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  • 1
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    Teff, an Orphan Cereal in the Chloridoideae, Provides Insights into the Evolution of Storage Proteins in Grasses (2016)
    Oxford University Press
    Details
    Publication Date: 2016-06-15
    Description: Seed storage proteins (SSP) in cereals provide essential nutrition for humans and animals. Genes encoding these proteins have undergone rapid evolution in different grass species. To better understand the degree of divergence, we analyzed this gene family in the subfamily Chloridoideae , where the genome of teff ( Eragrostis tef ) has been sequenced. We find gene duplications, deletions, and rapid mutations in protein-coding sequences. The main SSPs in teff, like other grasses, are prolamins, here called eragrostins. Teff has - and -prolamins, but has no β-prolamins. One -type prolamin (1) in teff has higher methionine (33%) levels than in maize (23–25%). The other -type prolamin (2) has reduced methionine residues (〈10%) and is phylogenetically closer to α prolamins. Prolamin 2 in teff represents an intermediate between and α types that appears to have been lost in maize and other Panicoideae , and was replaced by the expansion of α-prolamins. Teff also has considerably larger numbers of α-prolamin genes, which we further divide into five sub-groups, where α2 and α5 represent the most abundant α-prolamins both in number and in expression. In addition, indolines that determine kernel softness are present in teff and the panicoid cereal called foxtail millet ( Setaria italica ) but not in sorghum or maize, indicating that these genes were only recently lost in some members of the Panicoideae . Moreover, this study provides not only information on the evolution of SSPs in the grass family but also the importance of α-globulins in protein aggregation and germplasm divergence.
    Electronic ISSN: 1759-6653
    Topics: Biology
    Published by Oxford University Press
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  • 2
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    Comparative genomics of Oryza AA-genome species [Genetics] (2014)
    National Academy of Sciences
    Details
    Publication Date: 2014-11-19
    Description: Comparative genomic analyses among closely related species can greatly enhance our understanding of plant gene and genome evolution. We report de novo-assembled AA-genome sequences for Oryza nivara, Oryza glaberrima, Oryza barthii, Oryza glumaepatula, and Oryza meridionalis. Our analyses reveal massive levels of genomic structural variation, including segmental duplication and rapid...
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 3
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    The rice genome. Opening the door to comparative plant biology (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-04-06
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bennetzen, Jeffrey -- New York, N.Y. -- Science. 2002 Apr 5;296(5565):60-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA. maize@bilbo.bio.purdue.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11935009" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Arabidopsis/genetics ; Biological Evolution ; Chromosome Mapping ; Computational Biology ; Genes, Plant ; Genetic Variation ; *Genome, Plant ; Genomics ; Humans ; Oryza/*genetics ; Phylogeny ; Physical Chromosome Mapping ; Repetitive Sequences, Nucleic Acid ; *Sequence Analysis, DNA ; Species Specificity ; Synteny
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 4
    Electronic Resource
    Electronic Resource
    Single-stranded DNA transcription by yeast RNA polymerase B
    Amsterdam : Elsevier
    BBA Section Nucleic Acids And Protein Synthesis 656 (1981), S. 220-227 
    Details
    ISSN: 0005-2787
    Keywords: (Yeast) ; RNA polymerase B ; Single-stranded DNA ; Transcription
    Source: Elsevier Journal Backfiles on ScienceDirect 1907 - 2002
    Topics: Biology
    Type of Medium: Electronic Resource
    URL: http://linkinghub.elsevier.com/retrieve/pii/0005-2787(81)90090-3
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  • 5
    Electronic Resource
    Electronic Resource
    Genes, crops and the environment - by John Holden, James Peacock and Trevor Williams Cambridge University Press, 1993. (176 pages) £12.95/19.95 pbk ISBN 0 521 43737 7 £30.00/49.95 hbk ISBN 0 521 43137 9
    Amsterdam : Elsevier
    Trends in Genetics 10 (1994), S. 32 
    Details
    ISSN: 0168-9525
    Source: Elsevier Journal Backfiles on ScienceDirect 1907 - 2002
    Topics: Biology
    Type of Medium: Electronic Resource
    URL: http://linkinghub.elsevier.com/retrieve/pii/0168-9525(94)90017-5
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  • 6
    Electronic Resource
    Electronic Resource
    Genomic organization of the ribosomal DNA of sorghum and its close relatives (1989)
    Springer
    Theoretical and applied genetics 77 (1989), S. 844-850 
    Details
    ISSN: 1432-2242
    Keywords: Evolution ; Restriction fragment length polymorphism ; Grasses ; Maize ; Sugarcane
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The structure and organization of the ribosomal DNA (rDNA) of sorghum (Sorghum bicolor) and several closely related grasses were determined by gel blot hybridization to cloned maize rDNA. Monocots of the genus Sorghum (sorghum, shattercane, Sudangrass, and Johnsongrass) and the genus Saccharum (sugarcane species) were observed to organize their rDNA as direct tandem repeats of several thousand rDNA monomer units. For the eight restriction enzymes and 14 cleavage sites examined, no variations were seen within all of the S. bicolor races and other Sorghum species investigated. Sorghum, maize, and sugarcane were observed to have very similar rDNA monomer sizes and restriction maps, befitting their close common ancestry. The restriction site variability seen between these three genera demonstrated that sorghum and sugarcane are more closely related to each other than either is to maize. Variation in rDNA monomer lengths were observed frequently within the Sorghum genus. These size variations were localized to the intergenic spacer region of the rDNA monomer. Unlike many maize inbreds, all inbred Sorghum diploids were found to contain only one rDNA monomer size in an individual plant. These results are discussed in light of the comparative timing, rates, and modes of evolutionary events in Sorghum and other grasses. Spacer size variation was found to provide a highly sensitive assay for the genetic contribution of different S. bicolor races and other Sorghum species to a Sorghum population.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00268337
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  • 7
    Electronic Resource
    Electronic Resource
    Structure and evolution of the genomes ofsorghum bicolor andZea mays (1993)
    Springer
    Theoretical and applied genetics 86 (1993), S. 598-604 
    Details
    ISSN: 1432-2242
    Keywords: Maize-Sorghum-Restriction fragment length polymorphism ; Genetic maps ; Inversion ; Translocation ; Duplication
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Cloned maize genes and random maize genomic fragments were used to construct a genetic map of sorghum and to compare the structure of the maize and sorghum genomes. Most (266/280) of the maize DNA fragments hybridized to sorghum DNA and 145 of them detected polymorphisms. The segregation of 111 markers was analyzed in 55 F2 progeny. A genetic map was generated with 96 loci arranged in 15 linkage groups spanning 709 map units. Comparative genetic mapping of sorghum and maize is complicated by the fact that many loci are duplicated, often making the identification of orthologous sequences ambiguous. Relative map positions of probes which detect only a single locus in both species indicated that multiple rearrangements have occurred since their divergence, but that many chromosomal segments have conserved synteny. Some sorghum linkage groups were found to be composed of sequences that detect loci on two different maize chromosomes. The two maize chromosomes to which these loci mapped were generally those which commonly share duplicated sequences. Evolutionary models and implications are discussed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00838715
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  • 8
    Electronic Resource
    Electronic Resource
    The generation of Mutator transposable element subfamilies in maize (1994)
    Springer
    Theoretical and applied genetics 87 (1994), S. 657-667 
    Details
    ISSN: 1432-2242
    Keywords: Transposable elements ; Mutation ; Evolution ; DNA repair ; Gene conversion
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The mobile DNAs of the Mutator system of maize (Zea mays) are exceptional both in structure and diversity. So far, six subfamilies of Mu elements have been discovered; all Mu elements share highly conserved terminal inverted repeats (TIRs), but each sub-family is defined by internal sequences that are apparently unrelated to the internal sequences of any other Mu subfamily. The Mu1/Mu2 subfamily of elements was created by the acquisition of a portion of a standard maize gene (termed MRS-A) within two Mu TIRs. Beside the unusually long (185–359 bp) and diverse TIRs found on all of these elements, other direct and inverted repeats are often found either within the central portion of a Mu element or within a TIR. Our computer analyses have shown that sequence duplications (mostly short direct repeats interrupted by a few base pairs) are common in non-autonomous members of the Mutator, Ac/Ds, and Spm(En) systems. These duplications are often tightly associated with the element-internal end of the TIRs. Comparisons of Mu element sequences have indicated that they share more terminal components than previously reported; all subfamilies have at least the most terminal 215 bp, at one end or the other, of the 359-bp Mu5 TIR. These data suggest that many Mu element subfamilies were generated from a parental element that had termini like those of Mu5. With the Mu5 TIRs as a standard, it was possible to determine that elements like Mu4 could have had their unusual TIRs created through a three-step process involving (1) addition of sequences to interrupt one TIR, (2) formation of a stem-loop structure by one strand of the element, and (3) a subsequent DNA repair/gene conversion event that duplicated the insertion(s) within the other TIR. A similar repair/conversion extending from a TIR stem into loop DNA could explain the additional inverted repeat sequences added to the internal ends of the Mu4 and Mu7 TIRs. This same basic mechanism was found to be capable of generating new Mu element subfamilies. After endonucleolytic attack of the loop within the stem-loop structure, repair/conversion of the gap could occur as an intermolecular event to generate novel internal sequences and, therefore, a new Mu element subfamily. Evidence supporting and expanding this model of new Mu element subfamily creation was identified in the sequence of MRS-A.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00222890
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  • 9
    Electronic Resource
    Electronic Resource
    The Rp3 disease resistance gene of maize: mapping and characterization of introgressed alleles (1995)
    Springer
    Theoretical and applied genetics 91 (1995), S. 25-32 
    Details
    ISSN: 1432-2242
    Keywords: Restriction fragment length polymorphism ; Near-isogenic lines ; Puccinia sorghi ; Introgression ; Gene duplication
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The Rp3 locus of maize conditions race-specific resistance to a fungal rust pathogen, Puccinia sorghi. Both morphological and DNA markers were employed to characterize alleles of Rp3 and to accurately position Rp3 on the maize genetic map. DNA marker polymorphisms distinctive to each Rp3 allele were identified, allowing the identification of specific Rp3 alleles in cases where rust races that differentiate particular alleles are not available. In a population of 427 progeny, Rp3 and Rg1 were found to be completely linked, while Lg3 was approximately 3 cM proximal on the long arm of chromosome 3. In this same population, 12 RFLP markers were mapped relative to Rp3; the closest markers were UMC102 (about 1cM distal to Rp1) and NPI114 (1–2 cM proximal). These and additional DNA probes were used to characterize the nature and extent of flanking DNA that was carried along when six different Rp3 alleles were backcrossed into a single background. Depending upon the allele investigated, a minimum of 2–10cM of polymorphic DNA flanking the Rp3 locus was retained through the introgression process. In addition, many of the probes that map near Rp3 were found to detect an additional fragment in the Rp3 region, indicating that portions of this chromosomal segment have been tendemly duplicated. The materials and results generated will permit marker-assisted entry of Rp3 into different maize backgrounds and lay the foundation for the eventual map-based cloning of Rp3.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00220854
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  • 10
    Electronic Resource
    Electronic Resource
    Complex duplications in maize lines (1993)
    Springer
    Molecular genetics and genomics 239 (1993), S. 115-121 
    Details
    ISSN: 1617-4623
    Keywords: RFLP ; Disease resistance ; Duplicated sequence ; Recombination ; Linked repeats ; Hypervariable loci
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Rp1 is a disease resistance complex and is the terminal morphological marker on the short arm of maize chromosome 10. Several restriction fragment length polymorphisms (RFLPs), which map within 5 map units of Rp1, were examined to determine if they are also complex in structure. Two RFLP loci, which mapped distally to Rp1, BNL3.04 and PIO200075, existed in a single copy in all maize lines examined. These two loci cosegregated perfectly in 130 test cross progeny. Two RFLP loci that map proximally to Rp1 had unusual structures, which have not yet been reported for maize RFLPs; the loci were complex, with variable numbers of copies in different maize lines. One of the loci, NPI285, occasionally recombined in meiosis to yield changes in the number of copies of sequences homologous to the probe. The other proximal locus, detected by the probes NPI422, KSU3, and KSU4, was relatively stable in meiosis and no changes in the number of restriction fragments were observed. The similarity in map position between Rp1 and the complex RFLP loci indicate there may be genomic areas where variable numbers of repeated sequences are common. The structure of these complex loci may provide insight into the structure and evolution of Rp1.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00281609
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