Characterization of chromosomes and localization of the rDNA locus in the aye-aye (Daubentonia madagascariensis)

1990 ◽  
Vol 54 (1-2) ◽  
pp. 43-46 ◽  
Author(s):  
DA. Tagle ◽  
M. Goodman ◽  
DA. Miller
Keyword(s):  
Rdna Locus

scholarly journals Genetic characterization of Strongyloides spp. from captive, semi-captive and wild Bornean orangutans (Pongo pygmaeus) in Central and East Kalimantan, Borneo, Indonesia

Parasitology ◽  
2011 ◽  
Vol 138 (11) ◽  
pp. 1417-1422 ◽  
Author(s):  
E. M. LABES ◽  
N. WIJAYANTI ◽  
P. DEPLAZES ◽  
A. MATHIS
Keyword(s):  
18S Rrna ◽  
Genetic Characterization ◽  
18S Rrna Gene ◽  
Rdna Locus ◽  
Rrna Gene ◽  
Fecal Material ◽  
East Kalimantan ◽  
The One ◽  
Bornean Orangutans

SUMMARYOrangutans (Pongo spp.), Asia's only great apes, are threatened in their survival due to habitat loss, hunting and infections. Nematodes of the genus Strongyloides may represent a severe cause of death in wild and captive individuals. In order to better understand which Strongyloides species/subspecies infect orangutans under different conditions, larvae were isolated from fecal material collected in Indonesia from 9 captive, 2 semi-captive and 9 wild individuals, 18 captive groups of Bornean orangutans and from 1 human working with wild orangutans. Genotyping was done at the genomic rDNA locus (part of the 18S rRNA gene and internal transcribed spacer 1, ITS1) by sequencing amplicons. Thirty isolates, including the one from the human, could be identified as S. fuelleborni fuelleborni with 18S rRNA gene identities of 98·5–100%, with a corresponding published sequence. The ITS1 sequences could be determined for 17 of these isolates revealing a huge variability and 2 main clusters without obvious pattern with regard to attributes of the hosts. The ITS1 amplicons of 2 isolates were cloned and sequenced, revealing considerable variability indicative of mixed infections. One isolate from a captive individual was identified as S. stercoralis (18S rRNA) and showed 99% identity (ITS1) with S. stercoralis sequences from geographically distinct locations and host species. The findings are significant with regard to the zoonotic nature of these parasites and might contribute to the conservation of remaining orangutan populations.

Molecular and cytological characterization of genomic variability in hexaploid wheat 'Lindström'

Genome ◽  
2005 ◽  
Vol 48 (5) ◽  
pp. 895-904
Author(s):  
Pedro Costa-Nunes ◽  
Teresa Ribeiro ◽  
Margarida Delgado ◽  
Leonor Morais-Cecílio ◽  
Neil Jones ◽  
...  
Keyword(s):  
Molecular Weight ◽  
High Molecular Weight ◽  
Large Scale ◽  
Expression Patterns ◽  
5S Rdna ◽  
Rdna Locus ◽  
B Chromosomes ◽  
Addition Line ◽  
Rdna Loci

'Lindström' wheat (AABBDD + rye B chromosomes) was used to study the effects of alien chromatin introgressed into a wheat genetic background, subjecting the wheat genome to a new and transient allopolyploidisation episode. Using this experimental material, we have previously demonstrated that no large-scale chromosomal translocations occurred as a result of the genomic constitution of the addition line. However, we have shown that the presence of a number of rye B chromosomes is associated with changes in the interphase organization and expression patterns of wheat rDNA loci. We have now extended our studies to focus on a further characterization of 'Lindström' 5S rDNA loci and also on high molecular weight glutenin subunit (HMW-GS) patterns. In the process, we have uncovered an unusually large variant of the 5S rDNA locus on wheat chromosome 1B (not to be confused with rye B chromosomes) and 2 novel HMW glutenin y-type alleles. These changes are not directly related to variation in rye B chromosome number in the present material, but the fact that a new, and still segregating, 1Dy HMW-GS gene was identified indicates a recent timescale for its origin. Strikingly, the 'Lindström' 5S rDNA 1B locus integrates a unit sharing 94% homology with a rye 5S rDNA sequence, suggesting the possibility that the wheat locus was colonized by highly homologous rye sequences during the breeding of 'Lindström', when the rye and wheat genomes were together, albeit briefly, in the same nucleus.Key words: Triticum aestivum 'Lindström', allopolyploidisation, 5S rDNA, NTS, high molecular weight glutenin (HMW-GS).

scholarly journals Characterization of Active R2 Retrotransposition in the rDNA Locus ofDrosophila simulans

Genetics ◽  
2005 ◽  
Vol 170 (1) ◽  
pp. 195-205 ◽  
Author(s):  
Xian Zhang ◽  
Thomas H. Eickbush
Keyword(s):  
Rdna Locus

Molecular characterization of trypanosome species and subgroups within subgenus Nannomonas

Parasitology ◽  
1995 ◽  
Vol 111 (3) ◽  
pp. 301-312 ◽  
Author(s):  
L. H. Garside ◽  
W. C. Gibson
Keyword(s):  
Fragment Length Polymorphism ◽  
Genomic Library ◽  
Molecular Level ◽  
Pcr Amplification ◽  
Rflp Analysis ◽  
Rdna Locus ◽  
Kinetoplast Dna ◽  
Banding Patterns ◽  
High Level

SUMMARYRestriction fragment length polymorphism (RFLP) analysis of both genomic and kinetoplast DNA from representative stocks from 3 Trypanosoma congolense subgroups (Savannah, Forest, and Kilifi), T. simiae and T. godfreyi, was used to investigate the relatedness of the different groups within subgenus Nannomonas, DNA probes for β-tubulin and the ribosomal DNA (rDNA) locus were isolated from a T. congolense Savannah genomic library; additional probes were generated by PCR amplification of mini-exon and glutamate and alanine rich protein (GARP) gene sequences. Our results provide evidence that at the molecular level the T. congolense Savannah and Forest groups are the most closely related groups within the subgenus Nannomonas: the Savannah and the Forest groups had mini-exon gene repeats of identical size, which shared homology, had mini-circles of the same size and had a high level of similarity (63%) when the banding patterns produced with a tubulin and rDNA probe were subjected to numerical analysis. All other pairwise combinations of groups have very low percentage similarities of < 10%, suggesting that the Kilifi group trypanosomes, are as distantly related to the T. congolense Savannah and Forest groups as they are to T. simiae or T. godfreyi. The conservation of the GARP gene between the Savannah, Forest and Kilifi groups provides the only evidence linking the Kilifi trypanosomes to the other groups in T. congolense. We find no evidence for the presence of the GARP gene in the T. simiae or T. godfreyi group trypanosomes.

scholarly journals FISH-mapping of the 5S rDNA locus in chili peppers (Capsicum-Solanaceae)

2016 ◽  
Vol 88 (1) ◽  
pp. 117-125 ◽  
Author(s):  
PATRICIA M. AGUILERA ◽  
HUMBERTO J. DEBAT ◽  
MARISEL A. SCALDAFERRO ◽  
DARDO A. MARTÍ ◽  
MAURO GRABIELE
Keyword(s):  
Physical Mapping ◽  
Chromosome Pair ◽  
5S Rdna ◽  
Rdna Locus ◽  
Metacentric Chromosome ◽  
Haploid Genome ◽  
Fish Mapping ◽  
Chili Peppers

ABSTRACT We present here the physical mapping of the 5S rDNA locus in six wild and five cultivated taxa of Capsicum by means of a genus-specific FISH probe. In all taxa, a single 5S locus per haploid genome that persistently mapped onto the short arm of a unique metacentric chromosome pair at intercalar position, was found. 5S FISH signals of almost the same size and brightness intensity were observed in all the analyzed taxa. This is the first cytological characterization of the 5S in wild taxa of Capsicum by using a genus-derived probe, and the most exhaustive and comprehensive in the chili peppers up to now. The information provided here will aid the cytomolecular characterization of pepper germplasm to evaluate variability and can be instrumental to integrate physical, genetic and genomic maps already generated in the genus.

scholarly journals Tracking of quiescence in Leishmania by quantifying the expression of GFP in the ribosomal DNA locus

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Marlene Jara ◽  
Ilse Maes ◽  
Hideo Imamura ◽  
Malgorzata A. Domagalska ◽  
Jean Claude Dujardin ◽  
...  
Keyword(s):  
Molecular Level ◽  
Rdna Locus ◽  
Live Cells ◽  
Brdu Incorporation ◽  
Gfp Reporter ◽  
Gfp Reporter Gene ◽  
First Time ◽  
Quiescent Stage

AbstractUnder stressful conditions some microorganisms adopt a quiescent stage characterized by a reversible non or slow proliferative condition that allows their survival. This adaptation was only recently discovered in Leishmania. We developed an in vitro model and a biosensor to track quiescence at population and single cell levels. The biosensor is a GFP reporter gene integrated within the 18S rDNA locus, which allows monitoring the expression of 18S rRNA (rGFP expression). We showed that rGFP expression decreased significantly and rapidly during the transition from extracellular promastigotes to intracellular amastigotes and that it was coupled in vitro with a decrease in replication as measured by BrdU incorporation. rGFP expression was useful to track the reversibility of quiescence in live cells and showed for the first time the heterogeneity of physiological stages among the population of amastigotes in which shallow and deep quiescent stages may coexist. We also validated the use of rGFP expression as a biosensor in animal models of latent infection. Our models and biosensor should allow further characterization of quiescence at metabolic and molecular level.

scholarly journals Molecular Characterization of Novel Cryptosporidium Fish Genotypes in Edible Marine Fish

2020 ◽  
Vol 8 (12) ◽  
pp. 2014
Author(s):  
Gabriela Certad ◽  
Alireza Zahedi ◽  
Nausicaa Gantois ◽  
Manasi Sawant ◽  
Colette Creusy ◽  
...  
Keyword(s):  
Marine Fish ◽  
Current Knowledge ◽  
Phylogenetic Analyses ◽  
Genetic Distances ◽  
Rdna Locus ◽  
Genotype I ◽  
Separate Species ◽  
Genotype 2 ◽  
European Seas

Current knowledge of Cryptosporidium species/genotypes in marine fish is limited. Following phylogenetic analysis at the 18S rDNA locus, a recent study identified six new genotypes of Cryptosporidium colonizing edible fish found in European seas. Of these, five grouped in a clade together (#Cryptofish 1–5) and one grouped separately (#Cryptofish 7). In the present study, after phylogenetic analyses of #Cryptofish1, #Cryptofish2, #Cryptofish4, #Cryptofish5 and #Cryptofish7 at the actin locus, the presence of two major clades was confirmed. In addition, when possible, longer 18S amplicons were generated. In conclusion, the small genetic distances between these genotypes designated as a novel marine genotype I (#Cryptofish 1-5) suggest that they may be genetic variants of the same species, while the designated novel marine genotype 2 (#Cryptofish 7) is clearly representative of a separate species.

scholarly journals A Genetic Screen for Ribosomal DNA Silencing Defects Identifies Multiple DNA Replication and Chromatin-Modulating Factors

1999 ◽  
Vol 19 (4) ◽  
pp. 3184-3197 ◽  
Author(s):  
Jeffrey S. Smith ◽  
Emerita Caputo ◽  
Jef D. Boeke
Keyword(s):  
Dna Replication ◽  
Ribosomal Dna ◽  
Chromatin Structure ◽  
Position Effect ◽  
Reporter Genes ◽  
Rdna Locus ◽  
Genetic Screen ◽  
Regulator Genes ◽  
Dna Silencing

ABSTRACT Transcriptional silencing in Saccharomyces cerevisiaeoccurs at several genetic loci, including the ribosomal DNA (rDNA). Silencing at telomeres (telomere position effect [TPE]) and the cryptic mating-type loci (HML and HMR) depends on the silent information regulator genes, SIR1,SIR2, SIR3, and SIR4. However, silencing of polymerase II-transcribed reporter genes integrated within the rDNA locus (rDNA silencing) requires only SIR2. The mechanism of rDNA silencing is therefore distinct from TPE andHM silencing. Few genes other than SIR2 have so far been linked to the rDNA silencing process. To identify additional non-Sir factors that affect rDNA silencing, we performed a genetic screen designed to isolate mutations which alter the expression of reporter genes integrated within the rDNA. We isolated two classes of mutants: those with a loss of rDNA silencing (lrs) phenotype and those with an increased rDNA silencing (irs) phenotype. Using transposon mutagenesis,lrs mutants were found in 11 different genes, andirs mutants were found in 22 different genes. Surprisingly, we did not isolate any genes involved in rRNA transcription. Instead, multiple genes associated with DNA replication and modulation of chromatin structure were isolated. We describe these two gene classes, and two previously uncharacterized genes, LRS4 andIRS4. Further characterization of the lrs andirs mutants revealed that many had alterations in rDNA chromatin structure. Several lrs mutants, including those in the cdc17 and rfc1 genes, caused lengthened telomeres, consistent with the hypothesis that telomere length modulates rDNA silencing. Mutations in the HDB (RPD3) histone deacetylase complex paradoxically increased rDNA silencing by aSIR2-dependent, SIR3-independent mechanism. Mutations in rpd3 also restored mating competence selectively to sir3Δ MATα strains, suggesting restoration of silencing at HMR in a sir3mutant background.

scholarly journals Complex characterization of oat (Avena sativa L.) lines obtained by wide crossing with maize (Zea mays L.)

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5107 ◽  
Author(s):  
Edyta Skrzypek ◽  
Tomasz Warzecha ◽  
Angelika Noga ◽  
Marzena Warchoł ◽  
Ilona Czyczyło-Mysza ◽  
...  
Keyword(s):  
Zea Mays ◽  
Avena Sativa ◽  
Meiotic Chromosome ◽  
Rdna Locus ◽  
45S Rdna ◽  
Maize Hybrids ◽  
Complete Set ◽  
Dh Lines

Background The oat × maize addition (OMA) lines are used for mapping of the maize genome, the studies of centromere-specific histone (CENH3), gene expression, meiotic chromosome behavior and also for introducing maize C4 photosynthetic system to oat. The aim of our study was the identification and molecular-cytogenetic characterization of oat × maize hybrids. Methods Oat DH lines and oat × maize hybrids were obtained using the wide crossing of Avena sativa L. with Zea mays L. The plants identified as having a Grande-1 retrotransposon fragment, which produced seeds, were used for genomic in situ hybridization (GISH). Results A total of 138 oat lines obtained by crossing of 2,314 oat plants from 80 genotypes with maize cv. Waza were tested for the presence of maize chromosomes. The presence of maize chromatin was indicated in 66 lines by amplification of the PCR product (500 bp) generated using primers specific for the maize retrotransposon Grande-1. Genomic in situ hybridization (GISH) detected whole maize chromosomes in eight lines (40%). All of the analyzed plants possessed full complement of oat chromosomes. The number of maize chromosomes differed between the OMA lines. Four OMA lines possessed two maize chromosomes similar in size, three OMA—one maize chromosome, and one OMA—four maize chromosomes. In most of the lines, the detected chromosomes were labeled uniformly. The presence of six 45S rDNA loci was detected in oat chromosomes, but none of the added maize chromosomes in any of the lines carried 45S rDNA locus. Twenty of the analyzed lines did not possess whole maize chromosomes, but the introgression of maize chromatin in the oat chromosomes. Five of 66 hybrids were shorter in height, grassy type without panicles. Twenty-seven OMA lines were fertile and produced seeds ranging in number from 1–102 (in total 613). Sixty-three fertile DH lines, out of 72 which did not have an addition of maize chromosomes or chromatin, produced seeds in the range of 1–343 (in total 3,758). Obtained DH and OMA lines were fertile and produced seeds. Discussion In wide hybridization of oat with maize, the complete or incomplete chromosomes elimination of maize occur. Hybrids of oat and maize had a complete set of oat chromosomes without maize chromosomes, and a complete set of oat chromosomes with one to four retained maize chromosomes.

scholarly journals To Repeat or Not to Repeat: Repetitive Sequences Regulate Genome Stability in Candida albicans

Genes ◽  
2019 ◽  
Vol 10 (11) ◽  
pp. 866 ◽  
Author(s):  
Dunn ◽  
Anderson
Keyword(s):  
Candida Albicans ◽  
Genome Stability ◽  
Genome Instability ◽  
Repetitive Sequences ◽  
Gene Families ◽  
Rdna Locus ◽  
Repeat Sequence ◽  
Sequence Evolution ◽  
Adaptive Potential

Genome instability often leads to cell death but can also give rise to innovative genotypic and phenotypic variation through mutation and structural rearrangements. Repetitive sequences and chromatin architecture in particular are critical modulators of recombination and mutability. In Candida albicans, four major classes of repeats exist in the genome: telomeres, subtelomeres, the major repeat sequence (MRS), and the ribosomal DNA (rDNA) locus. Characterization of these loci has revealed how their structure contributes to recombination and either promotes or restricts sequence evolution. The mechanisms of recombination that give rise to genome instability are known for some of these regions, whereas others are generally unexplored. More recent work has revealed additional repetitive elements, including expanded gene families and centromeric repeats that facilitate recombination and genetic innovation. Together, the repeats facilitate C. albicans evolution through construction of novel genotypes that underlie C. albicans adaptive potential and promote persistence across its human host.

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