scholarly journals Regulation of nucleolar dominance in Drosophila melanogaster

2019 ◽  
Author(s):  
Natalie Warsinger-Pepe ◽  
Duojia Li ◽  
Yukiko M. Yamashita
Keyword(s):  
Ribosome Biogenesis ◽  
Chromosome Rearrangement ◽  
Rdna Locus ◽  
Rrna Genes ◽  
Nucleotide Polymorphisms ◽  
Developmentally Regulated ◽  
Nucleolar Dominance ◽  
Interspecies Hybrids ◽  
Sequence Variations ◽  
Rdna Loci

AbstractIn eukaryotic genomes, ribosomal RNA (rRNA) genes exist as tandemly repeated clusters, forming ribosomal DNA (rDNA) loci. Each rDNA locus typically contains hundreds of rRNA genes to meet the high demand of ribosome biogenesis. Nucleolar dominance is a phenomenon, whereby individual rDNA loci are entirely silenced or transcribed, and is believed to be a mechanism to control rRNA dosage. Nucleolar dominance was originally noted to occur in interspecies hybrids, and has been shown to occur within a species (i.e. non-hybrid contexts). However, studying nucleolar dominance within a species has been challenging due to the highly homogenous sequence across rDNA loci. By utilizing single nucleotide polymorphisms (SNPs) between X rDNA vs. Y rDNA loci in males, as well as sequence variations between two X rDNA loci in females, we conducted a thorough characterization of nucleolar dominance throughout development of D. melanogaster. We demonstrate that nucleolar dominance is a developmentally-regulated program, where Y rDNA dominance is established during male embryogenesis, whereas females normally do not exhibit dominance between two X rDNA loci. By utilizing various chromosomal complements (e.g. X/Y, X/X, X/X/Y) and a chromosome rearrangement, we show that Y chromosome rDNA likely contains cis elements that dictate its dominance over the X chromosome rDNA. Our study begins to reveal the mechanisms underlying the selection of rDNA loci for activation/silencing in nucleolar dominance.

scholarly journals Regulation of Nucleolar Dominance in Drosophila melanogaster

Genetics ◽  
2020 ◽  
Vol 214 (4) ◽  
pp. 991-1004 ◽  
Author(s):  
Natalie Warsinger-Pepe ◽  
Duojia Li ◽  
Yukiko M. Yamashita
Keyword(s):  
Drosophila Melanogaster ◽  
Ribosome Biogenesis ◽  
Chromosome Rearrangement ◽  
Rdna Locus ◽  
Rrna Genes ◽  
Nucleotide Polymorphisms ◽  
Developmentally Regulated ◽  
Nucleolar Dominance ◽  
Interspecies Hybrids ◽  
Rdna Loci

In eukaryotic genomes, ribosomal RNA (rRNA) genes exist as tandemly repeated clusters, forming ribosomal DNA (rDNA) loci. Each rDNA locus typically contains hundreds of rRNA genes to meet the high demand of ribosome biogenesis. Nucleolar dominance is a phenomenon whereby individual rDNA loci are entirely silenced or transcribed, and is believed to be a mechanism to control rRNA dosage. Nucleolar dominance was originally noted to occur in interspecies hybrids, and has been shown to occur within a species (i.e., nonhybrid context). However, studying nucleolar dominance within a species has been challenging due to the highly homogenous sequence across rDNA loci. By utilizing single nucleotide polymorphisms between X rDNA and Y rDNA loci in males, as well as sequence variations between two X rDNA loci in females, we conducted a thorough characterization of nucleolar dominance throughout development of Drosophila melanogaster. We demonstrate that nucleolar dominance is a developmentally regulated program that occurs in nonhybrid, wild-type D. melanogaster, where Y rDNA dominance is established during male embryogenesis, whereas females normally do not exhibit dominance between two X rDNA loci. By utilizing various chromosomal complements (e.g., X/Y, X/X, X/X/Y) and a chromosome rearrangement, we show that the short arm of the Y chromosome including the Y rDNA likely contains information that instructs the state of nucleolar dominance. Our study begins to reveal the mechanisms underlying the selection of rDNA loci for activation/silencing in nucleolar dominance in the context of nonhybrid D. melanogaster.

scholarly journals Epigenetic Regulation of Retrotransposons within the Nucleolus of Drosophila

2008 ◽  
Vol 28 (20) ◽  
pp. 6452-6461 ◽  
Author(s):  
Danna G. Eickbush ◽  
Junqiang Ye ◽  
Xian Zhang ◽  
William D. Burke ◽  
Thomas H. Eickbush
Keyword(s):  
Large Scale ◽  
Transcriptional Control ◽  
Rdna Locus ◽  
Rrna Genes ◽  
28S Rrna ◽  
Nucleolar Dominance ◽  
Retrotransposable Elements ◽  
Active Line ◽  
Interspecies Hybrids ◽  
Rdna Loci

ABSTRACT R2 retrotransposable elements exclusively insert into a conserved region of the tandemly organized 28S rRNA genes. Despite inactivating a subset of these genes, R2 elements have persisted in the ribosomal DNA (rDNA) loci of insects for hundreds of millions of years. Controlling R2 proliferation was addressed in this study using lines of Drosophila simulans previously shown to have either active or inactive R2 retrotransposition. Lines with active retrotransposition were shown to have high R2 transcript levels, which nuclear run-on transcription experiments revealed were due to increased transcription of R2-inserted genes. Crosses between R2 active and inactive lines indicated that an important component of this transcriptional control is linked to or near the rDNA locus, with the R2 transcription level of the inactive parent being dominant. Pulsed-field gel analysis suggested that the R2 active and inactive states were determined by R2 distribution within the locus. Molecular and cytological analyses further suggested that the entire rDNA locus from the active line can be silenced in favor of the locus from the inactive line. This silencing of entire rDNA loci represents an example of the large-scale epigenetic control of transposable elements and shares features with the nucleolar dominance frequently seen in interspecies hybrids.

Rates of R1 and R2 Retrotransposition and Elimination From the rDNA Locus of Drosophila melanogaster

Genetics ◽  
2002 ◽  
Vol 162 (2) ◽  
pp. 799-811 ◽  
Author(s):  
César E Pérez-González ◽  
Thomas H Eickbush
Keyword(s):  
Drosophila Melanogaster ◽  
Concerted Evolution ◽  
Inbred Lines ◽  
Rdna Locus ◽  
Mobile Elements ◽  
Rrna Genes ◽  
28S Rrna ◽  
Ltr Retrotransposons ◽  
A Genome ◽  
Rdna Loci

Abstract R1 and R2 elements are non-LTR retrotransposons that insert specifically into the 28S rRNA genes of arthropods. The process of concerted evolution of the rDNA locus should give rise to rapid turnover of these mobile elements compared to elements that insert at sites throughout a genome. To estimate the rate of R1 and R2 turnover we have examined the insertion of new elements and elimination of old elements in the Harwich mutation accumulation lines of Drosophila melanogaster, a set of inbred lines maintained for >350 generations. Nearly 300 new insertion and elimination events were observed in the 19 Harwich lines. The retrotransposition rate for R1 was 18 times higher than the retrotransposition rate for R2. Both rates were within the range previously found for retrotransposons that insert outside the rDNA loci in D. melanogaster. The elimination rates of R1 and R2 from the rDNA locus were similar to each other but over two orders of magnitude higher than that found for other retrotransposons. The high rates of R1 and R2 elimination from the rDNA locus confirm that these elements must maintain relatively high rates of retrotransposition to ensure their continued presence in this locus.

Nucleotide polymorphisms in three genes support host and geographic speciation in tree pathogens belonging toGremmeniellaspp.

2002 ◽  
Vol 80 (11) ◽  
pp. 1151-1159 ◽  
Author(s):  
M Dusabenyagasani ◽  
G Laflamme ◽  
R C Hamelin
Keyword(s):  
North America ◽  
Dna Sequences ◽  
North American ◽  
Abies Balsamea ◽  
Host Specialization ◽  
Rrna Genes ◽  
Nucleotide Polymorphisms ◽  
Group I ◽  
Geographic Separation ◽  
Pinus Spp

We detected nucleotide polymorphisms within the genus Gremmeniella in DNA sequences of β-tubulin, glyceraldehyde phosphate dehydrogenase, and mitochondrial small subunit rRNA (mtSSU rRNA) genes. A group-I intron was present in strains originating from fir (Abies spp.) in the mtSSU rRNA locus. This intron in the mtSSU rRNA locus of strains isolated from Abies sachalinensis (Fridr. Schmidt) M.T. Mast in Asia was also found in strains isolated from Abies balsamea (L.) Mill. in North America. Phylogenetic analyses yielded trees that grouped strains by host of origin with strong branch support. Asian strains of Gremmeniella abietina (Lagerberg) Morelet var. abietina isolated from fir (A. sachalinensis) were more closely related to G. abietina var. balsamea from North America, which is found on spruce (Picea spp.) and balsam fir, and European and North American races of G. abietina var. abietina from pines (Pinus spp.) were distantly related. Likewise, North American isolates of Gremmeniella laricina (Ettinger) O. Petrini, L.E. Petrini, G. Laflamme, & G.B. Ouellette, a pathogen of larch, was more closely related to G. laricina from Europe than to G. abietina var. abietina from North America. These data suggest that host specialization might have been the leading evolutionary force shaping Gremmeniella spp., with geographic separation acting as a secondary factor.Key words: Gremmeniella, geographic separation, host specialization, mitochondrial rRNA, nuclear genes.

scholarly journals Ribosomal DNA localization on Lathyrus species chromosomes by FISH

2020 ◽  
Vol 18 (1) ◽  
Author(s):  
Hoda B. M. Ali ◽  
Samira A. Osman
Keyword(s):  
Genome Mapping ◽  
Chromosome Complement ◽  
5S Rdna ◽  
Rdna Locus ◽  
5S Rrna ◽  
Rrna Genes ◽  
45S Rdna ◽  
Metaphase Chromosomes ◽  
Lathyrus Odoratus ◽  
5S Rrna Genes

Abstract Background Fluorescence In Situ Hybridization (FISH) played an essential role to locate the ribosomal RNA genes on the chromosomes that offered a new tool to study the chromosome structure and evolution in plant. The 45S and 5S rRNA genes are independent and localized at one or more loci per the chromosome complement, their positions along chromosomes offer useful markers for chromosome discriminations. In the current study FISH has been performed to locate 45S and 5S rRNA genes on the chromosomes of nine Lathyrus species belong to five different sections, all have chromosome number 2n=14, Lathyrus gorgoni Parl, Lathyrus hirsutus L., Lathyrus amphicarpos L., Lathyrus odoratus L., Lathyrus sphaericus Retz, Lathyrus incospicuus L, Lathyrus paranensis Burkart, Lathyrus nissolia L., and Lathyrus articulates L. Results The revealed loci of 45S and 5S rDNA by FISH on metaphase chromosomes of the examined species were as follow: all of the studied species have one 45S rDNA locus and one 5S rDNA locus except L. odoratus L., L. amphicarpos L. and L. sphaericus Retz L. have two loci of 5S rDNA. Three out of the nine examined species have the loci of 45S and 5S rRNA genes on the opposite arms of the same chromosome (L. nissolia L., L. amphicarpos L., and L. incospicuus L.), while L. hirsutus L. has both loci on the same chromosome arm. The other five species showed the loci of the two types of rDNA on different chromosomes. Conclusion The detected 5S and 45S rDNA loci in Lathyrus could be used as chromosomal markers to discriminate the chromosome pairs of the examined species. FISH could discriminate only one chromosome pair out of the seven pairs in three species, in L. hirsutus L., L. nissolia L. and L. incospicuus L., and two chromosome pairs in five species, in L. paranensis Burkart, L. odoratus L., L. amphicarpos L., L. gorgoni Parl. and L. articulatus L., while it could discriminate three chromosome pairs in L. sphaericus Retz. these results could contribute into the physical genome mapping of Lathyrus species and the evolution of rDNA patterns by FISH in the coming studies in future.

Detection of a variable number of 18S-5.8S-26S and 5S ribosomal DNA loci by fluorescent in situ hybridization in diploid and tetraploid Arachis species

Genome ◽  
1999 ◽  
Vol 42 (1) ◽  
pp. 52-59 ◽  
Author(s):  
S N Raina ◽  
Y Mukai
Keyword(s):  
In Situ Hybridization ◽  
5S Rdna ◽  
Gene Families ◽  
Ribosomal Gene ◽  
Rrna Genes ◽  
Tetraploid Species ◽  
Arachis Species ◽  
26S Rdna ◽  
Rdna Loci

In order to obtain new information on the genome organization of Arachis ribosomal DNA, more particularly among A. hypogaea and its close relatives, the distribution of the 18S-5.8S-26S and 5S ribosomal RNA gene families on the chromosomes of 21 diploid and tetraploid Arachis species, selected from six of nine taxonomic sections, was analyzed by in situ hybridization with pTa71 (18S-5.8S-26S rDNA) and pTa794 (5S rDNA) clones. Two major 18S-5.8S-26S rDNA loci with intense signals were found in the nucleolus organizer regions (NOR) of each of the diploid and tetraploid species. In addition to extended signals at major NORs, two to six medium and (or) minute-sized signals were also observed. Variability in the number, size, and location of 18S-5.8S-26S sites could generally distinguish species within the same genome as well as between species with different genomes. The use of double fluorescence in situ hybridization enabled us to locate the positions of 5S rRNA genes in relation to the chromosomal location of 18S-5.8S-26S rRNA genes in Arachis chromosomes which were difficult to karyotype. Two or four 5S rDNA loci and 18S-5.8S-26S rDNA loci were generally located on different chromosomes. The tandemly repeated 5S rDNA sites were diagnostic for T and C genomes. In one species, each of B and Am genomes, the two ribosomal gene families were observed to occur at the same locus. Barring A. ipaensis and A. valida, all the diploid species had characteristic centromeric bands in all the 20 chromosomes. In tetraploid species A. hypogaea and A. monticola only 20 out of 40 chromosomes showed centromeric bands. Comparative studies of distribution of the two ribosomal gene families, and occurrence of centromeric bands in only 20 chromosomes of the tetraploid species suggests that A. villosa and A. ipaensis are the diploid progenitors of A. hypogaea and A. monticola. This study excludes A. batizocoi as the B genome donor species for A. hypogaea and A. monticola.Key words: Arachis species, 5S rRNA, 18S-5.8S-26S rRNA, in situ hybridization, evolution.

scholarly journals Phylogenetic Relationship Among Brackishwater Vibrio Species

2020 ◽  
Vol 16 ◽  
pp. 117693432090328
Author(s):  
J Ashok Kumar ◽  
K Vinaya Kumar ◽  
S Avunje ◽  
V Akhil ◽  
S Ashok ◽  
...  
Keyword(s):  
16S Rrna ◽  
Vibrio Vulnificus ◽  
Single Copy ◽  
Vibrio Species ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Nucleotide Polymorphisms ◽  
Orthologous Genes ◽  
Phylogenetic Relations

Vibriosis is regarded as an important disease of penaeid shrimps affecting larvae in hatcheries. Among the Vibrio species, Vibrio parahaemolyticus, Vibrio vulnificus, Vibrio furnissii, Vibrio campbellii, Vibrio harveyi, Vibrio alginolyticus, and Vibrio anguillarum are often associated with diseases in finfish and shellfish of brackishwater ecosystem. Accurate species differentiating methods for the organisms present in an ecosystem are required for precise classification of the species and to take steps for their management. Conventional methods like 16s rRNA phylogeny and multilocus sequence typing (MLST) have often failed to correctly identify Vibrio species. This has necessitated a comprehensive investigation on methodologies available to distinguish Vibrio species associated with brackishwater aquaculture system. To achieve this, 35 whole genomes belonging to 7 Vibrio species were subjected to phylogenetic analysis based on 16s rRNA gene, MLST genes, single-copy orthologous genes, and single-nucleotide polymorphisms. In addition, genome-based similarity indices like average nucleotide identity (ANI) and in silico DNA-DNA hybridization (DDH) were computed as confirmatory tests to verify the phylogenetic relations. There were some misclassifications occurred regarding phylogenetic relations based on 16s rRNA genes and MLST genes, while phylogeny with single-copy orthologous genes produced accurate species-level clustering. Study reveals that the species identification based on whole genome-based estimates or genome-wide variants are more precise than the ones done with single or subset of genes.

scholarly journals Nucleotide polymorphisms upstream of the X-chromosome opsin gene array tune L:M cone ratio

2008 ◽  
Vol 25 (3) ◽  
pp. 265-271 ◽  
Author(s):  
KAREN L. GUNTHER ◽  
JAY NEITZ ◽  
MAUREEN NEITZ
Keyword(s):  
X Chromosome ◽  
Gene Array ◽  
Relative Number ◽  
Opsin Gene ◽  
Binding Affinities ◽  
Nucleotide Polymorphisms ◽  
Relative Probability ◽  
Sequence Variations ◽  
Protein Components ◽  
Genetically Determined

In support of the long-held idea that cone ratio is genetically determined by variation linked to the X-chromosome opsin gene locus, the present study identified nucleotide differences in DNA segments containing regulatory regions of the L and M opsin genes that are associated with significant differences in the relative number of L versus M cones. Specific haplotypes (combinations of genetic differences) were identified that correlated with high versus low L:M cone ratio. These findings are consistent with the biological principle that DNA sequence variations affect binding affinities for protein components of complexes that influence the relative probability that an L versus M opsin gene will be silenced during development, and in turn, produce variation in the proportion of L to M cones.

Chromosomal localization and characterization of rDNA loci in the Brassica A and C genomes

Genome ◽  
1997 ◽  
Vol 40 (4) ◽  
pp. 582-587 ◽  
Author(s):  
R. J. Snowdon ◽  
W. Köhler ◽  
A. Köhler
Keyword(s):  
In Situ Hybridization ◽  
Fluorescence In Situ Hybridization ◽  
Ribosomal Dna ◽  
Diploid Species ◽  
Rdna Locus ◽  
Chromosome Morphology ◽  
Rdna Site ◽  
A Genome ◽  
Rdna Loci

Using fluorescence in situ hybridization, we located ribosomal DNA loci on prometaphase chromosomes of the diploid species Brassica rapa and Brassica oleracea and their amphidiploid Brassica napus. Based on comparisons of chromosome morphology and hybridization patterns, we characterized the individual B. napus rDNA loci according to their presumed origins in the Brassica A and C genomes. As reported in other studies, the sum of rDNA loci observed on B. rapa (AA genome) and B. oleracea (CC genome) chromosomes was one greater than the total number of loci seen in their amphidiploid B. napus (AACC). Evidence is presented that this reduction in B. napus rDNA locus number results from the loss of the smallest A genome rDNA site in the amphidiploid.Key words: Brassica, fluorescence in situ hybridization, ribosomal DNA, rDNA.

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