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

Genome ◽  
2009 ◽  
Vol 52 (4) ◽  
pp. 361-380 ◽  
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.

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

Genome ◽  
2010 ◽  
Vol 53 (10) ◽  
pp. 769-777 ◽  
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.

scholarly journals Retention of relict satellite DNA sequences in Anemone (Ranunculaceae)

2013 ◽  
Vol 72 (1) ◽  
pp. 1-133 ◽  
Author(s):  
Višnja Besendorfer ◽  
Jelena Mlinarec
Keyword(s):  
Dna Sequences ◽  
Southern Hybridization ◽  
Repeat Unit ◽  
Similar Species ◽  
Genomic Component ◽  
Library Hypothesis ◽  
Species Specific ◽  
Eukaryotic Organisms ◽  
Fish Signal

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.

The use of double fluorescence in situ hybridization to physically map the positions of 5S rDNA genes in relation to the chromosomal location of 18S–5.8S–26S rDNA and a C genome specific DNA sequence in the genus Avena

Genome ◽  
1996 ◽  
Vol 39 (3) ◽  
pp. 535-542 ◽  
Author(s):  
Concha Linares ◽  
Juan González ◽  
Esther Ferrer ◽  
Araceli Fominaya
Keyword(s):  
In Situ Hybridization ◽  
Dna Sequence ◽  
Diploid Species ◽  
5S Rdna ◽  
Rdna Genes ◽  
26S Rdna ◽  
A Genome ◽  
Rdna Loci ◽  
C Genome

A physical map of the locations of the 5S rDNA genes and their relative positions with respect to 18S–5.8S–26S rDNA genes and a C genome specific repetitive DNA sequence was produced for the chromosomes of diploid, tetraploid, and hexaploid oat species using in situ hybridization. The A genome diploid species showed two pairs of rDNA loci and two pairs of 5S loci located on both arms of one pair of satellited chromosomes. The C genome diploid species showed two major pairs and one minor pair of rDNA loci. One pair of subtelocentric chromosomes carried rDNA and 5S loci physically separated on the long arm. The tetraploid species (AACC genomes) arising from these diploid ancestors showed two pairs of rDNA loci and three pairs of 5S loci. Two pairs of rDNA loci and 2 pairs of 5S loci were arranged as in the A genome diploid species. The third pair of 5S loci was located on one pair of A–C translocated chromosomes using simultaneous in situ hybridization with 5S rDNA genes and a C genome specific repetitive DNA sequence. The hexaploid species (AACCDD genomes) showed three pairs of rDNA loci and six pairs of 5S loci. One pair of 5S loci was located on each of two pairs of C–A/D translocated chromosomes. Comparative studies of the physical arrangement of rDNA and 5S loci in polyploid oats and the putative A and C genome progenitor species suggests that A genome diploid species could be the donor of both A and D genomes of polyploid oats. Key words : oats, 5S rDNA genes, 18S–5.8S–26S rDNA genes, C genome specific repetitive DNA sequence, in situ hybridization, genome evolution.

Variation in highly repetitive DNA composition of heterochromatin in rye studied by fluorescence in situ hybridization

Genome ◽  
1995 ◽  
Vol 38 (6) ◽  
pp. 1061-1069 ◽  
Author(s):  
A. Cuadrado ◽  
N. Jouve ◽  
C. Ceoloni
Keyword(s):  
In Situ Hybridization ◽  
Fluorescence In Situ Hybridization ◽  
Repetitive Dna ◽  
Dna Sequences ◽  
5S Rdna ◽  
Individual Identification ◽  
Highly Repetitive Dna ◽  
The Individual

The molecular characterization of heterochromatin in six lines of rye has been performed using fluorescence in situ hybridization (FISH). The highly repetitive rye DNA sequences pSc 119.2, pSc74, and pSc34, and the probes pTa71 and pSc794 containing the 25S–5.8S–18S rDNA (NOR) and the 5S rDNA multigene families, respectively, were used. This allowed the individual identification of all seven rye chromosomes and most chromosome arms in all lines. All varieties showed similar but not identical patterns. A standard in situ hybridization map was constructed following the nomenclature system recommended for C-bands. All FISH sites observed appeared to correspond well with C-band locations, but not all C-banding sites coincided with hybridization sites of the repetitive DNA probes used. Quantitative and qualitative differences between different varieties were found for in situ hybridization response at corresponding sites. Variation between plants and even between homologous chromosomes of the same plant was found in open-pollinated lines. In inbred lines, the in situ pattern of the homologues was practically identical and no variation between plants was detected. The observed quantitative and qualitative differences are consistent with a corresponding variation for C-bands detected both within and between cultivars.Key words: fluorescence in situ hybridization, repetitive DNA, rye, Secale cereale, polymorphism.

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

Genome ◽  
1996 ◽  
Vol 39 (2) ◽  
pp. 243-248 ◽  
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.

Chromosomal localization of two novel repetitive sequences isolated from the Chenopodium quinoa Willd. genome

Genome ◽  
2011 ◽  
Vol 54 (9) ◽  
pp. 710-717 ◽  
Author(s):  
B. Kolano ◽  
B.W. Gardunia ◽  
M. Michalska ◽  
A. Bonifacio ◽  
D. Fairbanks ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Repetitive Dna ◽  
Dna Sequences ◽  
Repetitive Sequences ◽  
Chenopodium Quinoa ◽  
5S Rdna ◽  
Rrna Gene ◽  
Fish Analysis ◽  
Rdna Loci

The chromosomal organization of two novel repetitive DNA sequences isolated from the Chenopodium quinoa Willd. genome was analyzed across the genomes of selected Chenopodium species. Fluorescence in situ hybridization (FISH) analysis with the repetitive DNA clone 18–24J in the closely related allotetraploids C. quinoa and Chenopodium berlandieri Moq. (2n = 4x = 36) evidenced hybridization signals that were mainly present on 18 chromosomes; however, in the allohexaploid Chenopodium album L. (2n = 6x = 54), cross-hybridization was observed on all of the chromosomes. In situ hybridization with rRNA gene probes indicated that during the evolution of polyploidy, the chenopods lost some of their rDNA loci. Reprobing with rDNA indicated that in the subgenome labeled with 18–24J, one 35S rRNA locus and at least half of the 5S rDNA loci were present. A second analyzed sequence, 12–13P, localized exclusively in pericentromeric regions of each chromosome of C. quinoa and related species. The intensity of the FISH signals differed considerably among chromosomes. The pattern observed on C. quinoa chromosomes after FISH with 12–13P was very similar to GISH results, suggesting that the 12–13P sequence constitutes a major part of the repetitive DNA of C. quinoa.

scholarly journals Use of Genomic in Situ Hybridization (GISH) to Track Genetic Introgression in Onion

HortScience ◽  
1997 ◽  
Vol 32 (3) ◽  
pp. 513B-513
Author(s):  
Anfu Hou ◽  
Ellen B. Peffley
Keyword(s):  
In Situ Hybridization ◽  
Dna Sequences ◽  
Genomic In Situ Hybridization ◽  
Genetic Introgression ◽  
A Genome

Introgression of genes in species crosses can be observed morphologically in backcrossed or selfed progenies, but the phenotype does not give information about the movement of DNAs. Cytogenetic markers allow for visualization of specific DNAs in a genome. Few cytogenetic markers are available in onion to monitor the introgression of DNA in species crosses. Genomic in situ hybridization (GISH) provides a way to locate unique DNA sequences contributed by parents. We are using GISH to monitor the movement of DNAs from A. fistulosum into A. cepa. Results of experiments using A. fistulosum as probe DNA, and A. cepa as blocking DNA will be reported. Also presented are hybridization sites observed in F1BC3 progeny of the GISH.

scholarly journals Genomic in situ hybridization in interspecific hybrids of scallops (Bivalvia, Pectinidae) and localization of the satellite DNA Cf303, and the vertebrate telomeric sequences (TTAGGG)n on chromosomes of scallop Chlamys farreri (Jones & Preston, 1904)

2018 ◽  
Vol 12 (1) ◽  
pp. 83-95
Author(s):  
Liping Hu ◽  
Liming Jiang ◽  
Ke Bi ◽  
Huan Liao ◽  
Zujing Yang ◽  
...  
Keyword(s):  
Interspecific Hybrids ◽  
Distribution Patterns ◽  
Mitotic Chromosomes ◽  
Chromosomal Distribution ◽  
Satellite Dnas ◽  
Banding Patterns ◽  
Telomeric Sequences ◽  
Specific Distribution ◽  
Species Specific

Mitotic chromosome preparations of the interspecific hybrids Chlamysfarreri (Jones & Preston, 1904) × Patinopectenyessoensis (Jay, 1857), C.farreri × Argopectenirradinas (Lamarck, 1819) and C.farreri × Mimachlamysnobilis (Reeve, 1852) were used to compare two different scallop genomes in a single slide. Although genomic in situ hybridization (GISH) using genomic DNA from each scallop species as probe painted mitotic chromosomes of the interspecific hybrids, the painting results were not uniform; instead it showed species-specific distribution patterns of fluorescent signals among the chromosomes. The most prominent GISH-bands were mainly located at centromeric or telomeric regions of scallop chromosomes. In order to illustrate the sequence constitution of the GISH-bands, the satellite Cf303 sequences of C.farreri and the vertebrate telomeric (TTAGGG)n sequences were used to map mitotic chromosomes of C.farreri by fluorescence in situ hybridization (FISH). The results indicated that the GISH-banding pattern presented by the chromosomes of C.farreri is mainly due to the distribution of the satellite Cf303 DNA, therefore suggesting that the GISH-banding patterns found in the other three scallops could also be the result of the chromosomal distribution of other species-specific satellite DNAs.

Fluorescence in situ hybridization mapping of Avena sativa L. cv. SunII and its monosomic lines using cloned repetitive DNA sequences

Genome ◽  
2002 ◽  
Vol 45 (6) ◽  
pp. 1230-1237 ◽  
Author(s):  
M L Irigoyen ◽  
C Linares ◽  
E Ferrer ◽  
A Fominaya
Keyword(s):  
In Situ Hybridization ◽  
Dna Sequences ◽  
Avena Sativa ◽  
Meiotic Chromosome ◽  
D Genome ◽  
Fish Mapping ◽  
Intergenomic Translocations ◽  
A Genome ◽  
C Genome

Fluorescent in situ hybridization (FISH) employing multiple probes was used with mitotic or meiotic chromosome spreads of Avena sativa L. cv. SunII and its monosomic lines to produce physical chromosome maps. The probes used were Avena strigosa pAs120a (which hybridizes exclusively to A-genome chromosomes), Avena murphyi pAm1 (which hybridizes exclusively to C-genome chromosomes), A. strigosa pAs121 (which hybridizes exclusively to A- and D-genome chromosomes), and the wheat rDNA probes pTa71 and pTa794. Simultaneous and sequential FISH employing two-by-two combinations of these probes allowed the unequivocal identification and genome assignation of all chromosomes. Ten pairs were found carrying intergenomic translocations: (i) between the A and C genomes (chromosome pair 5A); (ii) between the C and D genomes (pairs 1C, 2C, 4C, 10C, and 16C); and (iii) between the D and C genomes (pairs 9D, 11D, 13D, and 14D). The existence of a reciprocal intergenomic translocation (10C–14D) is also proposed. Comparing these results with those of other hexaploids, three intergenomic translocations (10C, 9D, and 14D) were found to be unique to A. sativa cv. SunII, supporting the view that 'SunII' is genetically distinct from other hexaploid Avena species and from cultivars of the A. sativa species. FISH mapping using meiotic and mitotic metaphases facilitated the genomic and chromosomal identification of the aneuploid chromosome in each monosomic line. Of the 18 analyzed, only 11 distinct monosomic lines were actually found, corresponding to 5 lines of the A genome, 2 lines of the C genome, and 4 lines of the D genome. The presence or absence of the 10C–14D interchange was also monitored in these lines.Key words: Avena sativa, monosomics, FISH mapping, genomic identification, intergenomic translocations.

Distribution of highly repeated DNA sequences in species of the genus Secale

Genome ◽  
1997 ◽  
Vol 40 (3) ◽  
pp. 309-317 ◽  
Author(s):  
Angeles Cuadrado ◽  
Nicolás Jouve
Keyword(s):  
In Situ Hybridization ◽  
Fluorescence In Situ Hybridization ◽  
Repetitive Dna ◽  
Dna Sequences ◽  
5S Rdna ◽  
Nucleotide Sequences ◽  
Repeated Dna ◽  
Accurate Identification ◽  
Highly Repetitive Dna

The presence and distribution of the most important highly repetitive DNA sequences of rye in cultivated and wild species of the genus Secale were investigated using fluorescence in situ hybridization. Accurate identification of individual chromosomes in the most commonly recognized species or subspecies of the genus Secale (S. cereale, S. ancestrale, S. segetale, S. afghanicum, S. dighoricum, S. montanum, S. montanum ssp. kuprijanovii, S. africanum, S. anatolicum, S. vavilovii, and S. silvestre) was achieved using three highly repetitive rye DNA sequences (probes pSc119.2, pSc74, and pSc34) and the 5S ribosomal DNA sequence pTa794. It is difficult to superimpose trends in the complexity of repetitive DNA during the evolution of the genus on conclusions from other cytogenetic and morphological assays. However, there are two clear groups. The first comprises the self-pollinated annuals S. silvestre and S. vavilovii that have few repeated nucleotide sequences of the main families of 120 and 480 bp. The second group presents amplification and interstitialization of the repeated nucleotide sequences and includes the perennials S. montanum, S. anatolicum, S. africanum, and S. kuprijanovii, as well as the annual and open-pollinated species S. cereale and its related weedy forms. The appearance of a new locus for 5S rRNA in S. cereale and S. ancestrale suggests that cultivated ryes evolved from this wild weedy species.Key words: rye, repeated nucleotide sequence, 5S rDNA, fluorescence in situ hybridization, FISH.

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