DNA Comparisons among Barley, Oats, Rye, and Wheat.
TL;DR: The present investigation was initiated to compare DNA base sequences within the Gramineae, a group of plants from which their taxonomic and supposed evolutionary relationships may be deduced.
Abstract: F all groups of plants, none can match the cereal grains in importance to O m a n . Their origins in cultivation have been traced back some 9,000 years to the beginnings of agriculture ( HELBAEK 1960). Extensive cytogenetic studies have been undertaken with this group of plants from which their taxonomic and supposed evolutionary relationships may be deduced (BELL 1965; RILEY 1965). Some of the relationships in the family to which the cultivated cereals belong are diagrammed in Figure 1 which includes only the relevant genera. The grass family, Gramineae, contains a very large number of polyploid forms. STEBBINS (1956b) has calculated that nearly 70% of grass species are polyploid, a value which is twice the average of flowering plants as a whole. In addition there has been a striking development of allopolyploid groups including the three major crop plants: barley, oats and wheat. STEBBIN'S (1956a,b) suggestions for a revision of the scheme presented in Figure 1 include the proposition that the tribe Triticeae be considered as a single genus. This change was proposed on the basis of cytological evidence and the uniquely high number of bigeneric hybrids. BOWDEN (1959) proposed on legal criteria that Triticum and Aegilops be considered as members of a single genus instead of separate genera in the subtribe Triticinae. They were so incorporated by MORRIS and SEARS (1967). The present investigation was initiated to compare DNA base sequences within the Gramineae. DNA comparisons can yield quantitative data on relatedness and divergence among organisms (SCHILDKRAUT et al. 1962; MCCARTHY and BOLTON 1963; HOYER, MCCARTHY and BOLTON 1964; LAIRD and MCCARTHY 1968). BENDICH and BOLTON (1967) have recently demonstrated the applicability of these same methods to plant material. The basis of this approach depends upon the accumulation of heritable changes in the genes of organisms manifested in the base sequence of DNA. Such changes occur in the sequential order of bases in the polynucleotide structure of DNA and in the number of similar regions of DNA created by gene duplication. By separating the two DNA strands of one organism and recombining them with separated DNA strands of another organism, a heteroduplex or hybrid DNA is produced. The quantity of hybrid DNA is easily measurable when one of the two DNAs is radiolabeled. It is generally recognized that the thermal stability of a DNA/DNA or RNA/
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TL;DR: The distance Wagner procedure is applicable to data matrices of immunological distance, such as that of Sarich (1969a), in which between-OTU comparisons are evaluated but for which no attributes of the OTUs themselves are directly observable.
Abstract: 1. The distance Wagner procedure, presented here, is a modification of the original Wagner algorithm of Kluge and Farris (1969). Unlike previous techniques for calculating most parsimonious trees, it does not require a character-state matrix for the OTUs, but depends only upon an OTU × OTU matrix of phenetic differences. For this reason, the distance Wagner procedure is applicable to data matrices of immunological distance, such as that of Sarich (1969a), in which between-OTU comparisons are evaluated but for which no attributes of the OTUs themselves are directly observable. The distance Wagner procedure has the advantage over other available techniques for processing such data that it is free of the assumption of homogeneity of evolutionary rates over phyletic lines. 2. The estimated evolutionary trees produced by the distance Wagner procedure are undirected. Their roots may be estimated either by assuming the evolutionary rates of the two most divergent phyletic lines on the tree to be equal, or by con...
1,218 citations
TL;DR: The process by which novel structure and function could have arisen during evolution are considered speculatively in terms of the authors' gene regulation theory.
Abstract: Recent experimental information on DNA sequence repetition is reviewed, and the significance of both repetitive and non-repetitive sequence considered. Included are a summary of data on the distribution of genome sizes in animals, new experiments on interspecific DNA homology, the distribution of sequence frequencies, and the interspersion of repetitive sequences within the genome. Aspects of the process of evolution are considered at the level of change in the DNA. the process by which novel structure and function could have arisen during evolution are considered speculatively in terms of the authors' gene regulation theory (Britten and Davidson, 1969).
753 citations
TL;DR: The complete nucleotide sequence of the transferred region of an octopine tumor inducing (Ti) plasmid from Agrobacterium tumefaciens (pTi15955) has been determined and it was revealed that recognition sites for 72 restriction endonucleases are present in the DNA sequence at least once.
Abstract: The complete nucleotide sequence of the transferred region (T-DNA) of an octopine tumor inducing (Ti) plasmid fromAgrobacterium tumefaciens (pTi15955) has been determined. A total of 24 595 nucleotides extending approximately 900 bases to either side of the outermost, T-DNA boundaries was sequenced. Computer analysis of the sequenced portion of the Ti plasmid revealed that recognition sites for 72 restriction endonucleases are present in the DNA sequence at least once; no site forEcoK exists in this DNA sequence. Two imperfect 24 base repeats border the T-DNA sequence; the left starts at position 909 and the right ends at position 23 782, giving the T-DNA region a total length, of 22 874 nucleotides. Another two similar 24 base repeats lie within T-DNA and divide it, into three distinct domains: T-left (TL-DNA) 13 175 bp of apparently eukaryotic origin; T-center (TC-DNA) 1816 bp of prokaryotic origin; and T-right (TR-DNA) 7 883 bp of eukaryotic origin. The T-DNA contains nine reported transcripts, however, 26 open reading frames longer than 300 bases that start with an ATG initiation codon were found. Fourteen open reading frames are bounded by putative eukaryotic promoters, ribosome binding sites, and poly(A) addition sites and occur only in TL-and TR-DNAs. No open reading frames showing eukaryotic promoter sequences are located within the TC-DNA.
412 citations
TL;DR: It is proposed that wheat and rye diverged after their common ancestor had diverged from the ancestor of barley, and a phylogenetic tree of cereal evolution constructed on the basis of the repeated sequence DNA homologies is proposed.
Abstract: The effect of DNA fragment size on the extent of hybridisation that occurs between repeated sequence DNAs from oats, barley, wheat and rye has been investigated. The extent of hybridisation is very dependent on fragment size, at least over the range of 200 to 1000 nucleotides. This is because only a fraction of each fragment forms duplex DNA during renaturation. From these results estimates of the proportions of repeated sequences of each of the cereal genomes that are homologous with repeated sequences in the other species have been determined and a phylogenetic tree of cereal evolution constructed on the basis of the repeated sequence DNA homologies. It is proposed that wheat and rye diverged after their common ancestor had diverged from the ancestor of barley. This was preceded by the divergence of the common ancestor of wheat, rye and barley and the ancestor of oats. Once introduced in Gramineae evolution most families of repeated sequences appear to have been maintained in all subsequently diverging species. — The repeated sequences of oats, barley, wheat and rye have been divided into Groups based upon their presence or absence in different species. Repeated sequences of related families are more closely related to one another within a species than between species. It is suggested that this is because repeated sequences have been involved in many rounds of amplification or quantitative change via unequal crossing over during species divergence in cereal evolution.
208 citations
TL;DR: It is suggested that repetitive DNA sequences in the terminal heterochromatin of rye chromosomes define a basic higher order structure and DNA loop domains of regions of Rye chromosomes consisting of arrays of tandemly organized sequences.
Abstract: Repetitive DNA sequences in the terminal heterochromatin of rye (Secale cereale) chromosomes have consequences for the structural and functional organization of chromosomes. The large-scale genomic organization of these regions was studied using the telomeric repeat from Arabidopsis and clones of three nonhomologous, tandemly repeated, subtelomeric DNA families with complex but contrasting higher order structural organizations. Polymerase chain reaction analysis with a single primer showed a fraction of the repeat units of one family organized in a "head-to-head" orientation. Such structures suggest evolution of chromosomes by chromatid-type breakage-fusion-bridge cycles. In situ hybridization and pulse field gel electrophoresis showed the order of the repeats and the heterogeneity in the lengths of individual arrays. After Xbal digestion and pulse field gel electrophoresis, the telomeric and two subtelomeric clones showed strong hybridization signals from 40 to 100 kb, with a maximum at 50 to 60 kb. We suggest that these fragments define a basic higher order structure and DNA loop domains of regions of rye chromosomes consisting of arrays of tandemly organized sequences.
202 citations
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3,603 citations
TL;DR: Hundreds of thousands of copies of DNA sequences have been incorporated into the genomes of higher organisms and used in medicine, science, and engineering.
Abstract: Hundreds of thousands of copies of DNA sequences have been incorporated into the genomes of higher organisms.
2,699 citations
TL;DR: An improved method for the formation of DNA—RNA hybrids is described, quantitatively more certain than annealing in liquid, since the competing DNA renaturation reaction is suppressed.
1,839 citations
TL;DR: It is proposed that the mechanism of the reaction involves the joining of short, homologous sites on the two strands followed by a fast, reversible zippering reaction with forward rate constant kt, which explains the temperature and the GC dependence.
1,355 citations
TL;DR: The present study explores in detail the relationships among the rate and specificity of reaction, the temperature, and the concentrations of formamide and salt.
Abstract: Conditions are described for effecting deoxyribonucleic acid renaturation and deoxyribonucleic acid-ribonucleic acid hybridization in formamide solutions at low temperatures. High specificity and rates of reaction can be achieved by appropriate choice of the formamide and salt conmalian nucleic acids. centrations and the temperature. Reaction conditions can be deduced from the relationship between formamide concentration and reduction in the thermal stability: 1 % formamide reduces the T,,, by 0.72'. These methods are valuable for studies of the prolonged reactions occurring between mamR e n a t u r a t i o n of DNA and hybridization of RNA with DNA are normally studied under reaction conditions involving elevated temperatures. The maximum rate of reaction occurs some 25 O below the T,, or mean thermal denaturation temperature (Marmur and Doty, 1961). However, in studies of nucleic acids of complex organisms where reaction times are prolonged, or where biological activity must be preserved, exposure of nucleic acids to high temperatures presents obvious disadvantages such as chain scission and depurination. These difficulties may be avoided by the use of high concentrations of certain salts, such as 6.2 M NaC104 (Thomas, 1966) or of aqueous solutions of various organic solvents in which the thermal stability of double-stranded polynucleotides is greatly reduced (Herskovits, 1962; Geiduschek, 1962; Levine et al., 1963). A particularly useful organic solvent is formamide in which DNA can be denatured and renatured at room temperature (Helmkamp and Ts'o, 1961 ; Marmur and Ts'o, 1961 ; Subirana and Doty, 1966). This principle has been exploited by Bonner et al. (1967) to allow the formation of DNA-RNA hybrids with filter-bound DNA at 25" in the presence of formamide. The present study explores in detail the relationships among the rate and specificity of reaction, the temperature, and the concentrations of formamide and salt. As a result of the incidence of partially related base sequences (Britten and Kohne, 1968), DNA renaturation or DNA-RNA hybridization reactions involving nucleic acids of mammals or other higher organisms may not display locus specificity. In fact, the extent of cross-reaction among related base sequences is dependent upon the reaction conditions such as temperature and ionic strength (McCarthy and McConaughy, 1968 ; Church and McCarthy, 1968). Thus it is important not only to establish conditions for high rates of reaction and species specificity but also to characterize the nature of the duplexes being formed. Although in aqueous solution cross-reaction among related base sequences is reduced at higher temperatures or lower ionic strengths (McCarthy and McConaughy, 1968), specificity conditions are much more easily adjusted by variation of ionic strength and formamide concentration. High specificity may be obtained at low temperatures, with rates of reaction several times higher than those obtained at 60 or 70" in aqueous solution. Materials and Methods Formamide. The formamide used in these studies was purchased from the Eastman Kodak Co. Optical studies in formamide solution require high solvent purity. The criterion applied was that the optical density of 100% formamide at 270 mp in 1-cm path-length cells not exceed 0.15. All of the experiments described here were carried out with formamide which meets these specifications. Isolation of Nucleic Acids. Bacillus subtilis DNA was prepared as described by Marmur (1961) and 3H-labeled DNA was extracted from cells grown in minimal medium to which 0.5 pCi/ml of thymidine-methyl-H3 was added per hour for 4 hr. * From the Departments of Microbiology and Genetics, University of Washington, Seattle, Washington 98105, and from the Department of DNA was isolated from Drosopl?i/a me/anogaster pupae by a procedure described elsewhere (Laird and McCarthy, 1968). Zoology, University of Texas, Austin, Texas. Received Apri l 18, 1969. Mouse and hamster DNA were extracted from liver as The work was supported in part by a research grant from the. U. S. Public Health Service, Institute of General Medical Sciences (GM 124491, in part by a grant from the National Science Foundation (GB 6099), and in part by National Institutes of Health postdoctoral funds, previously described by Church and McCarthy (1968). Labeled L cells grown in !-4Ci/m1 Of thymidine-methy1-3H added to the medium (McCarthy and McConaughy, 1968). DNA was prepared from with N U C L L I C A C I D R E A S S O C I A T I O N 3280
575 citations