Tandem repetitive Afa-family sequences from Leymus racemosus and Psathyrostachys juncea (Poaceae)

Genome ◽  
1999 ◽  
Vol 42 (6) ◽  
pp. 1258-1260 ◽  
Author(s):  
Kiyotaka Nagaki ◽  
Masahiro Kishii ◽  
Hisashi Tsujimoto ◽  
Tetsuo Sasakuma
Keyword(s):  
In Situ Hybridization ◽  
Phylogenetic Tree ◽  
Tandem Repeat ◽  
Related Species ◽  
Perennial Species ◽  
Elymus Trachycaulus ◽  
Psathyrostachys Juncea ◽  
Leymus Racemosus ◽  
Tribe Triticeae

Tandem repetitive Afa-family sequences of 340 bp are known to occur in wheat and related species of tribe Triticeae. We isolated six and three Afa-family sequences from Leymus racemosus and Psathyrostachys juncea, respectively, both of which are perennial species. The sequences account for 0.5% and 0.2% of L. racemosus and P. juncea genomes, respectively, and using in situ hybridization were located in subtelomeric and interstitial regions of L. racemosus chromosomes. These sequences are clustered with those of Elymus trachycaulus in the phylogenetic tree. Our findings indicate that the Afa-family sequences have been amplified at least twice in the lineage of L. racemosus, P. juncea, and E. trachycaulus.Key words: Triticeae, Leymus, Psathyrostachys, tandem repeat, Afa-family sequences.

Karyotypes and Distribution of Tandem Repeat Sequences in Brassica nigra Determined by Fluorescence in situ Hybridization

2017 ◽  
Vol 152 (3) ◽  
pp. 158-165 ◽  
Author(s):  
Gui-xiang Wang ◽  
Qun-yan He ◽  
Jiri Macas ◽  
Petr Novák ◽  
Pavel Neumann ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Fluorescence In Situ Hybridization ◽  
Fluorescence Intensity ◽  
Tandem Repeat ◽  
Brassica Nigra ◽  
Metaphase Chromosomes ◽  
Repeat Sequences ◽  
Tandem Repeat Sequences ◽  
Black Mustard

Whole-genome shotgun reads were analyzed to determine the repeat sequence composition in the genome of black mustard, Brassica nigra (L.) Koch. The analysis showed that satellite DNA sequences are very abundant in the black mustard genome. The distribution pattern of 7 new tandem repeats (BnSAT13, BnSAT28, BnSAT68, BnSAT76, BnSAT114, BnSAT180, and BnSAT200) on black mustard chromosomes was visualized using fluorescence in situ hybridization (FISH). The FISH signals of BnSAT13 and BnSAT76 provided useful cytogenetic markers; their position and fluorescence intensity allowed for unambiguous identification of all 8 somatic metaphase chromosomes. A karyotype showing the location and fluorescence intensity of these tandem repeat sequences together with the position of rDNAs and centromeric retrotransposons of Brassica (CRB) was constructed. The establishment of the FISH-based karyotype in B. nigra provides valuable information that can be used in detailed analyses of B. nigra accessions and derived allopolyploid Brassica species containing the B genome.

scholarly journals UNDER-REPLICATION OF RIBOSOMAL CISTRONS IN POLYTENE CHROMOSOMES OF RHYNCHOSCIARA

1974 ◽  
Vol 62 (1) ◽  
pp. 215-222 ◽  
Author(s):  
A. G. Gambarini ◽  
F. J. S. Lara
Keyword(s):  
Salivary Gland ◽  
In Situ Hybridization ◽  
Xenopus Laevis ◽  
Related Species ◽  
Polytene Chromosomes ◽  
Chromosome X ◽  
Heterologous Hybridization ◽  
Ribosomal Cistrons ◽  
Rhynchosciara Americana

DNA preparations obtained from several tissues of Rhynchosciara americana and two related species, R. milleri and R. papaveroi, were hybridized to R. americana rRNA. The percentage of hybridization was found to be higher in tissues with low polyteny than in tissues with high polyteny, suggesting a relationship between the amount of rDNA and the tissue polyteny. This could be explained by under-replication of ribosomal cistrons in polytene cells, such as those from the salivary gland. Only slight tissue-dependent changes in the percentages of hybridization can be observed in heterologous hybridization using Xenopus laevis rRNA. The possibility that these experiments could not detect differences in the amount of ribosomal cistrons among tissues is discussed. The female:male ratio for the percentages of hybridization in the salivary gland of R. americana agrees with the results obtained by in situ hybridization experiments (16, 17) which have shown that the rRNA cistrons are distributed among chromosomes other than chromosome X.

The pericentromeric heterochromatin of the grass Zingeria biebersteiniana (2n = 4) is composed of Zbcen1-type tandem repeats that are intermingled with accumulated dispersedly organized sequences

Genome ◽  
2001 ◽  
Vol 44 (6) ◽  
pp. 955-961 ◽  
Author(s):  
Verity A Saunders ◽  
Andreas Houben
Keyword(s):  
In Situ Hybridization ◽  
Tandem Repeat ◽  
Tandem Repeats ◽  
Repetitive Sequences ◽  
Pericentromeric Region ◽  
Pericentromeric Heterochromatin ◽  
Repeat Family ◽  
Dna Reassociation ◽  
Copy Dna

DNA reassociation and hydroxyapatite chromatography were used to isolate high-copy DNA of the grass Zingeria biebersteiniana (2n = 4). In situ hybridization demonstrated that the DNA isolated was enriched for pericentromere-specific repetitive sequences. One abundant pericentromere-specific component is the differentially methylated tandem-repeat family Zbcen1. Other sequences isolated, Zb46 and Zb47A, are dispersed and display similarity to parts of the gypsy- and copia-like retrotransposable elements of other grasses. In situ hybridization with the copia-like sequence Zb47A resulted in dispersed labelling along the chromosome arms, with a significant signal accumulation in the pericentromeric region of all chromosomes. It is concluded that the pericentromeric heterochromatin of Z. biebersteiniana is composed of members of the Zbcen1 tandem repeat family and that these tandem arrays are intermingled with accumulated putative copia-like retrotransposon sequences. An observed Rabl interphase orientation suggests that the length of the chromosomes rather than the genome size is the determining factor of the Rabl phenomenon.Key Words: centromere, heterochromatin, tandemly repeated DNA, retrotransposon-like, DNA reassociation.

scholarly journals Development of Specific Thinopyrum Cytogenetic Markers for Wheat-Wheatgrass Hybrids Using Sequencing and qPCR Data

2020 ◽  
Vol 21 (12) ◽  
pp. 4495
Author(s):  
Ekaterina Nikitina ◽  
Victoria Kuznetsova ◽  
Pavel Kroupin ◽  
Gennady I. Karlov ◽  
Mikhail G. Divashuk
Keyword(s):  
In Situ Hybridization ◽  
Fluorescence In Situ Hybridization ◽  
Tandem Repeat ◽  
Cytogenetic Study ◽  
Breeding Programs ◽  
Thinopyrum Ponticum ◽  
Model Object ◽  
Wide Hybrids ◽  
Fundamental Values

The cytogenetic study of wide hybrids of wheat has both practical and fundamental values. Partial wheat-wheatgrass hybrids (WWGHs) are interesting as a breeding bridge to confer valuable genes to wheat genome, as well as a model object that contains related genomes of Triticeae. The development of cytogenetic markers is a process that requires long and laborious fluorescence in situ hybridization (FISH) testing of various probes before a suitable probe is found. In this study, we aimed to find an approach that allows to facilitate this process. Based on the data sequencing of Thinopyrum ponticum, we selected six tandem repeat (TR) clusters using RepeatExplorer2 pipeline and designed primers for each of them. We estimated the found TRs’ abundance in the genomes of Triticum aestivum, Thinopyrum ponticum, Thinopyrum intermedium and four different WWGH accessions using real-time qPCR, and localized them on the chromosomes of the studied WWGHs using fluorescence in situ hybridization. As a result, we obtained three tandem repeat cytogenetic markers that specifically labeled wheatgrass chromosomes in the presence of bread wheat chromosomes. Moreover, we designed and tested primers for these repeats, and demonstrated that they can be used as qPCR markers for quick and cheap monitoring of the presence of certain chromosomes of wheatgrass in breeding programs.

scholarly journals The Two Nuclei of Giardia Each Have Complete Copies of the Genome and Are Partitioned Equationally at Cytokinesis

2002 ◽  
Vol 1 (2) ◽  
pp. 191-199 ◽  
Author(s):  
Li Zhi Yu ◽  
C. William Birky ◽  
Rodney D. Adam
Keyword(s):  
In Situ Hybridization ◽  
Cell Division ◽  
Phylogenetic Tree ◽  
Fluorescence In Situ Hybridization ◽  
Giardia Lamblia ◽  
Daughter Cell ◽  
The World ◽  
Single Nucleus

ABSTRACT Giardia lamblia is medically important as a cause of diarrhea and malabsorption throughout the world and is thought to be one of the earliest-branching eukaryotes on a phylogenetic tree. Nevertheless, the mechanisms of inheritance are largely unknown. The trophozoites of Giardia and other diplomonads are interesting in their possession of two nuclei that are identical or similar in several respects. They replicate at nearly the same time, have similar quantities of DNA, and are both transcriptionally active. We used fluorescence in situ hybridization to demonstrate that genes from each of the five chromosomes are found in both nuclei, confirming that each nucleus has at least one complete copy of the genome. This raises a second question. The alleles of a gene in different nuclei are expected to accumulate different mutations, but surprisingly, the degree of heterozygosity in a clone is very low. One possible mechanism for eliminating sequence differences between nuclei is that each daughter cell receives two copies of the same nucleus at cell division. We used trophozoites with a plasmid transfected into a single nucleus to demonstrate that the two nuclei are partitioned equationally at cytokinesis. The mechanism(s) by which homozygosity is maintained will require further investigation.

Phylogenetic distribution of TTAGG telomeric repeats in insects

Genome ◽  
2004 ◽  
Vol 47 (1) ◽  
pp. 163-178 ◽  
Author(s):  
Radmila Frydrychová ◽  
Petr Grossmann ◽  
Pavel Trubac ◽  
Magda Vítková ◽  
František Marec
Keyword(s):  
In Situ Hybridization ◽  
Phylogenetic Tree ◽  
Fluorescence In Situ Hybridization ◽  
Southern Hybridization ◽  
Published Data ◽  
Phylogenetic Distribution ◽  
Telomeric Repeats ◽  
Insect Evolution ◽  
Single Primer

We examined the presence of TTAGG telomeric repeats in 22 species from 20 insect orders with no or inconclusive information on the telomere composition by single-primer polymerase chain reaction with (TTAGG)6 primers, Southern hybridization of genomic DNAs, and fluorescence in situ hybridization of chromosomes with (TTAGG)n probes. The (TTAGG)n sequence was present in 15 species and absent in 7 species. In a compilation of new and published data, we combined the distribution of (TTAGG)n telomere motif with the insect phylogenetic tree. The pattern of phylogenetic distribution of the TTAGG repeats clearly supported a hypothesis that the sequence was an ancestral motif of insect telomeres but was lost repeatedly during insect evolution. The motif was conserved in the "primitive" apterous insect orders, the Archaeognatha and Zygentoma, in the "lower" Neoptera (Plecoptera, Phasmida, Orthoptera, Blattaria, Mantodea, and Isoptera) with the exception of Dermaptera, and in Paraneoptera (Psocoptera, Thysanoptera, Auchenorrhyncha, and Sternorrhyncha) with the exception of Heteroptera. Surprisingly, the (TTAGG)n motif was not found in the "primitive" pterygotes, the Palaeoptera (Ephemeroptera and Odonata). The Endopterygota were heterogeneous for the occurrence of TTAGG repeats. The motif was conserved in Hymenoptera, Lepidoptera, and Trichoptera but was lost in one clade formed by Diptera, Siphonaptera, and Mecoptera. It was also lost in Raphidioptera, whereas it was present in Megaloptera. In contrast with previous authors, we did not find the motif in Neuroptera. Finally, both TTAGG-positive and TTAGG-negative species were reported in Coleoptera. The repeated losses of TTAGG in different branches of the insect phylogenetic tree and, in particular, in the most successful lineage of insect evolution, the Endopterygota, suggest a backup mechanism in the genome of insects that enabled them frequent evolutionary changes in telomere composition.Key words: chromosomes, fluorescence in situ hybridization, FISH, insects, phylogeny, single primer PCR, Southern hybridization, telomere, telomeric repeats.

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