Characterization of the DNA from the dinoflagellate crypthecodinium cohnii and implications for nuclear organization

Allen, James; Roberts, Thomas M.; Loeblich, Alfred R.; Klotz, Lynn C.

doi:10.1016/0092-8674(75)90006-9

Cited by 95 publications

(42 citation statements)

References 30 publications

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“…Furthermore, the DNA content can vary substantially not only from species to species but also between growth phases. In several autotrophic dinoflagellate species, cells in logarithmic phase were found to contain a twofold-larger amount of DNA than those in stationary phase (1). In most eukaryotes, rRNA genes are organized in tandemly repeated units (14), for example, 100 to 200 copies are present in yeast and 50 to 10,000 copies are present in mammals.…”

Section: Discussionmentioning

confidence: 99%

“…This estimate is consistent with the value obtained by DNA extraction and quantification by optical density at 260 nm (4 to 6 pg of DNA/cell), although it is in the lower range of DNA content (5.2 to 9.4 pg of DNA/cell) as measured by fluorescent staining of DNA (46). Dinoflagellates contain large amounts of DNA, ranging from 3.8 pg per cell in Crypthecodinium cohnii and 33 pg in Gyrodinium resplendens to 200 pg per cell in G. polyedra (1,28). These values are greater than the DNA contents of any other unicellular eukaryotes characterized so far (0.046 to 3 pg/nucleus) (48).…”

Section: Discussionmentioning

confidence: 99%

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Characterization of the rRNA Locus of Pfiesteria piscicida and Development of Standard and Quantitative PCR-Based Detection Assays Targeted to the Nontranscribed Spacer

Saito

Drgon

Robledo

et al. 2002

Appl Environ Microbiol

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Pfiesteria piscicida is a heterotrophic dinoflagellate widely distributed along the middle Atlantic shore of the United States and associated with fish kills in the Neuse River (North Carolina) and the Chesapeake Bay (Maryland and Virginia). We constructed a genomic DNA library from clonally cultured P. piscicida and characterized the nontranscribed spacer (NTS), small subunit, internal transcribed spacer 1 (ITS1), 5.8S region, ITS2, and large subunit of the rRNA gene cluster. Based on the P. piscicida ribosomal DNA sequence, we developed a PCR-based detection assay that targets the NTS. The assay specificity was assessed by testing clonal P. piscicida and Pfiesteria shumwayae, 35 additional dinoflagellate species, and algal prey (Rhodomonas sp.). Only P. piscicida and nine presumptive P. piscicida isolates tested positive. All PCR-positive products yielded identical sequences for P. piscicida, suggesting that the PCR-based assay is species specific. The assay can detect a single P. piscicida zoospore in 1 ml of water, 10 resting cysts in 1 g of sediment, or 10 fg of P. piscicida DNA in 1 g of heterologous DNA. An internal standard for the PCR assay was constructed to identify potential false-negative results in testing of environmental sediment and water samples and as a competitor for the development of a quantitative competitive PCR assay format. The specificities of both qualitative and quantitative PCR assay formats were validated with >200 environmental samples, and the assays provide simple, rapid, and accurate methods for the assessment of P. piscicida in water and sediments.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Characterization of the rRNA Locus of Pfiesteria piscicida and Development of Standard and Quantitative PCR-Based Detection Assays Targeted to the Nontranscribed Spacer

Saito

Drgon

Robledo

et al. 2002

Appl Environ Microbiol

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“…Using renaturation kinetic analysis, the complexity of total cellular dinoflagellate DNA has been studied by several investigators (3,23,26). These studies indicated that 55 to 60% of the total DNA in C. cohnii and Prorocentrum cassubicum consisted of repetitive sequences.…”

Section: Discussionmentioning

confidence: 99%

Characterization of Satellite DNA from Three Marine Dinoflagellates (Dinophyceae): Glenodinium sp. and Two Members of the Toxic Genus, Protogonyaulax

Boczar

Liston²,

Cattolico³

1991

Plant Physiol.

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Using CsCI-Hoechst dye or CsCI-ethidium bromide gradients, satellite and nuclear DNAs were separated and characterized in three marine dinoflagellates: Glenodinium sp., and two toxic dinoflagellates, Protogonyaulax tamarensis and Protogonyaulax catenella. In all three dinoflagellates, the lowest density fraction, satellite DNA1, hybridized to chloroplast genes derived from terrestrial plants and/or other algae. Dinoflagellate chloroplast DNAs exhibited molecular sizes of 114 to 125 kilobase pairs, which is consistent with plastid sizes determined for other chromophytic algae (120-150 kilobase pairs). Mitochondrial DNA was not resolved from nuclear DNA in this system. Two additional satellite DNAs, satellite DNA2 and satellite DNA3, recovered from P. tamarensis and P. catenella were similar to one another, both within and between species, when characterized by restriction enzyme analysis. These satellites were 85 to 95 kilobase pairs in size, and exhibited restriction fragments that hybridized to yeast nuclear ribosomal RNA genes. Restriction enzyme analyses and DNA hybridization studies of cpDNA document that the two Protogonyaulax isolates are not evolutionarily identical.The Dinophyceae is a group of unicellular, eukaryotic organisms that is composed of photosynthetic, heterotrophic, phagocytic, and saprophytic forms. These algae are second only to diatoms in their contribution to primary production in marine and freshwater ecosystems. In addition, species of photosynthetic dinoflagellates have been identified as the dominant organisms comprising the toxic "red tides" that periodically close shellfish aquaculture facilities on both the East and West Coasts.Dinoflagellates possess unique DNA characteristics. Cells of this taxonomic group frequently contain very high levels (32-200 pg/cell) of DNA packaged into chromosomes that lack classic histone-like proteins. These chromosomes remain condensed throughout cellular interphase (28) and contain an '

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“…[13] Using Eqs. 7, 9, and 12 to get the corrected difference matrix, D', we have [15] x= S [a+b+c+2y]+d, [16] 3 and X' is again given by Eq. 13.…”

Section: The Methodsmentioning

confidence: 99%

Calculation of evolutionary trees from sequence data.

Klotz¹,

Komar²,

Blanken³

et al. 1979

Proc. Natl. Acad. Sci. U.S.A.

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Evolutionary trees are usually calculated from comparisons of protein or nucleic acid sequences. from present-day organisms by use of algorithms that use only the difference matrix, where the difference matrix is constructed from the sequence differences between pairs of sequences from the organisms. The difference matrix alone cannot.define uniquely the correct position of the ancestor of the present-day organisms (root of the tree). Furthermore, methods using the difference matrix alone often fail to give the correct pattern of tree branching (topology) when the different sequences evolve at different rates. Only for equal rates of evolution can the difference matrix (when used with the so-called matrix method) yield exactly the correct topology and root. In this paper we present a method for calculating evolutionary trees from sequence data that uses, along with the difference matrix, the rate of evolution of the various sequences from their common ancestor. It is proven analytically that this method uniquely determines both the correct tree topology and root in theory for unequal rates of sequence evolution. How one would estimate an ancestral sequence to be used in the method is discussed in particular fox the 5S RNA sequences from prokaryotes and eukaryotes and for ferredoxin sequences. The recent proliferation of protein and nucleic acid sequences, due in part to the development of new sequencing techniques (1, 2), has led to a renewed interest in the evolution of these sequences and the organisms from which they came. We wish to discuss here some problems with the commonly used method (3, 4) (the matrix method) for calculating evolutionary trees from molecular sequence data and to present an alternative method that, in theory, eliminates these problems. Because the analytic proof of our method depends on a knowledge of existing methods, we will briefly review what is necessary from the existing literature, then discuss the problems with the matrix method in some detail.An evolutionary tree representation of nucleic acid or protein sequence differences among several organisms should give the following information: (I) the correct pattern of branching of the various present-day organisms from one another (that is, the correct tree "topology"); (ii) the correct position on the tree of the common ancestor to all the present-day organisms (that is, the correct tree "root"); and (iii) of secondary importance, a reasonable estimate of the number of mutations along each of the tree branches (branch mutations).One type of such a representation is presented in Fig. la for five hypothetical present-day organisms, A, B, C, D, and E, and their common ancestor X. In this representation, the topology is shown by the order in which the branches connect: C and D are most closely related in the sense that they connect first, then CD connects to E, and A connects to B. The root of the tree with the common ancestor X is shown to be between the groups AB and CDE. This pictorial representation may also be represented...

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Characterization of the DNA from the dinoflagellate crypthecodinium cohnii and implications for nuclear organization

Cited by 95 publications

References 30 publications

Characterization of the rRNA Locus of Pfiesteria piscicida and Development of Standard and Quantitative PCR-Based Detection Assays Targeted to the Nontranscribed Spacer

Characterization of the rRNA Locus of Pfiesteria piscicida and Development of Standard and Quantitative PCR-Based Detection Assays Targeted to the Nontranscribed Spacer

Characterization of Satellite DNA from Three Marine Dinoflagellates (Dinophyceae): Glenodinium sp. and Two Members of the Toxic Genus, Protogonyaulax

Calculation of evolutionary trees from sequence data.

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