PHYLOGEOGRAPHY OF AEGILOPS TAUSCHII COSS. AS REVEALED BY GOT2 DNA SEQUENCES

2018 ◽  
Author(s):  
A. DUDNIKOV ◽  
Keyword(s):  
Dna Sequences ◽  
Aegilops Tauschii

Identification of the entire chromosome complement of bread wheat by two-colour FISH

Genome ◽  
1997 ◽  
Vol 40 (5) ◽  
pp. 589-593 ◽  
Author(s):  
C. Pedersen ◽  
P. Langridge
Keyword(s):  
In Situ Hybridization ◽  
Fluorescence In Situ Hybridization ◽  
Dna Sequences ◽  
Banding Pattern ◽  
Aegilops Tauschii ◽  
Chromosome Complement ◽  
Chromosome Identification ◽  
Satellite Sequence ◽  
Entire Chromosome

Using the Aegilops tauschii clone pAs1 together with the barley clone pHvG38 for two-colour fluorescence in situ hybridization (FISH) the entire chromosome complement of hexaploid wheat was identified. The combination of the two probes allowed easy discrimination of the three genomes of wheat. The banding pattern obtained with the pHvG38 probe containing the GAA-satellite sequence was identical to the N-banding pattern of wheat. A detailed idiogram was constructed, including 73 GAA bands and 48 pAs1 bands. Identification of the wheat chromosomes by FISH will be particularly useful in connection with the physical mapping of other DNA sequences to chromosomes, or for chromosome identification in general, as an alternative to C-banding.Key words: Triticum aestivum, chromosome identification, fluorescence in situ hybridization, repetitive DNA sequences.

scholarly journals The homoeologous genes for the Rec8-like meiotic cohesin in wheat: structure, function, and evolutionary implication

2018 ◽  
Author(s):  
Guojia Ma ◽  
Wei Zhang ◽  
Liwang Liu ◽  
Wun S. Chao ◽  
Yong Qiang Gu ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Hexaploid Wheat ◽  
Expression Patterns ◽  
Aegilops Tauschii ◽  
Tetraploid Wheat ◽  
Nucleotide Polymorphisms ◽  
Origin And Evolution ◽  
Homoeologous Genes ◽  
The One ◽  
Functional Analyses

ABSTRACTThe Rec8-like cohesin is a cohesion protein essential for orderly chromosome segregation in meiosis. Here, we cloned two Rec8-like homoeologous genes (homoeoalleles) from tetraploid wheat (TtRec8-A1 and TtRec8-B1) and one from hexaploid wheat (TaRec8-D1), and performed expression and functional analyses of the homoeoalleles. Also, we identified other two Rec8 homoeoalleles in hexaploid wheat (TaRec8-A1 and TaRec8-B1) and the one in Aegilops tauschii (AetRec8-D1) by comparative analysis. The coding DNA sequences (CDS) of these six Rec8 homoeoalleles are all 1,827 bp in length, encoding 608 amino acids. They differed from each other primarily in introns although single nucleotide polymorphisms were detected in CDS. Substantial difference was observed between the homoeoalleles from the subgenome B (TtRec8-B1 and TaRec8-B1) and those from the subgenomes A and D (TtRec8-A1, TaRec8-A1, and TaRec8-D1). TtRec8-A1 expressed dominantly over TtRec8-B1, but comparably to TaRec8-D1. Therefore, the Rec8 homoeoalleles from the subgenomes A and D may be functionally more active than the one from the subgenome B in wheat. The structural variation and differential expression of the Rec8 homoeoalleles indicate a unique cross-genome coordination of the homoeologous genes in the polyploid, and imply the distinction of the wheat subgenome B from other subgenomes in the origin and evolution.HIGHLIGHTThis work revealed the structural and expression patterns of the Rec8-like homoeologous genes in polyploid wheat, implying a unique origin and evolutionary route of the wheat B subgenome.

scholarly journals Differentially Amplified Repetitive Sequences Among Aegilops tauschii Subspecies and Genotypes

2021 ◽  
Vol 12 ◽  
Author(s):  
Rahman Ebrahimzadegan ◽  
Fatemeh Orooji ◽  
Pengtao Ma ◽  
Ghader Mirzaghaderi
Keyword(s):  
Dna Sequences ◽  
Tandem Repeats ◽  
Repetitive Sequences ◽  
Aegilops Tauschii ◽  
Distribution Patterns ◽  
Snp Analysis ◽  
Specific Sequence ◽  
Factors Affecting ◽  
Illumina Sequence ◽  
Species Specific

Genomic repetitive sequences commonly show species-specific sequence type, abundance, and distribution patterns, however, their intraspecific characteristics have been poorly described. We quantified the genomic repetitive sequences and performed single nucleotide polymorphism (SNP) analysis between 29 Ae. tauschii genotypes and subspecies using publicly available raw genomic Illumina sequence reads and used fluorescence in situ hybridization (FISH) to experimentally analyze some repeats. The majority of the identified repetitive sequences had similar contents and proportions between anathera, meyeri, and strangulata subspecies. However, two Ty3/gypsy retrotransposons (CL62 and CL87) showed significantly higher abundances, and CL1, CL119, CL213, CL217 tandem repeats, and CL142 retrotransposon (Ty1/copia type) showed significantly lower abundances in subspecies strangulata compared with the subspecies anathera and meyeri. One tandem repeat and 45S ribosomal DNA (45S rDNA) abundances showed a high variation between genotypes but their abundances were not subspecies specific. Phylogenetic analysis using the repeat abundances of the aforementioned clusters placed the strangulata subsp. in a distinct clade but could not discriminate anathera and meyeri. A near complete differentiation of anathera and strangulata subspecies was observed using SNP analysis; however, var. meyeri showed higher genetic diversity. FISH using major tandem repeats couldn’t detect differences between subspecies, although (GAA)10 signal patterns generated two different karyotype groups. Taken together, the different classes of repetitive DNA sequences have differentially accumulated between strangulata and the other two subspecies of Ae. tauschii that is generally in agreement with spike morphology, implying that factors affecting repeatome evolution are variable even among highly closely related lineages.

The Ha locus of wheat: Identification of a polymorphic region for tracing grain hardness in crosses

Genome ◽  
1999 ◽  
Vol 42 (6) ◽  
pp. 1242-1250 ◽  
Author(s):  
M Turner ◽  
Y Mukai ◽  
P Leroy ◽  
B Charef ◽  
R Appels ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Hexaploid Wheat ◽  
Aegilops Tauschii ◽  
Grain Hardness ◽  
High Sequence Identity ◽  
D Genome ◽  
Sequence Identity ◽  
Group 5 ◽  
Grain Softness ◽  
Puroindoline A

The grain softness proteins or friabilins are known to be composed of three main components: puroindoline a, puroindoline b, and GSP-1. cDNAs for GSP-1 have previously been mapped to group-5 chromosomes and their location on chromosome 5D is closely linked to the grain hardness (Ha) locus of hexaploid wheat. A genomic DNA clone containing the GSP-1 gene (wGSP1-A1) from hexaploid wheat has been identified by fluorescent in situ hybridization as having originated from the distal end of the short arm of chromosome 5A. A genomic clone containing the gene (wGSP1-D1) was also isolated from Aegilops tauschii, the donor of the D genome to bread wheat. There are no introns in the GSP-1 genes, and there is high sequence identity between wGSP1-A1 and wGSP1-D1 up to 1 kb 5' and 300 bp 3' to wGSP1-D1. However, regions further upstream and downstream of wGSP1-D1 share no significant sequence identity to corresponding sequences in wGSP1-A1. These regions therefore identified potentially valuable sequences for tracing the Ha locus through assaying polymorphic DNA sequences. The sequence from 300 to 500 bp 3' to wGSP1-D1 (wGSP1-D13) was mapped to the Ha locus in a mapping population. wGSP1-D13 was also tightly linked to genes for puroindoline a and puroindoline b which have been previously mapped to be at the Ha locus. In addition wGSP1-D13 was used to detect RFLPs between near isogenic soft and hard Falcon lines and in a random selection of soft and hard wheats.Key words: wheat, grain hardness, chromosome 5, puroindoline, GSP-1.

Aphid feeding response and microsatellite-based genetic diversity among diploid Brachypodium distachyon (L.) Beauv accessions

2009 ◽  
Vol 7 (1) ◽  
pp. 72-79 ◽  
Author(s):  
Perumal Azhaguvel ◽  
Wanlong Li ◽  
Jackie C. Rudd ◽  
Bikram S. Gill ◽  
G. J. Michels ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Common Wheat ◽  
Dna Sequences ◽  
Expressed Sequence Tag ◽  
Brachypodium Distachyon ◽  
Aegilops Tauschii ◽  
Cereal Aphid ◽  
D Genome ◽  
Geographical Distances ◽  
Brome Grass

False brome grass, Brachypodium distachyon (L.) Beauv, has been proposed as a new model species to bridge rice and temperate cereal crops for genomics research. However, much basic information for this species is still lacking. In this study, six diploid B. distachyon (2n = 2x = 10) accessions (Bd1-1, Bd2-3, Bd3-1, Bd18-1, Bd21 and BD29) were evaluated for their response to infestation by two cereal aphid pests of common wheat (Triticum aestivum L.): the greenbug, Schizaphis graminum Rondani, and the Russian wheat aphid (RWA), Diuraphis noxia Mordvilko. Through database mining of B. distachyon expressed sequence tag (EST) and genomic DNA sequences, 160 EST- and 21 genomic microsatellite markers were developed and used to evaluate genetic diversity among the B. distachyon accessions. All six accessions were resistant to RWA biotype RWA1 but showed distinct responses to feeding by greenbug biotypes C and E, as well as RWA2 RWAs. Although microsatellite-based genetic diversity among different accessions was generally low, Bd1-1 and BD29 were the most diverged from the other four lines. The genetic divergence was correlated with geographical distances between the Brachypodium accessions. Comparison of simple sequence repeat polymorphisms in three inbred lines (Bd2-3, Bd3-1 and Bd18-1) with their respective original parental lines revealed no effect of inbreeding on genetic diversity. Phylogenetic analysis suggested that Aegilops tauschii (Coss.) Schmal., the D genome donor of common wheat, was closer to B. distachyon than to rice. The greenbug - B. distachyon system seems to be a model of choice for plant–aphid interaction studies in the grass genome.

Transcription factor/DNA interactions visualized by electron spectroscopic imaging

1992 ◽  
Vol 50 (1) ◽  
pp. 450-451
Author(s):  
David P. Bazett-Jones ◽  
Mark L. Brown
Keyword(s):  
Transcription Factor ◽  
Dna Sequences ◽  
Transcription Initiation ◽  
Molecular Mechanisms ◽  
Phosphorus Content ◽  
Spectroscopic Imaging ◽  
Electron Spectroscopic Imaging ◽  
Dna Backbone ◽  
Two Parameters ◽  
High Level

A multisubunit RNA polymerase enzyme is ultimately responsible for transcription initiation and elongation of RNA, but recognition of the proper start site by the enzyme is regulated by general, temporal and gene-specific trans-factors interacting at promoter and enhancer DNA sequences. To understand the molecular mechanisms which precisely regulate the transcription initiation event, it is crucial to elucidate the structure of the transcription factor/DNA complexes involved. Electron spectroscopic imaging (ESI) provides the opportunity to visualize individual DNA molecules. Enhancement of DNA contrast with ESI is accomplished by imaging with electrons that have interacted with inner shell electrons of phosphorus in the DNA backbone. Phosphorus detection at this intermediately high level of resolution (≈lnm) permits selective imaging of the DNA, to determine whether the protein factors compact, bend or wrap the DNA. Simultaneously, mass analysis and phosphorus content can be measured quantitatively, using adjacent DNA or tobacco mosaic virus (TMV) as mass and phosphorus standards. These two parameters provide stoichiometric information relating the ratios of protein:DNA content.

DNA sequence mapping in interphase and metaphase chromosomes by fluorescence in situ hybridization

1992 ◽  
Vol 50 (1) ◽  
pp. 496-497
Author(s):  
Barbara Trask ◽  
Susan Allen ◽  
Anne Bergmann ◽  
Mari Christensen ◽  
Anne Fertitta ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Dna Sequence ◽  
Dna Sequences ◽  
Dual Band ◽  
Nick Translation ◽  
Metaphase Chromosomes ◽  
Band Pass ◽  
Texas Red ◽  
Fluorescent Spot

Using fluorescence in situ hybridization (FISH), the positions of DNA sequences can be discretely marked with a fluorescent spot. The efficiency of marking DNA sequences of the size cloned in cosmids is 90-95%, and the fluorescent spots produced after FISH are ≈0.3 μm in diameter. Sites of two sequences can be distinguished using two-color FISH. Different reporter molecules, such as biotin or digoxigenin, are incorporated into DNA sequence probes by nick translation. These reporter molecules are labeled after hybridization with different fluorochromes, e.g., FITC and Texas Red. The development of dual band pass filters (Chromatechnology) allows these fluorochromes to be photographed simultaneously without registration shift.

Three-Dimensional Structure of Cloned T3 Connector Protein at 1.6nm Resolution

1990 ◽  
Vol 48 (1) ◽  
pp. 282-283
Author(s):  
José L. Carrascosa ◽  
José M. Valpuesta ◽  
Hisao Fujisawa
Keyword(s):  
Dna Sequences ◽  
Expression Vector ◽  
Three Dimensional ◽  
Deae Cellulose ◽  
Dna Packaging ◽  
Dimensional Structure ◽  
Two Dimensional ◽  
Freezing And Thawing ◽  
Three Dimensional Structure ◽  
Dimensional Reconstruction

The head to tail connector of bacteriophages plays a fundamental role in the assembly of viral heads and DNA packaging. In spite of the absence of sequence homology, the structure of connectors from different viruses (T4, Ø29, T3, P22, etc) share common morphological features, that are most clearly revealed in their three-dimensional structure. We have studied the three-dimensional reconstruction of the connector protein from phage T3 (gp 8) from tilted view of two dimensional crystals obtained from this protein after cloning and purification.DNA sequences including gene 8 from phage T3 were cloned, into Bam Hl-Eco Rl sites down stream of lambda promotor PL, in the expression vector pNT45 under the control of cI857. E R204 (pNT89) cells were incubated at 42°C for 2h, harvested and resuspended in 20 mM Tris HC1 (pH 7.4), 7mM 2 mercaptoethanol, ImM EDTA. The cells were lysed by freezing and thawing in the presence of lysozyme (lmg/ml) and ligthly sonicated. The low speed supernatant was precipitated by ammonium sulfate (60% saturated) and dissolved in the original buffer to be subjected to gel nitration through Sepharose 6B, followed by phosphocellulose colum (Pll) and DEAE cellulose colum (DE52). Purified gp8 appeared at 0.3M NaCl and formed crystals when its concentration increased above 1.5 mg/ml.

DNA methylation in satellite repeats disorders

2019 ◽  
Vol 63 (6) ◽  
pp. 757-771 ◽  
Author(s):  
Claire Francastel ◽  
Frédérique Magdinier
Keyword(s):  
Dna Methylation ◽  
Human Genome ◽  
Repetitive Dna ◽  
Dna Sequences ◽  
Satellite Repeats ◽  
Tremendous Progress ◽  
Genes Encoding ◽  
Dna Elements ◽  
Near Future

Abstract Despite the tremendous progress made in recent years in assembling the human genome, tandemly repeated DNA elements remain poorly characterized. These sequences account for the vast majority of methylated sites in the human genome and their methylated state is necessary for this repetitive DNA to function properly and to maintain genome integrity. Furthermore, recent advances highlight the emerging role of these sequences in regulating the functions of the human genome and its variability during evolution, among individuals, or in disease susceptibility. In addition, a number of inherited rare diseases are directly linked to the alteration of some of these repetitive DNA sequences, either through changes in the organization or size of the tandem repeat arrays or through mutations in genes encoding chromatin modifiers involved in the epigenetic regulation of these elements. Although largely overlooked so far in the functional annotation of the human genome, satellite elements play key roles in its architectural and topological organization. This includes functions as boundary elements delimitating functional domains or assembly of repressive nuclear compartments, with local or distal impact on gene expression. Thus, the consideration of satellite repeats organization and their associated epigenetic landmarks, including DNA methylation (DNAme), will become unavoidable in the near future to fully decipher human phenotypes and associated diseases.

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