Molecular Cytogenetic Mapping of Satellite DNA Sequences in Aegilops geniculata and Wheat

Fluorescence in situ hybridization (FISH) provides an efficient system for cytogenetic analysis of wild relatives of wheat for individual chromosome identification, elucidation of homoeologous relationships, and for monitoring alien gene transfers into wheat. This study is aimed at developing cytogenetic markers for chromosome identification of wheat and Aegilops geniculata (2n = 4x = 28, UgUgMgMg) using satellite DNAs obtained from flow-sorted chromosome 5Mg. FISH was performed to localize the satellite DNAs on chromosomes of wheat and selected Aegilops species. The FISH signals for satellite DNAs on chromosome 5Mg were generally associated with constitutive heterochromatin regions corresponding to C-band-positive chromatin including telomeric, pericentromeric, centromeric, and interstitial regions of all the 14 chromosome pairs of Ae. geniculata. Most satellite DNAs also generated FISH signals on wheat chromosomes and provided diagnostic chromosome arm-specific cytogenetic markers that significantly improved chromosome identification in wheat. The newly identified satellite DNA CL36 produced localized Mg genome chromosome-specific FISH signals in Ae. geniculata and in the M genome of the putative diploid donor species Ae. comosa subsp. subventricosa but not in Ae. comosa subsp. comosa, suggesting that the Mg genome of Ae. geniculata was probably derived from subsp. subventricosa.

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The molecular structure, chromosomal organization, and interspecies distribution of a family of tandemly repeated DNA sequences of Antirrhinum majus L.

Genome ◽

10.1139/g96-033 ◽

1996 ◽

Vol 39 (2) ◽

pp. 243-248 ◽

Cited By ~ 7

Author(s):

Thomas Schmidt ◽

Jörg Kudla

Keyword(s):

In Situ Hybridization ◽

Dna Sequences ◽

Satellite Dna ◽

Antirrhinum Majus ◽

Repeated Dna ◽

Satellite Dnas ◽

Repeated Dna Sequences ◽

The North ◽

Tandemly Repeated Dna

Monomers of a major family of tandemly repeated DNA sequences of Antirrhinum majus have been cloned and characterized. The repeats are 163–167 bp long, contain on average 60% A + T residues, and are organized in head-to-tail orientation. According to site-specific methylation differences two subsets of repeating units can be distinguished. Fluorescent in situ hybridization revealed that the repeats are localized at centromeric regions of six of the eight chromosome pairs of A. majus with substantial differences in array size. The monomeric unit shows no homologies to other plant satellite DNAs. The repeat exists in a similar copy number and conserved size in the genomes of six European species of the genus Antirrhinum. Tandemly repeated DNA sequences with homology to the cloned monomer were also found in the North American section Saerorhinum, indicating that this satellite DNA might be of ancient origin and was probably already present in the ancestral genome of both sections. Key words : Antirrhinum majus, satellite DNA, repetitive DNA, methylation, in situ hybridization.

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Satellite DNA in Plants: More than Just Rubbish

Cytogenetic and Genome Research ◽

10.1159/000437008 ◽

2015 ◽

Vol 146 (2) ◽

pp. 153-170 ◽

Cited By ~ 64

Author(s):

Manuel A. Garrido-Ramos

Keyword(s):

Dna Sequences ◽

Satellite Dna ◽

Dna Repeats ◽

Satellite Dnas ◽

Factors Affecting ◽

Functional Roles ◽

Tandem Repeat Sequences ◽

Satellite Repeats ◽

History Of ◽

Main Components

For decades, satellite DNAs have been the hidden part of genomes. Initially considered as junk DNA, there is currently an increasing appreciation of the functional significance of satellite DNA repeats and of their sequences. Satellite DNA families accumulate in the heterochromatin in different parts of the eukaryotic chromosomes, mainly in pericentromeric and subtelomeric regions, but they also span the functional centromere. Tandem repeat sequences may spread from subtelomeric to interstitial loci, leading to the formation of chromosome-specific loci or to the accumulation in equilocal sites in different chromosomes. They also appear as the main components of the heterochromatin in the sex-specific region of sex chromosomes. Satellite DNA, required for chromosome organization, also plays a role in pairing and segregation. Some satellite repeats are transcribed and can participate in the formation and maintenance of heterochromatin structure and in the modulation of gene expression. In addition to the identification of the different satellite DNA families, their characteristics and location, we are interested in determining their impact on the genomes, by identifying the mechanisms leading to their appearance and amplification as well as in understanding how they change over time, the factors affecting these changes, and the influence exerted by the evolutionary history of the organisms. On the other hand, satellite DNA sequences are rapidly evolving sequences that may cause reproductive barriers between organisms and promote speciation. The accumulation of experimental data collected in recent years and the emergence of new approaches based on next-generation sequencing and high-throughput genome analysis are opening new perspectives that are changing our understanding of satellite DNA. This review examines recent data to provide a timely update on the overall information gathered about this part of the genome, focusing on the advances in the knowledge of its origin, its evolution, and its potential functional roles.

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Sequence Analysis and FISH Mapping of Four Satellite DNA Families among Cervidae

Genes ◽

10.3390/genes11050584 ◽

2020 ◽

Vol 11 (5) ◽

pp. 584

Author(s):

Miluse Vozdova ◽

Svatava Kubickova ◽

Halina Cernohorska ◽

Jan Fröhlich ◽

Natália Martínková ◽

...

Keyword(s):

Dna Sequences ◽

Satellite Dna ◽

Phylogenetic Trees ◽

In Situ Hybridisation ◽

Gc Content ◽

Copy Number Variations ◽

Binding Motif ◽

Fluorescence In Situ Hybridisation ◽

Chromosomal Distribution ◽

Satellite Dnas

Centromeric and pericentromeric chromosome regions are occupied by satellite DNA. Satellite DNAs play essential roles in chromosome segregation, and, thanks to their extensive sequence variability, to some extent, they can also be used as phylogenetic markers. In this paper, we isolated and sequenced satellite DNA I-IV in 11 species of Cervidae. The obtained satellite DNA sequences and their chromosomal distribution were compared among the analysed representatives of cervid subfamilies Cervinae and Capreolinae. Only satI and satII sequences are probably present in all analysed species with high abundance. On the other hand, fluorescence in situ hybridisation (FISH) with satIII and satIV probes showed signals only in a part of the analysed species, indicating interspecies copy number variations. Several indices, including FISH patterns, the high guanine and cytosine (GC) content, and the presence of centromere protein B (CENP-B) binding motif, suggest that the satII DNA may represent the most important satellite DNA family that might be involved in the centromeric function in Cervidae. The absence or low intensity of satellite DNA FISH signals on biarmed chromosomes probably reflects the evolutionary reduction of heterochromatin following the formation of chromosome fusions. The phylogenetic trees constructed on the basis of the satellite I-IV DNA relationships generally support the present cervid taxonomy.

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The DNA sequences of cloned complex satellite DNAs from Hawaiian Drosophila and their bearing on satellite DNA sequence conservation

Chromosoma ◽

10.1007/bf00285766 ◽

1981 ◽

Vol 82 (3) ◽

pp. 409-427 ◽

Cited By ~ 18

Author(s):

George L. Gabor Miklos ◽

Amanda Clare Gill

Keyword(s):

Dna Sequence ◽

Dna Sequences ◽

Satellite Dna ◽

Sequence Conservation ◽

Satellite Dnas ◽

Hawaiian Drosophila

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Differential sensitivity of some human alphoid and classical satellite DNA regions from lymphocyte chromosomes to in situ exonuclease III digestion

Genome ◽

10.1139/g96-153 ◽

1996 ◽

Vol 39 (6) ◽

pp. 1210-1213

Author(s):

José Luis Fernández ◽

Carmen López-Fernández ◽

Jaime Gosálvez ◽

Vicente Goyanes

Keyword(s):

Dna Sequences ◽

Satellite Dna ◽

Fluorescent In Situ Hybridization ◽

Human Lymphocytes ◽

Differential Sensitivity ◽

Satellite Dnas ◽

Exonuclease Iii ◽

Human Cytogenetics ◽

Structural Differences

Fluorescent in situ hybridization of alphoid and classical satellite III DNA sequences was performed on fixed chromosomes from human lymphocytes that were previously digested in situ with exonuclease III to produce single-stranded DNA motifs. Digital image analysis showed that while labeled alphoid satellite DNAs produced signals of similar strength to thermally denatured chromosomes, those of classical satellite III DNAs of chromosomes 9 and Yq were around 50% weaker. This result shows a differential sensitivity of these satellite DNA regions to in situ exonuclease III digestion and suggests structural differences in the higher-order organization of both subchromosomal constitutive heterochromatic regions. Key words : alphoid sequences, classical satellite, exonuclease III, FISH, human cytogenetics, satellite DNA.

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Distribution and complex organization of satellite DNA sequences in Aveneae species

Genome ◽

10.1139/g96-131 ◽

1996 ◽

Vol 39 (6) ◽

pp. 1045-1050 ◽

Cited By ~ 19

Author(s):

Bärbel Grebenstein ◽

Oliver Grebenstein ◽

Wilhelm Sauer ◽

Vera Hemleben

Keyword(s):

Repetitive Dna ◽

Dna Sequences ◽

Satellite Dna ◽

Sequence Similarity ◽

Satellite Dnas ◽

A Genome ◽

Complex Organization ◽

Dna Elements ◽

Taxonomic Groups ◽

Dna Components

Distribution, organization, and molecular analysis of four unrelated satellite DNA components in Aveneae species are described. Highly repeated DNA elements were cloned from Helictotrichon convolutum (CON1 and CON2) and Helictotrichon compression (COM1 and COM2). The lengths of the repeat monomers are 365 bp (CON1), 562 bp (CON2), 346 bp (COM1), and 476 bp (COM2). Similar repeats were detected by dot blots, Southern blots, and by DNA sequencing in other species of the genus Helictotrichon, in Aveneae species, and in species of the tribes Andropogoneae and Oryzeae. All four satellite DNAs are differently distributed in the taxonomic groups mentioned above. Remarkably, the longer elements are built up in a complex pattern of either shorter subrepeats arranged in tandem (COM2) or by duplications inserted into an original 369-bp element (CON2). Shorter representatives, 190 bp, similar to CON1 elements occur in Holcus species. In Koeleria species, COM1-related repeats are only 180 bp in length. No similarity was found among the sequences CON2, COM1, and COM2 or with sequences of other repetitive DNA elements of the grasses, but CON1 shows sequence similarity to an A genome specific repetitive DNA of Oryza (rice). Key words : genome evolution, grasses, Poaceae, repetitive DNA, wild oats.

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Sequence, Chromatin and Evolution of Satellite DNA

International Journal of Molecular Sciences ◽

10.3390/ijms22094309 ◽

2021 ◽

Vol 22 (9) ◽

pp. 4309

Author(s):

Jitendra Thakur ◽

Jenika Packiaraj ◽

Steven Henikoff

Keyword(s):

Dna Sequences ◽

Satellite Dna ◽

Tandem Repeats ◽

Large Fraction ◽

Dna Curvature ◽

Sequence Motifs ◽

Specific Sequence ◽

Satellite Dnas ◽

Dna Repeat ◽

Species Specific

Satellite DNA consists of abundant tandem repeats that play important roles in cellular processes, including chromosome segregation, genome organization and chromosome end protection. Most satellite DNA repeat units are either of nucleosomal length or 5–10 bp long and occupy centromeric, pericentromeric or telomeric regions. Due to high repetitiveness, satellite DNA sequences have largely been absent from genome assemblies. Although few conserved satellite-specific sequence motifs have been identified, DNA curvature, dyad symmetries and inverted repeats are features of various satellite DNAs in several organisms. Satellite DNA sequences are either embedded in highly compact gene-poor heterochromatin or specialized chromatin that is distinct from euchromatin. Nevertheless, some satellite DNAs are transcribed into non-coding RNAs that may play important roles in satellite DNA function. Intriguingly, satellite DNAs are among the most rapidly evolving genomic elements, such that a large fraction is species-specific in most organisms. Here we describe the different classes of satellite DNA sequences, their satellite-specific chromatin features, and how these features may contribute to satellite DNA biology and evolution. We also discuss how the evolution of functional satellite DNA classes may contribute to speciation in plants and animals.

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