from Elymus and from most of the monogenomic genera of the Triticeae in an attempt to identify the maternal genome donor of Elymus.
		We also present a cpDNA phylogeny for the monogenomic genera that includes more data than, and thus builds on, those previously published.
		Within the monogenomic Triticeae, the problematic group Thinopyrum is resolved as monophyletic on the chloroplast DNA tree.
	www.uic.edu /labs/bios/robie/Abstracts/AbstrElycpDNA.htm (191 words)

	Gillespie, Lynn J. and Robert J. Soreng.*
		A new phylogenetic study of Poa, based on data from restriction site analysis of PCR amplified regions of chloroplast DNA (cpDNA) (trnT-trnF, trnF-trnV, trnV-rbcL, rbcL-ORF106, trnH-trnK), expands sampling to where about 1/6 of the species have been characterized for cpDNA types.
		The new analysis suggests that divergence in morphology and ecology is often decoupled from the frequency of fixation of phylogenetically informative cpDNA variation.
		Some species groups are widely distributed with strikingly disparate morphology and ecology, yet have diverged little in their cpDNA profiles, whereas the opposite pattern occurs in other groups.
	www.botany2001.org /section12/abstracts/266.shtml (318 words)

	Coreopsis grandiflora (Site not responding. Last check: 2007-10-26)
		Thirteen distinct cpDNA haplotypes were detected, differing by as many as 22 restriction site changes, or an estimated 0.674% nucleotide sequence divergence.
		The survey detected sufficient cpDNA variation for analyses of intraspecific and intrapopulational genetic structure, and yielded evidence for interpopulational gene flow, a cpDNA polymorphism that transcends the species boundary, and possible cpDNA introgression.
		Patterns of genetic diversity do not strictly correspond to either morphological variation or to geographical distribution; this may be a result of either cpDNA introgression or the maintenance of a cpDNA polymorphism through the speciation event that gave rise to C.
	www.uic.edu /labs/bios/robie/Abstracts/AbstrCoreo.htm (143 words)

	cpDNA_protocols.html (Site not responding. Last check: 2007-10-26)
		Described below is a procedure commonly used in the Palmer lab to purify chloroplast DNA from land plants.
		Prior to extraction, place plants in the dark for 1-4 days to reduce chloroplast starch levels.
		Approximately 100 g or more of leaf tissue is required to get sufficient quantities of cpDNA.
	evogen.jgi.doe.gov /second_levels/chloroplasts/jansen_project_home/cpDNA_protocols.html (1783 words)

	Organelle DNA Diversity among Buffalograsses from the Great Plains of North America Determined by cpDNA and mtDNA RFLPs ...
		UPGMA dendrogram of 56 buffalograsses and two outgroups based on analysis of 36 monomorphic and 189 polymorphic fragments from 6 cpDNA and 3 mtDNA sequences.
		The cpDNA was found to be maternally inherited in buffalograsses
		Verification of maternal inheritance of cpDNA in buffalograsses by using cpDNA PCR-RFLPs with primers psbC-trnS and HaeIII.
	crop.scijournals.org /cgi/content/full/45/1/186 (2801 words)

	Meiotic Stability, Chloroplast DNA Polymorphisms, and Morphological Traits of Upland Lowland Switchgrass Reciprocal ...
		of inheritance of the cpDNA in switchgrass which was not known.
		DNA was digested with BamHI restriction endonuclease and hybridized with the spinach cpDNA probe pRR12.
		J to N was the same as that observed in the maternal parent
	crop.scijournals.org /cgi/content/full/41/5/1579 (2494 words)

	Complete chloroplast DNA sequence of the moss Physcomitrella patens: evidence for the loss and relocation of rpoA from ...
		Among the bryophytes, the cpDNA (121 024 bp) of the liverwort
		Arrows indicate positions of the endpoint of large inversion relative to liverwort M.polymorpha and hornwort A.formosae cpDNA.
		the hornwort A.formosae cpDNA (8), are absent from P.patens
	nar.oxfordjournals.org /cgi/content/full/31/18/5324 (4133 words)

	Cytogenomic Analyses Reveal the Structural Plasticity of the Chloroplast Genome in Higher Plants -- Lilly et al. 13 ...
		PFGE was used to estimate the sizes of cpDNA molecules present
		PFGE conditions were 5 to 120 sec of pulse time at 4.5 V/cm, with a total run time of 46 hr.
		A similar diversity of cpDNA structures was observed in Arabidopsis.
	www.plantcell.org /cgi/content/full/13/2/245 (4127 words)

	Phylogeography of the Arctic-Alpine Saxifraga oppositifolia (Saxifragaceae) and some related taxa based on cpDNA and ...
		Localities and distribution of psbA–trnH cpDNA haplotypes of 19 samples of Saxifraga oppositifolia (circles) and of one sample each of S.
		In contrast to maternally inherited cpDNA, biparentally inherited
		Widmer A. Baltisberger 1999 Extensive intraspecific chloroplast DNA (cpDNA) variation in the alpine Draba aizoides L. (Brassicaceae): haplotype relationships and population structure.
	www.amjbot.org /cgi/content/full/90/6/931 (3380 words)

	Projects
		In Chlamydomonas reinhardtii the chloroplast DNA (cpDNA) of meiotic progeny is inherited exclusively from the parent that carries the plus mating type allele.
		Although both plus and minus parents contribute cpDNA to the zygote, the minus parental cpDNA is selectively destroyed within hours of mating.
		While the prevailing model for uniparental cpDNA inheritance invokes a methylation-restriction system, our work on cpDNA methylation rules out that model and instead points to a role for methylation in regulating cpDNA replication in germinating zygotes.
	www.salk.edu /labs/pbio-u/projects.html (316 words)

	Nonreciprocal Recombination between Alleles of the Chloroplast 23S rRNA Gene in Interspecific Chlamydomonas Crosses -- ...
		The inheritance of six polymorphic loci mapping in the rRNA-encoding (rDNA) region of the inverted repeat sequence of chloroplast DNA (cpDNA) was scored in hybrid subclones derived from reciprocal interspecific crosses between the green algae Chlamydomonas eugametos and Chlamydomonas moewusii.
		(ii) Only one allele of each polymorphic cpDNA locus was ever detected in the hybrids, thus suggesting that newly recombined rDNA sequences in one copy of the inverted repeat are rapidly spread to the other by a copy-correction mechanism.
		(iv) cpDNA markers associated with a putative intron of the C. eugametos 23S rRNA gene were inherited by all 17 hybrids.
	www.pnas.org /cgi/content/abstract/84/12/4166 (525 words)

	PCR-RFLP ANALYSIS OF CHLOROPLAST DNA IN LEUCADENDRON (PROTEACEAE)
		The mode of chloroplast DNA (cpDNA) inheritance was studied in Leucadendron (Proteaceae) using polymerase chain reaction amplification of chloroplast DNA followed by restriction fragment length analysis of the amplified products (PCR-RFLP).
		It was found that by testing 100 progeny from five interspecific crosses, the inheritance of cpDNA in Leucadendron was predominantly maternal.
		Based on the cpDNA variation detected, sixteen haplotypes were recognized among the 21 Leucadendron species studied.
	www.actahort.org /books/716/716_6.htm (95 words)

	Heredity - Abstract of article: Genetic variation of Ginkgo biloba L. (Ginkgoaceae) based on cpDNA PCR-RFLPs: inference ...
		biloba, we examined the genetic structure of eight potential refugial populations and plantations using chloroplast DNA (cpDNA) with eight size variants in the trnK1-trnK2 fragment.
		The majority of the cpDNA haplotypes are restricted to minor portions of the geographical range.
		This area is a current biodiversity hotspot of global importance, and may have been protected from the extremes of climatic fluctuations during the Pleistocene.
	www.nature.com /cgi-taf/DynaPage.taf?file=/hdy/journal/v94/n4/abs/6800616a.html (298 words)

	Circular Chloroplast Chromosomes: The Grand Illusion -- Bendich 16 (7): 1661 -- THE PLANT CELL
		The first to adapt these procedures for cpDNA were Deng et al.
		This ethidium-stained structure was obtained from meristematic tissue of maize.
		To summarize, it is replication driven by recombination that
	www.plantcell.org /cgi/content/full/16/7/1661 (3583 words)

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