Genus-specific localization of the TaiI family of tandem-repetitive sequences in either the centromeric or subtelomeric regions in Triticeae species (Poaceae) and its evolution in wheat

Genome ◽  
2002 ◽  
Vol 45 (5) ◽  
pp. 946-955 ◽  
Author(s):  
Masahiro Kishii ◽  
Hisashi Tsujimoto
Keyword(s):  
Common Wheat ◽  
Dna Sequences ◽  
Repetitive Sequences ◽  
Chromosomal Distribution ◽  
B Genome ◽  
Triticeae Species ◽  
Copy Numbers ◽  
Specific Localization ◽  
Mixed Origin ◽  
Subtelomeric Regions

The TaiI family sequences are classified as tandem repetitive DNA sequences present in the genome of tribe Triticeae, and are localized in the centromeric regions of common wheat, but in the subtelomeric heterochromatic regions of Leymus racemosus and related species. In this study, we investigated the chromosomal distribution of TaiI family sequences in other Triticeae species. The results demonstrated a centromeric localization in genera Triticum and Aegilops and subtelomeric localization in other genera, thus showing a genus-dependent localization of TaiI family sequences in one or the other region. The copy numbers of TaiI family sequences in species in the same genus varied greatly, whether in the centromeric or subtelomeric regions (depending on genus). We also examined the evolution of TaiI family sequences during polyploidization of hexaploid common wheat. A comparison of chromosomal locations of the major TaiI family signals in common wheat and in its ancestral species suggested that the centromeric TaiI family sequences in common wheat were inherited from its ancestors with little modification, whereas a mixed origin for the B genome of common wheat was indicated.Key words: TaiI family, tandem repeat, centromere, subtelomere, Triticeae.

scholarly journals Heteroalleles in Common Wheat: Multiple Differences between Allelic Variants of the Gli-B1 Locus

2021 ◽  
Vol 22 (4) ◽  
pp. 1832
Author(s):  
Eugene Metakovsky ◽  
Laura Pascual ◽  
Patrizia Vaccino ◽  
Viktor Melnik ◽  
Marta Rodriguez-Quijano ◽  
...  
Keyword(s):  
Common Wheat ◽  
Dna Sequences ◽  
Fragment Length Polymorphism ◽  
Snp Markers ◽  
Group Iv ◽  
Nucleotide Polymorphisms ◽  
High Genetic Diversity ◽  
Single Nucleotide ◽  
Allelic Variants ◽  
B Genome

The Gli-B1-encoded γ-gliadins and non-coding γ-gliadin DNA sequences for 15 different alleles of common wheat have been compared using seven tests: electrophoretic mobility (EM) and molecular weight (MW) of the encoded major γ-gliadin, restriction fragment length polymorphism patterns (RFLPs) (three different markers), Gli-B1-γ-gliadin-pseudogene known SNP markers (Single nucleotide polymorphisms) and sequencing the pseudogene GAG56B. It was discovered that encoded γ-gliadins, with contrasting EM, had similar MWs. However, seven allelic variants (designated from I to VII) differed among them in the other six tests: I (alleles Gli-B1i, k, m, o), II (Gli-B1n, q, s), III (Gli-B1b), IV (Gli-B1e, f, g), V (Gli-B1h), VI (Gli-B1d) and VII (Gli-B1a). Allele Gli-B1c (variant VIII) was identical to the alleles from group IV in four of the tests. Some tests might show a fine difference between alleles belonging to the same variant. Our results attest in favor of the independent origin of at least seven variants at the Gli-B1 locus that might originate from deeply diverged genotypes of the donor(s) of the B genome in hexaploid wheat and therefore might be called “heteroallelic”. The donor’s particularities at the Gli-B1 locus might be conserved since that time and decisively contribute to the current high genetic diversity of common wheat.

scholarly journals Organization and Chromosomal Distribution of Histone Genes and Transposable Rex Elements in the Genome of Astyanax bockmanni (Teleostei, Characiformes)

2015 ◽  
Vol 146 (4) ◽  
pp. 311-318 ◽  
Author(s):  
Sandro N. Daniel ◽  
Manolo Penitente ◽  
Duílio M.Z.A. Silva ◽  
Diogo T. Hashimoto ◽  
Daniela C. Ferreira ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Dna Sequences ◽  
Repetitive Sequences ◽  
B Chromosome ◽  
Gene Probe ◽  
Histone Genes ◽  
Chromosomal Distribution ◽  
Evolutionary Mechanisms ◽  
Small Sites ◽  
Eukaryotic Organisms

An important feature of eukaryotic organisms is the number of different repetitive DNA sequences in their genome, a feature not observed in prokaryotes. These sequences are considered to be important components for understanding evolutionary mechanisms and the karyotypic differentiation processes. Thus, we aimed to physically map the histone genes and transposable elements of the Rex family in 6 fish populations of Astyanax bockmanni. FISH results using a histone H1 gene probe showed fluorescent clusters in 2 chromosome pairs in all 6 samples analyzed. In contrast, FISH with a histone H3 probe showed conspicuous blocks in 4 chromosomes in 5 of the 6 populations analyzed. The sixth population revealed 7 chromosomes marked with this probe. Probes for the transposable elements Rex1 and Rex6 showed small sites dispersed on most chromosomes of the 6 populations, and the Rex3 element is located in a big block concentrated in only 1 acrocentric chromosome of 2 populations. As for the other populations, a Rex3 probe showed large blocks in more than 1 chromosome. Fish from Alambari and Campo Novo Stream have Rex3 elements dispersed along most of the chromosomes. Additionally, the conspicuous signals of Rex1, Rex3, and Rex6 were identified in the acrocentric B microchromosome of A. bockmanni found only in individuals of the Alambari River. Thus, we believe that different mechanisms drive the spread of repetitive sequences among the populations analyzed, which appear to be organized differently in the genome of A. bockmanni. The presence of transposable elements in the B chromosome also suggests that these sequences could play a role in the origin and maintenance of the supernumerary element in the genome of this species.

Possible repetitive DNA markers for Eusorghum and Parasorghum and their potential use in examining phylogenetic hypotheses on the origin of Sorghum species

Genome ◽  
1991 ◽  
Vol 34 (2) ◽  
pp. 241-250 ◽  
Author(s):  
Hoang-Tang ◽  
Shyam K. Dube ◽  
George H. Liang ◽  
Shain-Dow Kung
Keyword(s):  
Repetitive Dna ◽  
Dna Sequences ◽  
Meiotic Chromosome ◽  
Repetitive Sequences ◽  
Copy Numbers ◽  
Major Species ◽  
Strong Homology ◽  
Genome Phylogeny ◽  
Genomic Dnas ◽  
Phylogenetic Hypotheses

Genomic structures of two major species in section Eusorghum (Sorghum), Sorghum bicolor and Sorghum halepense, and their phylogenetic relationships with a species in section Parasorghum, Sorghum versicolor, were studied by using cloned repetitive DNA sequences from the three species. Of the five repetitive DNA clones isolated from S. bicolor and S. halepense, four produced qualitatively similar hybridization patterns with detectable variations in copy numbers of some of the restriction fragments on the Southern blots of the two genomic DNAs. One clone was shown to be diagnostic for S. halepense. Molecular analysis at the DNA level indicates that S. bicolor and S. halepense have similar but not identical genomes, consonant with differences in karyotypes, meiotic chromosome behaviors, morphology, and physiology of the species. In addition to five repetitive clones isolated from S. bicolor and S. halepense, eight more sequences were cloned from S. versicolor. Nine clones were found to be specific for either S. bicolor and S. halepense or S. versicolor. The remaining four had a moderate to strong homology with sequences present in all Sorghum species studied. We speculate that the genome in the common ancestor of Sorghum has differentiated to give rise to genomes of at least three major chromosome sizes; large, medium, and small, as seen at present. Amplifications, eliminations, rearrangements, and new syntheses of repetitive sequences may have been involved in genome differentiation of these species. The results also suggest that the S. versicolor genome has strongly diverged from the genomes of the two species in section Eusorghum.Key words: repetitive DNA, genome, phylogeny, Eusorghum, Parasorghum, Sorghum.

scholarly journals Sequence Composition Underlying Centromeric and Heterochromatic Genome Compartments of the Pacific Oyster Crassostrea gigas

Genes ◽  
2020 ◽  
Vol 11 (6) ◽  
pp. 695
Author(s):  
Monika Tunjić Cvitanić ◽  
Tanja Vojvoda Zeljko ◽  
Juan J. Pasantes ◽  
Daniel García-Souto ◽  
Tena Gržan ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Crassostrea Gigas ◽  
Pacific Oyster ◽  
Repetitive Sequences ◽  
Genetic Material ◽  
Chromosomal Distribution ◽  
Sequence Composition ◽  
Specific Distribution ◽  
The Pacific ◽  
Associated Sequences

Segments of the genome enriched in repetitive sequences still present a challenge and are omitted in genome assemblies. For that reason, the exact composition of DNA sequences underlying the heterochromatic regions and the active centromeres are still unexplored for many organisms. The centromere is a crucial region of eukaryotic chromosomes responsible for the accurate segregation of genetic material. The typical landmark of centromere chromatin is the rapidly-evolving variant of the histone H3, CenH3, while DNA sequences packed in constitutive heterochromatin are associated with H3K9me3-modified histones. In the Pacific oyster Crassostrea gigas we identified its centromere histone variant, Cg-CenH3, that shows stage-specific distribution in gonadal cells. In order to investigate the DNA composition of genomic regions associated with the two specific chromatin types, we employed chromatin immunoprecipitation followed by high-throughput next-generation sequencing of the Cg-CenH3- and H3K9me3-associated sequences. CenH3-associated sequences were assigned to six groups of repetitive elements, while H3K9me3-associated-ones were assigned only to three. Those associated with CenH3 indicate the lack of uniformity in the chromosomal distribution of sequences building the centromeres, being also in the same time dispersed throughout the genome. The heterochromatin of C. gigas exhibited general paucity and limited chromosomal localization as predicted, with H3K9me3-associated sequences being predominantly constituted of DNA transposons.

TAS49—a dispersed repetitive sequence isolated from subtelomeric regions of Nicotiana tomentosiformis chromosomes

Genome ◽  
2000 ◽  
Vol 43 (2) ◽  
pp. 273-284
Author(s):  
Mirka Horáková ◽  
Jirí Fajkus
Keyword(s):  
Dna Sequences ◽  
Repetitive Sequence ◽  
Repetitive Sequences ◽  
Reading Frame ◽  
Diploid Genome ◽  
Nicotiana Tomentosiformis ◽  
Dna Repeat ◽  
The Family ◽  
A Subunit ◽  
Subtelomeric Regions

We have isolated and characterized a new repetitive sequence, TAS49, from terminal restriction fragments of Nicotiana tomentosiformis genomic DNA by means of a modified vectorette approach. The TAS49 was found directly attached to telomeres of N. tabacum and one of its ancestors, N. tomentosiformis, and also at inner chromosome locations. No association with telomeres was detected neither in N. otophora nor in the second tobacco ancestor, N. sylvestris. PCR and Southern hybridization reveal similarities in the arrangement of TAS49 on the chromosomes of 9 species of the genus Nicotiana, implying its occurrence as a subunit of a conserved complex DNA repeat. TAS49 belongs to the family of dispersed repetitive sequences without features of transposons. The copy number of TAS49 varies widely in the genomes of 8 species analyzed being lowest in N. sylvestris, with 3300 copies per diploid genome. In N. tomentosiformis, TAS49 forms about 0.56% of the diploid genome, corresponding to 17 400 copies. TAS49 units are about 460 bp long and show about 90% of mutual homology, but no significant homology to DNA sequences deposited in GenBank and EMBL. Although genomic clones of TAS49 contain an open reading frame encoding a proline-rich protein similar to plant extensins, no mRNA transcript was detected. TAS49 is extensively methylated at CpG and CpNpG sites and its chromatin forms nucleosomes phased with a 170 ± 8 bp periodicity. Key words: repetitive DNA sequence, subtelomere, plant, Nicotiana.

CUMULATIVE SPECTRAL REPEAT FINDER (CSRF): A SPECTRAL APPROACH FOR IDENTIFYING THE LENGTH OF REPEATS IN DNA SEQUENCES

2011 ◽  
Vol 20 (01) ◽  
pp. 179-194
Author(s):  
R. M. CHEN ◽  
M. T. HOU ◽  
N. W. CHANG ◽  
Y. T. CHEN ◽  
JEFFREY J. P. TSAI
Keyword(s):  
Dna Sequence ◽  
Gibbs Sampler ◽  
Dna Sequences ◽  
Repetitive Sequences ◽  
Exact Method ◽  
Spectral Approach ◽  
Copy Numbers ◽  
Rules Of Thumb

Repetitive sequences of DNA are meaningful and of great importance to human functions. Previous researchers have proposed various methods to discover repetitive sequences in DNA sequence. However, the unknown lengths for repetitive sequences are usually predicted randomly or determined by rules of thumb rather than using a systematical criterion. We propose a new algorithm based on the cumulative Fourier spectral contents of DNA sequence to identify the candidate lengths of repetitive sequences or repeats in DNA sequences. After the candidate lengths of repeats are known, one can identify the repeats and their copy numbers using an exact method. Both of the simulated and real datasets are used to illustrate the performance of the proposed algorithm. The results are also compared to two well-known methods such as Spectral Repeat Finder (SRF) and Gibbs sampler. Furthermore, we demonstrate the use of CSRF in some well-known repeats-finding methods such as SRF, Gibbs sampler, MEME.

Organization and evolution of two repetitive sequences, 18-24J and 12-13P, in the genome of Chenopodium (Amaranthaceae)

Genome ◽  
2018 ◽  
Vol 61 (9) ◽  
pp. 643-652 ◽  
Author(s):  
Maja Orzechowska ◽  
Maciej Majka ◽  
Hanna Weiss-Schneeweiss ◽  
Ales Kovařík ◽  
Natalia Borowska-Zuchowska ◽  
...  
Keyword(s):  
Repetitive Sequences ◽  
Diploid Species ◽  
Chromosomal Marker ◽  
Polyploid Species ◽  
Chromosomal Distribution ◽  
Chromosomal Organization ◽  
Molecular Analyses ◽  
B Genome ◽  
A Genome ◽  
Eurasian Species

The abundance and chromosomal organization of two repetitive sequences named 12-13P and 18-24J were analyzed in 24 diploid and nine polyploid species of Chenopodium s.l., with special attention to Chenopodium s.s. Both sequences were predominantly present in species of Chenopodium s.s.; however, differences in the amplification levels were observed among the species. The 12-13P repeat was highly amplified in all of the analyzed Eurasian species, whereas the American diploids showed a marked variation in the amplification levels. The 12-13P repeat contains a tandemly arranged 40 bp minisatellite element forming a large proportion of the genome of Chenopodium (up to 3.5%). FISH revealed its localization to the pericentromeric regions of the chromosomes. The chromosomal distribution of 12-13P delivered additional chromosomal marker for B-genome diploids. The 18-24J repeat showed a dispersed organization in all of the chromosomes of the analyzed diploid species and the Eurasian tetraploids. In the American allotetraploids (C. quinoa, C. berlandieri) and Eurasian allohexaploids (e.g., C. album) very intense hybridization signals of 18-24J were observed only on 18 chromosomes that belong to the B subgenome of these polyploids. Combined cytogenetic and molecular analyses suggests that reorganization of these two repeats accompanied the diversification and speciation of diploid (especially A genome) and polyploid species of Chenopodium s.s.

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