scholarly journals Chromosomal characterization and physical mapping of the 5S and the 18S-5.8S-25S ribosomal DNA in Helianthus argophyllus, with new data from Helianthus annuus

Genome ◽  
1999 ◽  
Vol 42 (1) ◽  
pp. 110-115 ◽  
Author(s):  
T Cuéllar ◽  
J Orellana ◽  
E Belhassen ◽  
J L Bella
Keyword(s):  
Ribosomal Dna ◽  
Physical Mapping ◽  
Dna Sequences ◽  
5S Rdna ◽  
The Other ◽  
Mitotic Chromosomes ◽  
Introgression Breeding ◽  
C Banding ◽  
Interspecific Differences ◽  
Secondary Constrictions

The characterization of the mitotic chromosomes of Helianthus argophyllus by means of Feulgen staining, Giemsa C-banding, and the usual DNA sequence-specific fluorochromes allows a chromosomal classification of this species, and shows that two kinds of heterochromatin co-exist equilocally in its chromosomes. One type is confined to the pericentromeric areas of all the chromosomes and the other is associated with the secondary constrictions of the satellite chromosomes. This species is evolutionarily very close to H. annuus with which it is involved in introgression breeding programs. Since these two species show no intra- or interspecific differences with the above treatments, we have used C-banding followed by DAPI, chromomycin A3 or Acridine Orange, and the fluorescent in situ hybridization (FISH) with 5S and 18S-25S ribosomal DNA probes to characterize further the chromosomes of both species in an attempt to find practically applicable chromosomal markers. Our results confirm the heterogeneity of the heterochromatin in these species and show that neither its distribution nor its response to distinct fluorochrome treatments allows better discrimination of the chromosomes within or between the species. On the other hand, the 18S-5.8S-25S rDNA arrays are located in the secondary constrictions of the satellited SM7, SM10, and ST13 pairs and the 5S-rDNA genes are interstitially placed on the short arm of the SM7 and SM11 chromosomes in both species. This permits these chromosomes to be distinguished and provides markers which may be helpful for further physical mapping of DNA sequences in these species.Key words: chromosome banding, sunflower cytogenetics, heterochromatin, ribosomal DNA mapping, FISH.

Sequence characterization and phylogenetic analysis of the 5S ribosomal DNA in species of the family Batrachoididae

Genome ◽  
2010 ◽  
Vol 53 (9) ◽  
pp. 723-730 ◽  
Author(s):  
María Úbeda-Manzanaro ◽  
Manuel Alejandro Merlo ◽  
José Luis Palazón ◽  
Carmen Sarasquete ◽  
Laureana Rebordinos
Keyword(s):  
Phylogenetic Analysis ◽  
Ribosomal Dna ◽  
5S Rdna ◽  
Purifying Selection ◽  
The Other ◽  
Fish Family ◽  
Sequence Characterization ◽  
Rdna Sequences ◽  
The Family ◽  
Clear Differentiation

5S ribosomal DNA (rDNA) sequences were analyzed in four species belonging to different genera of the fish family Batrachoididae. Several 5S rDNA variants differing in their non-transcribed spacers (NTSs) were found and were grouped into two main types. Two species showed both types of 5S rDNA, whereas the other two species showed only one type. One type of NTS of Amphichthys cryptocentrus showed a high polymorphism due to several deletions and insertions, and phylogenetic analysis showed a between-species clustering of this type of NTS in Amphichthys cryptocentrus. These results suggest a clear differentiation in the model of 5S rDNA evolution of these four species of Batrachoididae, which appear to have been subject to processes of concerted evolution and birth-and-death evolution with purifying selection.

Genomic organization and evolution of the 5S ribosomal DNA in the ancient fish sturgeon

Genome ◽  
2005 ◽  
Vol 48 (1) ◽  
pp. 18-28 ◽  
Author(s):  
Francisca Robles ◽  
Roberto de la Herrán ◽  
Arne Ludwig ◽  
Carmelo Ruiz Rejón ◽  
Manuel Ruiz Rejón ◽  
...  
Keyword(s):  
Gene Conversion ◽  
Ribosomal Dna ◽  
5S Rdna ◽  
Rrna Genes ◽  
Coding Region ◽  
Coding Regions ◽  
Interspecific Differences ◽  
Sturgeon Species ◽  
Selective Forces ◽  
5S Gene

Ribosomal DNA in sturgeon is informative when analyzed at the molecular level because it bears unique characteristics that are, to a certain extent, ancestral within vertebrates. In this paper, we examine the structure and the molecular evolution of the 5S ribosomal DNA (rDNA) region in 13 sturgeon species, comparing both the 5S ribosomal RNA (rRNA) genes and the non-transcribed spacer (NTS) sequences between the coding regions. We have found that different NTS and 5S gene variants are intermixed in the 5S rDNA arrays of the different sturgeon species and that all variants are ancestral, having been maintained over many millions of years. Using predictive models, we have found similar levels of sequence diversity in the coding regions, as well as in the non-coding region, but fixed interspecific differences are underrepresented for 5S genes. However, contrary to the expectations, we have not found fixed differences between NTS sequences when comparing many pairs of species. Specifically, when they belong to the same phylogeographic clade of the four into which the sturgeon is divided, but fixation of mutations and divergence is found between species belonging to different phylogeographic clades. Our results suggest that the evolution of the two parts of the 5S rDNA region cannot be explained exclusively as the outcome of a balance between mutational, homogenizing (i.e., gene conversion as a predominant force in sturgeon), and selective forces. Rather, they suggest that other factors (i.e., hybridization) might be superimposed over those forces and thus could to some extent be masking their effects.Key words: sturgeon, 5S rDNA, NTS sequence, 5S gene, concerted evolution, sequence homogenization, gene conversion, hybridization.

scholarly journals Ribosomal DNA revealed an extensive role of allopolyploidy in the radiation of Ulex L

2021 ◽  
Author(s):  
João P. Fonseca ◽  
Ana Pereira ◽  
Joana I. Robalo ◽  
Carlos Neto ◽  
José C. Costa
Keyword(s):  
Ribosomal Dna ◽  
Dna Markers ◽  
Intergenic Spacer ◽  
5S Rdna ◽  
The Other ◽  
Phylogenetic Position ◽  
Early Hypothesis ◽  
Center Of Diversity ◽  
Suitable Marker

AbstractWe studied the phylogeny of Ulex L., a genus of spiny legumes, which its center of diversity in the Iberian Peninsula, using ribosomal DNA markers (rDNA), namely ETS, 5.8S and ITS (45S), and 5S intergenic spacer regions. One of the main findings was the presence of very different haplotypes in 5S-IGS genes and, to a less extent, in ETS and ITS, in seven polyploid taxa. We interpreted these results as an indication of hybrid origins and proposed allopolyploidy for U. argenteus ssp. subsericeus, U. australis ssp. australis, U. australis ssp. welwitschianus, U. densus, U. europaeus ssp. europaeus, U. europaeus ssp. latebracteatus, and U. jussiaei. These results reinforce an early hypothesis which stated that the radiation of Ulex occurred mainly by polyplodization.Phylograms showed two main clades, one grouping the hydrophilic U. gallii, U. breoganii and U. minor, and the other grouping the southern, xerophytic, taxa. The putative allopolyploids showed haplotypes, which grouped in both clades, indicating that allopolyploidy, occurred through hybridization from these hydrophilic and xerophytic lineages.The phylogenetic position of U. micranthus is not certain and it is discussed. The 5S-IGS showed to retain more polymorphisms than ETS gene or ITS markers. This result is compatible with the hypothesis that 5S rDNA region is less vulnerable to inter-loci concerted evolution than 45S, providing a more suitable marker for reconstructing histories of allopolyploid species. We discuss the taxonomic consequences of these results.

scholarly journals Prins and C-PRINS: Promising tools for the physical mapping of the lupin genome

2007 ◽  
Vol 12 (1) ◽  
Author(s):  
Anna Kaczmarek ◽  
Barbara Naganowska ◽  
Bogdan Wolko
Keyword(s):  
Vicia Faba ◽  
Physical Mapping ◽  
Dna Sequences ◽  
Molecular Cytogenetics ◽  
Chromosome Identification ◽  
Prins Reaction ◽  
Mitotic Chromosomes ◽  
Coding Sequences ◽  
Dna Labeling

AbstractTwo molecular cytogenetics methods, PRINS (primed in situ DNA labeling) and C-PRINS (cycling PRINS), were optimized for the physical mapping of several types of DNA sequences on the mitotic chromosomes of the narrow-leafed lupin (Lupinus angustifolius L.). The fragment of the FokI element from Vicia faba was localised by indirect PRINS reaction. Two other sequences, fragments of the coding sequences of L. luteus and of L. angustifolius, were localised by indirect C-PRINS. These techniques are faster and more sensitive than FISH, and they allowed the mapping of short DNA fragments. The data obtained shows that both types of PRINS are valuable tools for chromosome identification in lupin.

The Organization of Repetitive DNA in the Genomes of Amazonian Lizard Species in the Family Teiidae

2015 ◽  
Vol 147 (2-3) ◽  
pp. 161-168 ◽  
Author(s):  
Natalia D.M. Carvalho ◽  
Vanessa S.S. Pinheiro ◽  
Edson J. Carmo ◽  
Leonardo G. Goll ◽  
Carlos H. Schneider ◽  
...  
Keyword(s):  
Repetitive Dna ◽  
Dna Sequences ◽  
Genome Organization ◽  
Repetitive Sequences ◽  
5S Rdna ◽  
Distinct Pattern ◽  
Structural Function ◽  
Mitotic Chromosomes ◽  
Lizard Species ◽  
Evolutionary Diversification

Repetitive DNA is the largest fraction of the eukaryote genome and comprises tandem and dispersed sequences. It presents variations in relation to its composition, number of copies, distribution, dynamics, and genome organization, and participates in the evolutionary diversification of different vertebrate species. Repetitive sequences are usually located in the heterochromatin of centromeric and telomeric regions of chromosomes, contributing to chromosomal structures. Therefore, the aim of this study was to physically map repetitive DNA sequences (5S rDNA, telomeric sequences, tropomyosin gene 1, and retroelements Rex1 and SINE) of mitotic chromosomes of Amazonian species of teiids (Ameiva ameiva, Cnemidophorus sp. 1, Kentropyx calcarata, Kentropyx pelviceps, and Tupinambis teguixin) to understand their genome organization and karyotype evolution. The mapping of repetitive sequences revealed a distinct pattern in Cnemidophorus sp. 1, whereas the other species showed all sequences interspersed in the heterochromatic region. Physical mapping of the tropomyosin 1 gene was performed for the first time in lizards and showed that in addition to being functional, this gene has a structural function similar to the mapped repetitive elements as it is located preferentially in centromeric regions and termini of chromosomes.

scholarly journals Molecular systematics of the Phyllachorales (ascomycota, fungi) based on 18S ribosomal DNA sequences

2003 ◽  
Vol 46 (3) ◽  
pp. 315-322 ◽  
Author(s):  
Denise Wanderlei-Silva ◽  
Eduardo Ramalho Neto ◽  
Richard Hanlin
Keyword(s):  
Molecular Systematics ◽  
Ribosomal Dna ◽  
Dna Sequences ◽  
18S Rdna ◽  
18S Rrna ◽  
18S Rrna Gene ◽  
The Other ◽  
Maximum Parsimony Analysis ◽  
Rrna Gene ◽  
Parsimony Analysis

In order to evaluate the monophyly of the Phyllachorales from a molecular standpoint and elucidate its phylogenetic relationships with other orders, a segment of the 18S rRNA gene from several representatives of the Phyllachorales, including species of Glomerella, Phyllachora, Coccodiella (=Coccostroma), Sphaerodothis, Ophiodothella, as well as Magnaporthe was sequenced. Maximum Parsimony analysis revealed that the Phyllachorales was a polyphyletic assemblage of taxa. None of the other members of the Phyllachorales, which produced either a clypeus or stroma, clustered with Glomerella. Of the taxa examined, was Coccodiella the closest relative of Phyllachora. Magnaporthe was closely related to the Diaporthales. Our 18S rDNA data highly supported Glomerella being accommodated in a separate family.

Parental origin and genome evolution of several Eurasian hexaploid species of Chenopodium (Chenopodiaceae)

Phytotaxa ◽  
2019 ◽  
Vol 392 (3) ◽  
pp. 163 ◽  
Author(s):  
BOZENA KOLANO ◽  
JAMIE McCANN ◽  
MAJA OSKĘDRA ◽  
MARCELINA CHRAPEK ◽  
MAGDALENA ROJEK ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Analyses ◽  
5S Rdna ◽  
The Other ◽  
Parental Origin ◽  
B Genome ◽  
Rdna Loci ◽  
History Of ◽  
35S Rdna

Hybridization and polyploidization appear to be ubiquitous in the evolution of Chenopodium s.s., but the origin and the evolutionary history of the polyploid chenopods is still poorly understood. Phylogenetic analyses of DNA sequences of nrITS, four plastid regions, and 5S rDNA spacer region (NTS) of five Eurasian hexaploid chenopods (2n = 6x = 54), C. album, C. giganteum, C. pedunculare C. formosanum and C. opulifolium, and their diploid and tetraploid relatives as well as genomic in situ hybridization (GISH) indicate their allohexaploid origin. The origin of all the analyzed hexaploids have been inferred to have involved B-genome diploid. The identity of the other parent/parents is more elusive. In the case of C. album, C. giganteum and C. pedunculare the second maternal parent seems to be similar to extant C. strictum or C. striatiforme or Asian diploids (e.g. C. acuminatum). In genomes of allohexaploid C. album, C. giganteum and C. pedunculare half of the rDNA were located in the chromosomes of B-subgenome. The remaining rDNA loci were placed in chromosomes originating from the other parent/parents. Although 35S rDNA loci inherited from two parental species seems to be present in these hexaploids, only one ribotype of nrITS was detected.

Distribution of highly repeated DNA sequences in species of the genus Lens Miller

Genome ◽  
2003 ◽  
Vol 46 (6) ◽  
pp. 1118-1124 ◽  
Author(s):  
Incoronata Galasso
Keyword(s):  
Dna Sequences ◽  
Lens Culinaris ◽  
Repetitive Sequences ◽  
5S Rdna ◽  
Chromosome Identification ◽  
Mitotic Chromosomes ◽  
Genomic Relationships ◽  
Lens Nigricans ◽  
25S Rdna

Multiple-target fluorescence in situ hybridization (FISH) was applied on mitotic chromosomes of seven Lens taxa using two highly repetitive sequences (pLc30 and pLc7) isolated from the cultivated lentil and the multigene families for the 18S–5.8S–25S (pTa71) and 5S rRNA (pTa794) from wheat simultaneously as probes. The number and location of pLc30 and pLc7 sites on chromosomes varied markedly among the species, whereas the hybridization pattern of 5S rDNA and 18S–5.8S–25S rDNA was less variable. In general, each species showed a typical FISH karyotype and few differences were observed among accessions belonging to the same species, except for the accessions of Lens odemensis. The most similar FISH karyotype to the cultivated lentil is that of Lens culinaris subsp. orientalis, whereas Lens nigricans and Lens tomentosus are the two species that showed the most divergent FISH patterns compared with all taxa for number and location of pLc30 and 18S–5.8S–25S rDNA sites.Key words: chromosome identification, comparative FISH karyotype, wild Lens species, genomic relationships.

Phylogenetic studies on nuclear large subunit ribosomal DNA sequences of smut fungi and related taxa

1997 ◽  
Vol 75 (12) ◽  
pp. 2045-2056 ◽  
Author(s):  
Dominik Begerow ◽  
Robert Bauer ◽  
Franz Oberwinkler
Keyword(s):  
Molecular Phylogeny ◽  
Ribosomal Dna ◽  
Dna Sequences ◽  
Large Subunit ◽  
The Other ◽  
Lsu Rdna ◽  
Smut Fungi ◽  
Neighbor Joining ◽  
Phylogenetic Studies ◽  
Key Words Basidiomycete

To show phylogenetic relationships among the smut fungi and their relatives, we sequenced a part of the nuclear LSU rDNA from 43 different species of smut fungi and related taxa. Our data were combined with the existing sequences of seven further smut fungi and 17 other basidiomycetes. Two sets of sequences were analyzed. The first set with a representative number of simple septate basidiomycetes, complex septate basidiomycetes, and smut fungi was analyzed with the neighbor-joining method to estimate the general topology of the basidiomycetes phylogeny and the positions of the smut fungi. The tripartite subclassification of the basidiomycetes into the Urediniomycetes, Ustilaginomycetes, and Hymenomycetes was confirmed and two groups of smut fungi appeared. The smut genera Aurantiosporium, Microbotryum, Fulvisporium, and Ustilentyloma are members of the Urediniomycetes, whereas the other smut species tested are members of the Ustilaginomycetes with Entorrhiza as a basal taxon. The second set of 46 Ustilaginomycetes was analyzed using the neighbor-joining and the maximum parsimony methods to show the inner topology of the Ustilaginomycetes. The results indicated three major lineages among Ustilaginomycetes corresponding to the Entorrhizomycetidae, Exobasidiomycetidae, and Ustilaginomycetidae. The Entorrhizomycetidae are represented by Entorrhiza species. The Ustilaginomycetidae contain at least two groups, the Urocystales and Ustilaginales. The Exobasidiomycetidae include five orders, i.e., Doassansiales, Entylomatales, Exobasidiales, Georgefischeriales, and Tilletiales, and Graphiola phoenicis and Microstroma juglandis. Our results support a classification mainly based on ultrastructure. The description of the Glomosporiaceae is emended. The Doassansiopsaceae, Melanotaeniaceae, and Urocystaceae are proposed as new taxa. Key words: basidiomycete systematics, LSU rDNA, Microbotryales, molecular phylogeny, smut fungi, Ustilaginomycetes.

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