scholarly journals Molecular Cytogenetic Mapping of Chromosomal Fragments and Immunostaining of Kinetochore Proteins in Beta

2009 ◽  
Vol 2009 ◽  
pp. 1-12 ◽  
Author(s):  
Daryna Dechyeva ◽  
Thomas Schmidt
Keyword(s):  
Repetitive Dna ◽  
Small Chromosome ◽  
Rrna Genes ◽  
Fish Analysis ◽  
Addition Lines ◽  
Multicolor Fish ◽  
Active Involvement ◽  
Chromosome Fragments ◽  
In The Wild ◽  
Wild Beet

By comparative multicolor FISH, we have physically mapped small chromosome fragments in the sugar beet addition lines PRO1 and PAT2 and analyzed the distribution of repetitive DNA families in species of the section Procumbentes of the genus Beta. Six repetitive probes were applied, including genotype-specific probes—satellites pTS4.1, pTS5, and pRp34 and a dispersed repeat pAp4, the telomere (TTTAGGG)n, and the conserved 18S-5.8S-25S rRNA genes. Pachytene-FISH analysis of the native centromere organization allowed proposing the origin of PRO1 and PAT2 fragments. Comparative analysis of the repetitive DNA distribution and organization in the wild beet and in the addition lines allowed the development of a physical model of the chromosomal fragments. Immunostaining revealed that the PRO1 chromosome fragment binds α-tubulin and the serine 10-phosphorylated histone H3 specific for the active centromere. This is the first experimental detection of the kinetochore proteins in Beta showing their active involvement in chromosome segregation in mitosis.

scholarly journals Isolation of a Pericentromeric Satellite DNA Family in Chnootriba argus (Henosepilachna argus) with an Unusual Short Repeat Unit (TTAAAA) for Beetles

Insects ◽  
2019 ◽  
Vol 10 (9) ◽  
pp. 306 ◽  
Author(s):  
Pablo Mora ◽  
Jesús Vela ◽  
Areli Ruiz-Mena ◽  
Teresa Palomeque ◽  
Pedro Lorite
Keyword(s):  
Repetitive Dna ◽  
Satellite Dna ◽  
Repeat Unit ◽  
Pericentromeric Region ◽  
Fish Analysis ◽  
Agricultural Pests ◽  
Base Pairs ◽  
Satellite Dnas ◽  
Repeat Units

Ladybird beetles (Coccinellidae) are one of the largest groups of beetles. Among them, some species are of economic interest since they can act as a biological control for some agricultural pests whereas other species are phytophagous and can damage crops. Chnootriba argus (Coccinellidae, Epilachnini) has large heterochromatic pericentromeric blocks on all chromosomes, including both sexual chromosomes. Classical digestion of total genomic DNA using restriction endonucleases failed to find the satellite DNA located on these heterochromatic regions. Cloning of C0t-1 DNA resulted in the isolation of a repetitive DNA with a repeat unit of six base pairs, TTAAAA. The amount of TTAAAA repeat in the C. argus genome was about 20%. Fluorescence in situ hybridization (FISH) analysis and digestion of chromosomes with the endonuclease Tru9I revealed that this repetitive DNA could be considered as the putative pericentromeric satellite DNA (satDNA) in this species. The presence of this satellite DNA was tested in other species of the tribe Epilachnini and it is also present in Epilachna paenulata. In both species, the TTAAAA repeat seems to be the main satellite DNA and it is located on the pericentromeric region on all chromosomes. The size of this satDNA, which has only six base pairs is unusual in Coleoptera satellite DNAs, where satDNAs usually have repeat units of a much larger size. Southern hybridization and FISH proved that this satDNA is conserved in some Epilachnini species but not in others. This result is in concordance with the controversial phylogenetic relationships among the genera of the tribe Epilachnini, where the limits between genera are unclear.

scholarly journals Multicolor FISH Analysis of Chromosomal Breaks, Duplications, Deletions, and Numerical Abnormalities in the Sperm of Healthy Men

2000 ◽  
Vol 67 (4) ◽  
pp. 862-872 ◽  
Author(s):  
Eddie D. Sloter ◽  
Xiu Lowe ◽  
Dan H. Moore ◽  
Joginder Nath ◽  
Andrew J. Wyrobek
Keyword(s):  
Fish Analysis ◽  
Multicolor Fish ◽  
Healthy Men ◽  
Chromosomal Breaks

Identification of prevalent microbial communities in a municipal solid waste landfill

2006 ◽  
Vol 53 (8) ◽  
pp. 139-147 ◽  
Author(s):  
B. Calli ◽  
S. Durmaz ◽  
B. Mertoglu
Keyword(s):  
16S Rrna ◽  
Municipal Solid Waste ◽  
Microbial Communities ◽  
Solid Waste ◽  
Molecular Techniques ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Fish Analysis ◽  
Municipal Solid Waste Landfill ◽  
Waste Landfill

To identify the microbial communities in Istanbul, Odayeri Municipal Solid Waste Landfill, leachate samples were collected from different sections at different stabilization phases. In identification of microbial communities in leachate samples, molecular techniques such as FISH, DGGE and cloning based on 16S rRNA and mcrA genes were used. As the chemical and microbiological compositions of the samples were compared, obvious correlations were found between the stability of the landfill section and abundance of active methanogens. On the other hand, there were considerable differences between acidogenic and mature leachate samples in DGGE profiles of archaeal and bacterial 16S rRNA genes. Moreover, in acidogenic leachate samples having BOD5/COD ratio of about 0.5 acetate utilizing Methanosarcina and Methanosaeta species were intensively detected in FISH. Although only very few H2-utilizing methanogens were identified with FISH analysis, most of the clones isolated from mature leachate samples clustered within H2-utilizing Methanobacteriales and Methanomicrobiales according to phylogenetic analysis of 16S rRNA and mcrA clones, respectively.

Integrated Karyotyping of Woodland Strawberry (Fragaria vesca) with Oligopaint FISH Probes

2017 ◽  
Vol 153 (3) ◽  
pp. 158-164 ◽  
Author(s):  
Manman Qu ◽  
Kunpeng Li ◽  
Yanli Han ◽  
Lei Chen ◽  
Zongyun Li ◽  
...  
Keyword(s):  
Draft Genome ◽  
5S Rdna ◽  
Fish Analysis ◽  
Fragaria Vesca ◽  
Chromosome Identification ◽  
Multicolor Fish ◽  
Metaphase Chromosomes ◽  
Cross Species Chromosome Painting ◽  
Simultaneous Identification

Chromosome identification is critical for many aspects of cytogenetic research. However, for Fragaria vesca, definite identification of individual chromosomes is almost impossible because of their small size and high similarity. Here, we demonstrate that bulked oligonucleotide (oligo) probes can be used as chromosome-specific DNA markers for chromosome identification in F. vesca. Oligos specific to entire pseudochromosomes in the draft genome of F. vesca were identified and synthesized as libraries. In all, we synthesized 6 oligo libraries corresponding to 6 pseudochromosomes of F. vesca. These libraries were amplified and labeled as probes for fluorescence in situ hybridization (FISH). Two rounds of multicolor FISH analysis were sequentially conducted on the same metaphase cells with each round including 3 probe libraries, which permitted simultaneous identification of all chromosomes of F. vesca. Moreover, 45S and 5S rDNA were mapped to chromosomes 1, 2, and 7, respectively. A karyotype of metaphase chromosomes was constructed, representing the first FISH-based molecular cytogenetic karyotype of F. vesca. Our study can serve as a basis for future comparative cytogenetic research through cross-species chromosome painting using bulked oligo probes and will facilitate the application of breeding technologies that rely on the identification of chromosomes in the genus Fragaria.

Investigations of 5S rDNA of Vitis vinifera L.: sequence analysis and physical mapping

Genome ◽  
2007 ◽  
Vol 50 (10) ◽  
pp. 927-938 ◽  
Author(s):  
E. Falistocco ◽  
V. Passeri ◽  
G. Marconi
Keyword(s):  
Vitis Vinifera ◽  
Repeat Unit ◽  
5S Rdna ◽  
Nucleotide Composition ◽  
Large Deletion ◽  
Rrna Genes ◽  
Vitis Vinifera L ◽  
Fish Analysis ◽  
Rdna Sequences ◽  
Short Repeat

Here we report the first results of a study of 5S rDNA of Vitis vinifera . 5S rDNA sequences from seven genotypes were amplified by PCR, cloned, and sequenced. Three types of repeats were found. Two variants, denominated long repeat and short repeat, appeared to be the main components of the 5S rDNA of this species, since they were found in all genotypes analyzed. They differed markedly from each other in both the length and the nucleotide composition of the spacers. The third variant, classified as DEL short repeat, differs from the short repeat owing to a large deletion in the spacer region. It appears to be the most recent repeat type, since it was identified in only one genotype. The organization of the 5S rDNA repeat unit variants was investigated by amplifying the genomic DNA with primers designed on the sequence of the long and short spacers. The PCR-amplified fragments showed that the long repeat is associated with the other two repeats, indicating that in V. vinifera different repeat units coexist within the same tandem array. FISH analysis demonstrated that 5S rRNA genes are localized at a single locus. The variability of 5S rDNA repeats is discussed in relation to the putative allopolyploid origin of V. vinifera.

Molecular and cytological characterization of ribosomal RNA genes in Chenopodium quinoa and Chenopodium berlandieri

Genome ◽  
2006 ◽  
Vol 49 (7) ◽  
pp. 825-839 ◽  
Author(s):  
P J Maughan ◽  
B A Kolano ◽  
J Maluszynska ◽  
N D Coles ◽  
A Bonifacio ◽  
...  
Keyword(s):  
Ribosomal Rna ◽  
Organizer Region ◽  
Nucleolus Organizer Region ◽  
Chenopodium Quinoa ◽  
Nucleolus Organizer ◽  
5S Rrna ◽  
Rrna Genes ◽  
Fish Analysis ◽  
General Sequence ◽  
Sequence Composition

The nucleolus organizer region (NOR) and 5S ribosomal RNA (rRNA) genes are valuable as chromosome landmarks and in evolutionary studies. The NOR intergenic spacers (IGS) and 5S rRNA nontranscribed spacers (NTS) were PCR-amplified and sequenced from 5 cultivars of the Andean grain crop quinoa (Chenopodium quinoa Willd., 2n = 4x = 36) and a related wild ancestor (C. berlandieri Moq. subsp. zschackei (Murr) A. Zobel, 2n = 4x = 36). Length heterogeneity observed in the IGS resulted from copy number difference in subrepeat elements, small re arrangements, and species-specific indels, though the general sequence composition of the 2 species was highly similar. Fifteen of the 41 sequence polymorphisms identified among the C. quinoa lines were synapomorphic and clearly differentiated the highland and lowland ecotypes. Analysis of the NTS sequences revealed 2 basic NTS sequence classes that likely originated from the 2 allopolyploid subgenomes of C. quinoa. Fluorescence in situ hybridization (FISH) analysis showed that C. quinoa possesses an interstitial and a terminal pair of 5S rRNA loci and only 1 pair of NOR, suggesting a reduction in the number of rRNA loci during the evolution of this species. C. berlandieri exhibited variation in both NOR and 5S rRNA loci without changes in ploidy.Key words: rDNA, NOR, IGS, 5S NTS, FISH, Chenopodium.

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.

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