Retention of relict satellite DNA sequences in Anemone (Ranunculaceae)

Abstract Satellite DNAis a genomic component present in virtually all eukaryotic organisms. The turnover of highly repetitive satellite DNAis an important element in genome organization and evolution in plants. Here we study the presence, physical distribution and abundance of the satellite DNAfamily AhTR1 in Anemone. Twenty-two Anemone accessions were analyzed by PCR to assess the presence of AhTR1, while fluorescence in situ hybridization and Southern hybridization were used to determine the abundance and genomic distribution of AhTR1. The AhTR1 repeat unit was PCR-amplified only in eight phylogenetically related European Anemone taxa of the Anemone section. FISH signal with AhTR1 probe was visible only in A. hortensis and A. pavonina, showing localization of AhTR1 in the regions of interstitial heterochromatin in both species. The absence of a FISH signal in the six other taxa as well as weak signal after Southern hybridization suggest that in these species AhTR1 family appears as relict sequences. Thus, the data presented here support the »library hypothesis« for AhTR1 satellite evolution in Anemone. Similar species-specific satellite DNAprofiles in A. hortensis and A. pavonina support the treatment of A. hortensis and A. pavonina as one species, i.e. A. hortensis s.l.

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Species-diagnostic and species-specific DNA sequences evenly distributed throughout pine and spruce chromosomes

Genome ◽

10.1139/g10-065 ◽

2010 ◽

Vol 53 (10) ◽

pp. 769-777 ◽

Cited By ~ 1

Author(s):

Melanie Mehes-Smith ◽

Paul Michael ◽

Kabwe Nkongolo

Keyword(s):

Dna Sequences ◽

Random Amplified Polymorphic Dna ◽

Inter Simple Sequence Repeat ◽

Issr Markers ◽

Pinus Monticola ◽

The Family ◽

Species Specific ◽

Rapd And Issr ◽

Specific Sequences

Genome organization in the family Pinaceae is complex and largely unknown. The main purpose of the present study was to develop and physically map species-diagnostic and species-specific molecular markers in pine and spruce. Five RAPD (random amplified polymorphic DNA) and one ISSR (inter-simple sequence repeat) species-diagnostic or species-specific markers for Picea mariana , Picea rubens , Pinus strobus , or Pinus monticola were identified, cloned, and sequenced. In situ hybridization of these sequences to spruce and pine chromosomes showed the sequences to be present in high copy number and evenly distributed throughout the genome. The analysis of centromeric and telomeric regions revealed the absence of significant clustering of species-diagnostic and species-specific sequences in all the chromosomes of the four species studied. Both RAPD and ISSR markers showed similar patterns.

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Chromosome evolution in wild oat grasses (Aveneae) revealed by molecular phylogeny

Genome ◽

10.1139/g09-012 ◽

2009 ◽

Vol 52 (4) ◽

pp. 361-380 ◽

Cited By ~ 12

Author(s):

Grit Winterfeld ◽

Elke Döring ◽

Martin Röser

Keyword(s):

Molecular Phylogeny ◽

Dna Sequences ◽

Chromosome Evolution ◽

5S Rdna ◽

Fluorochrome Staining ◽

Satellite Dnas ◽

A Genome ◽

Satellite Chromosomes ◽

Species Specific

Karyotype structures revealed by in situ hybridization with ribosomal and satellite DNAs and fluorochrome staining of AT- or GC-rich regions are reported for 23 diploid to tetraploid taxa of Aveneae genera Arrhenatherum , Avena , Helictotrichon , and Pseudarrhenatherum . Chromosomal features are compared with a molecular phylogeny generated on nuclear ribosomal (ITS, 5S) and chloroplast (matK) DNA sequences. Ancestral chromosomal character states are (1) two satellite chromosomes per set of x = 7, (2) 5S rDNA localized in nonsatellite chromosomes, (3) large chromosomes with (4) rather equal lengths of their respective chromosome arms, (5) sets with strong variance of chromosome lengths, (6) absence or small amounts of heterochromatin, and (7) absence or no detectable amplification of the satellite DNAs tested. Overall, most karyotype characteristics are species specific, but common patterns were found for the species of two large subgenera of Helictotrichon. Pseudarrhenatherum, although nested in the molecular phylogeny within Helictotrichon subgenus Helictotrichon, deviates strongly in karyotype characters such as Arrhenatherum as sister of Avena. The karyotype of Helictotrichon jahandiezii , sister to the clade of Helictotrichon subgenera Helictotrichon, Avena, and Arrhenatherum, strongly resembles that of Avena macrostachya . Karyotype features suggest that perennial A. macrostachya and H. jahandiezii are close to the C-genome species of annual Avena, whereas the Avena A genome resembles that of Arrhenatherum.

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Organization of highly repeated sequences in surface-spread pachytene chromosomes of rye

Genome ◽

10.1139/g00-064 ◽

2000 ◽

Vol 43 (6) ◽

pp. 945-948 ◽

Cited By ~ 2

Author(s):

N Cuñado ◽

J Barrios ◽

J L Santos

Keyword(s):

In Situ Hybridization ◽

Fluorescence In Situ Hybridization ◽

Repetitive Dna ◽

Dna Sequences ◽

Repeated Dna ◽

Telomeric Sequences ◽

Different Types ◽

Surface Spread ◽

Fish Signal

A method of preparing two-dimensional surface spreads of plant synaptonemal complexes (SCs) associated with fluorescence in situ hybridization (FISH) has been applied to analyze the location and organization of five different highly repeated DNA sequences in rye. Our observations indicate that, depending on the type of sequence, the chromatin displays different types of organization. Telomeric sequences were seen tightly associated with the SC while other repetitive DNA sequences were found to form loops that are associated with SCs only at their bases. On the contrary, the FISH signal of a centromeric satellite had a granular appearance, reflecting that the hybridization occurs only with parts of the chromatin loops.Key words: fluorescence in situ hybridization, meiosis, repetitive DNA, rye, synaptonemal complex.

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Species-specific DNA probes for the identification of African trypanosomes in tsetse flies

Parasitology ◽

10.1017/s0031182000066749 ◽

1988 ◽

Vol 97 (1) ◽

pp. 63-73 ◽

Cited By ~ 84

Author(s):

W. C. Gibson ◽

P. Dukes ◽

J. K. Gashumba

Keyword(s):

Repeat Unit ◽

Blot Hybridization ◽

Dna Probes ◽

Tsetse Flies ◽

Dot Blot ◽

Specific Group ◽

African Trypanosomes ◽

Dot Blot Hybridization ◽

Species Specific

SUMMARYWe have obtained 5 specific DNA probes for African trypanosomes of the subgenera Trypanozoon and Nannomonas. Each probe consists of one repeat unit of the major repetitive DNA (satellite DNA) of each species or intra-specific group. One probe hybridized with all members of subgenus Trypanozoon (except T. equiperdum which was not tested). In subgenus Nannomonas, one probe recognized T. simiae, but 3 probes were needed to identify all stocks of T. congolense available. Each of the 3 latter probes recognized trypanosomes from one of the 3 major groups of T. congolense previously defined by isoenzyme characterization, i.e. savannah, forest and Kenya coast types. As few as 100 trypanosomes could be unequivocally identified by dot blot hybridization and individual trypanosomes could be identified by in situ hybridization. We show how this simple methodology can be used in the field for the identification of immature and mature trypanosome infections in tsetse.

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Physical localisation of repetitive DNA sequences in Alstroemeria: karyotyping of two species with species-specific and ribosomal DNA

Genome ◽

10.1139/g97-086 ◽

1997 ◽

Vol 40 (5) ◽

pp. 652-658 ◽

Cited By ~ 22

Author(s):

Silvan A. Kamstra ◽

Anja G. J. Kuipers ◽

Marjo J. De Jeu ◽

M. S. Ramanna ◽

Evert Jacobsen

Keyword(s):

In Situ Hybridization ◽

Fluorescence In Situ Hybridization ◽

Repetitive Dna ◽

Ribosomal Dna ◽

Dna Sequences ◽

Repetitive Dna Sequences ◽

Metaphase Chromosomes ◽

Rdna Sites ◽

Species Specific

Fluorescence in situ hybridization (FISH) was used to localise two species-specific repetitive DNA sequences, A001-I and D32-13, and two highly conserved 25S and 5S rDNA sequences on the metaphase chromosomes of two species of Alstroemeria. The Chilean species, Alstroemeria aurea (2n = 16), has abundant constitutive heterochromatin, whereas the Brazilian species, Alstroemeria inodora, has hardly any heterochromatin. The A. aurea specific A001-I probe hybridized specifically to the C-band regions on all chromosomes. The FISH patterns on A. inodora chromosomes using species-specific probe D32–13 resembled the C-banding pattern and the A001-I pattern on A. aurea chromosomes. There were notable differences in number and distribution of rDNA sites between the two species. The 25S rDNA probe revealed 16 sites in A. aurea that closely colocalised with A001-I sites and 12 in A. inodora that were predominantly detected in the centromeric regions. FISH karyotypes of the two Alstroemeria species were constructed accordingly, enabling full identification of all individual chromosomes. These FISH karyotypes will be useful for monitoring the chromosomes of both Alstroemeria species in hybrids and backcross derivatives.Key words: Alstroemeria, fluorescence in situ hybridization, FISH, repetitive DNA, ribosomal DNA, karyotype.

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Molecular characterization and chromosomal distribution of species-specific repetitive DNA sequences from Beta corolliflora, a wild relative of sugar beet

Genome ◽

10.1139/g00-084 ◽

2000 ◽

Vol 43 (6) ◽

pp. 1073-1080 ◽

Cited By ~ 17

Author(s):

D Gao ◽

T Schmidt ◽

C Jung

Keyword(s):

Sugar Beet ◽

Repetitive Dna ◽

Dna Sequences ◽

Genomic Dna ◽

Southern Hybridization ◽

Repetitive Dna Sequences ◽

Wild Relative ◽

Chromosomal Distribution ◽

Species Specific ◽

Specific Sequences

Repetitive DNA sequences have been isolated from a Sau3AI plasmid library of tetraploid Beta corolliflora (2n = 4x = 36), a wild relative of sugar beet (B. vulgaris). The library was screened by differential hybridization with genomic DNA of B. corolliflora and B. vulgaris. When used as probes for Southern hybridization of genomic DNA, six clones were determined to represent highly repetitive DNA families present only in the B. corolliflora genome. Five other sequences were highly repetitive in B. corolliflora and low or single copy in B. vulgaris. The insert size varied between 43 bp and 448 bp. Two sequences pBC1279 and pBC1944 displayed strong homology to a previously cloned satellite DNA from B. nana. With one exception, sequences are tandemly arranged as revealed by a typical ladder pattern after genomic Southern hybridization. The chromosomal distribution of five probes was determined by fluorescence in situ hybridization (FISH) of mitotic metaphases from B. corolliflora and a triploid hybrid between B. vulgaris and B. corolliflora. Three sequences were spread along all chromosome arms of B. corolliflora while one sequence was present on only six chromosomes. The chromosome-specific sequence pBC216 was found in close vicinity to the 5S rDNA located on B. corolliflora chromosome IV. This set of species-specific sequences has the potential to be used as probes for the identification of monosomic alien addition lines and for marker-assisted gene transfer from wild beet to cultivated beet.Key words: Beta vulgaris, FISH, repetitive DNA, species-specific sequences.

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Repetitive DNA sequences in Crocus vernus Hill (Iridaceae): The genomic organization and distribution of dispersed elements in the genus Crocus and its allies

Genome ◽

10.1139/g00-044 ◽

2000 ◽

Vol 43 (5) ◽

pp. 902-909 ◽

Cited By ~ 14

Author(s):

S Frello ◽

J S Heslop-Harrison

Keyword(s):

In Situ Hybridization ◽

Sequence Analysis ◽

Repetitive Dna ◽

Dna Sequences ◽

Southern Hybridization ◽

Genomic Organization ◽

Organizer Region ◽

Nucleolar Organizer Region ◽

Taxonomic Structure

Eight clones of repetitive DNA were isolated from Crocus vernus Hill. The genomic organization of the clones was analyzed by in situ hybridization to C. vernus and Southern hybridization to a range of Crocus and other species. Seven clones were used for in situ hybridization. Sequence analysis showed that all eight clones were nonhomologous, and thus represented eight different sequence-families. In situ hybridization showed that six were dispersed in high copy numbers on all chromosomes of the C. vernus genome, whereas one was localized proximal to the secondary constriction, at the NOR (nucleolar organizer region) and was not further analyzed, as it was considered part of the 18S-25S rDNA repeat. Except for short palindromes, none of the sequences showed notable internal structures. Clone pCvKB4 showed homology to the reverse transcriptase gene of Ty1-copia-like retrotransposons; the others showed no homology to known sequences. When used as probes for Southern hybridization, four showed a ladder of 3-4 bands superimposed by irregular patterns, indicating organization in short tandem arrays. Each clone had a unique distribution among Crocus species (12-16 species analyzed with each clone) and six species of Iridaceae, Liliaceae, and Amaryllidaceae; all seven investigated sequences were Iridaceae specific and four were Crocus specific. The species distribution of these seven clones showed notable discrepancies with the taxonomic subdivision of the genus at the subgenus, section, and series levels. The results suggest that the phylogeny and taxonomic structure of the genus Crocus might need reconsideration. The analysis of repetitive DNA as a major and rapidly evolving part of the genome could contribute to the study of species relationships and evolution.Key words: phylogeny, evolution, in situ hybridization, sequence analysis, dispersed elements.

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Isolation, characterization, and analysis of Leymus-specific DNA sequences

Genome ◽

10.1139/g03-029 ◽

2003 ◽

Vol 46 (4) ◽

pp. 673-682 ◽

Cited By ~ 22

Author(s):

Sigridur Klara Bödvarsdóttir ◽

Kesara Anamthawat-Jónsson

Keyword(s):

Dna Sequences ◽

Genomic Dna ◽

Southern Hybridization ◽

Genetic Relatedness ◽

Repetitive Sequences ◽

Nucleolar Organiser Regions ◽

Basic Genome ◽

Specific Sequences ◽

Leymus Mollis

Genomic Southern hybridization using labeled total genomic DNA of Leymus mollis as probe showed intense hybridization signals on all restriction enzyme digested DNA from five species of Leymus Hochst., and four species of Psathyrostachys Nevski. Experiments using the same L. mollis probe, but with unlabeled blocking DNA from Psathyrostachys, showed no hybridization at all. These two genera evidently had the same genomic content. Southern hybridization without blocking allowed identification of DNA fragments abundant in Leymus and Psathyrostachys. Fragments potentially specific to Leymus were cloned. Five repetitive DNA clones from L. mollis and L. arenarius were characterized: pLmIs1, pLmIs44, pLmIs51, pLmIs53, and pLaIs56. These clones hybridized to both Leymus and Psathyrostachys on Southern blots no clone hybridized to only one of these genera. Both Southern blot and fluorescence in situ hybridization (FISH) experiments showed that all the clones contained dispersed repetitive sequences. They painted all and whole chromosomes uniformly except at centromeres, telomeres, and nucleolar organiser regions. Three of these clones, i.e., pLmIs1, pLmIs44, and pLmIs53, were essentially specific to Leymus and Psathyrostachys little or no hybridization was detected in other genera such as Triticum, Hordeum, Thinopyrum, or Elymus. Sequence analysis further revealed that the clones were part of retroelements. In particular, the clone pLmIs44 produced hybridization profiles suitable for analysis of genetic relatedness among species. The present study shows that Leymus and Psathyrostachys share the same basic genome, Ns, and therefore provides strong evidence for combining these two genera.Key words: Triticeae, Leymus, Psathyrostachys, genome-specific sequences, retrotransposons.

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Cytogenetic Characterization of Seven Novel satDNA Markers in Two Species of Spined Loaches (Cobitis) and Their Clonal Hybrids

Genes ◽

10.3390/genes11060617 ◽

2020 ◽

Vol 11 (6) ◽

pp. 617

Author(s):

Anatolie Marta ◽

Dmitry Dedukh ◽

Oldřich Bartoš ◽

Zuzana Majtánová ◽

Karel Janko

Keyword(s):

Interspecific Hybridization ◽

Dna Sequences ◽

Species Determination ◽

Closely Related Species ◽

Evolutionary Force ◽

Identification Of Species ◽

Cytogenetic Characterization ◽

Species Specific

Interspecific hybridization is a powerful evolutionary force. However, the investigation of hybrids requires the application of methodologies that provide efficient and indubitable identification of both parental subgenomes in hybrid individuals. Repetitive DNA, and especially the satellite DNA sequences (satDNA), can rapidly diverge even between closely related species, hence providing a useful tool for cytogenetic investigations of hybrids. Recent progress in whole-genome sequencing (WGS) offers unprecedented possibilities for the development of new tools for species determination, including identification of species-specific satDNA markers. In this study, we focused on spined loaches (Cobitis, Teleostei), a group of fishes with frequent interspecific hybridization. Using the WGS of one species, C. elongatoides, we identified seven satDNA markers, which were mapped by fluorescence in situ hybridization on mitotic and lampbrush chromosomes of C. elongatoides, C. taenia and their triploid hybrids (C. elongatoides × 2C. taenia). Two of these markers were chromosome-specific in both species, one had centromeric localization in multiple chromosomes and four had variable patterns between tested species. Our study provided a novel set of cytogenetic markers for Cobitis species and demonstrated that NGS-based development of satDNA cytogenetic markers may provide a very efficient and easy tool for the investigation of hybrid genomes, cell ploidy, and karyotype evolution.

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Molecular cytogenetic analysis of DNA sequences with flanking telomeric repeats inTriticum aestivumcv. Begra

Genome ◽

10.1139/g00-093 ◽

2001 ◽

Vol 44 (1) ◽

pp. 133-136

Author(s):

Marta Dobrzanska ◽

Elzbieta Kraszewska ◽

Maria Bucholc ◽

Glyn Jenkins

Keyword(s):

Triticum Aestivum ◽

Dna Sequences ◽

Genomic Dna ◽

Repeat Unit ◽

Chromosome Complement ◽

Mobile Dna ◽

Chromosomal Distribution ◽

Telomeric Sequences ◽

Dna Fragment

A cloned genomic DNA fragment (pTa241) formerly derived from a DNA fraction obtained from isolated nuclei of embryos of a Polish cultivar of wheat (Triticum aestivum cv. Begra) comprises a tandem repeat of the telomeric array CCCTAAA, and hybridizes in situ exclusively to the telomeres of all chromosome arms of the somatic chromosome complement of wheat. A second cloned fragment (pTa637) derived from the same fraction is 637 bp long, flanked by 28 bp of the same telomeric repeat unit, and hybridizes in situ to the entire lengths of all the chromosomes of the complement. The same pattern of hybridization was observed when the flanking telomeric sequences were removed. A third DNA fragment (pTa1439), derived from unfractionated genomic DNA and flanked with 62 bp of the same telomeric unit, showed the same patterns of distribution. Together with additional evidence from Southern analysis, these observations were interpreted to mean that these sequences are associated with mobile DNA elements and are distributed widely throughout the genome. The chromosomal distribution of the non-telomeric parts of the clones is consistent with the dispersed genomic distribution characteristic of transposons and retroelements.Key words: wheat, Triticum aestivum cv. Begra, mobile elements, telomeric DNA sequence, FISH.

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