TAS49—a dispersed repetitive sequence isolated from subtelomeric regions of Nicotiana tomentosiformis chromosomes

Genome ◽  
2000 ◽  
Vol 43 (2) ◽  
pp. 273-284
Author(s):  
Mirka Horáková ◽  
Jirí Fajkus
Keyword(s):  
Dna Sequences ◽  
Repetitive Sequence ◽  
Repetitive Sequences ◽  
Reading Frame ◽  
Diploid Genome ◽  
Nicotiana Tomentosiformis ◽  
Dna Repeat ◽  
The Family ◽  
A Subunit ◽  
Subtelomeric Regions

We have isolated and characterized a new repetitive sequence, TAS49, from terminal restriction fragments of Nicotiana tomentosiformis genomic DNA by means of a modified vectorette approach. The TAS49 was found directly attached to telomeres of N. tabacum and one of its ancestors, N. tomentosiformis, and also at inner chromosome locations. No association with telomeres was detected neither in N. otophora nor in the second tobacco ancestor, N. sylvestris. PCR and Southern hybridization reveal similarities in the arrangement of TAS49 on the chromosomes of 9 species of the genus Nicotiana, implying its occurrence as a subunit of a conserved complex DNA repeat. TAS49 belongs to the family of dispersed repetitive sequences without features of transposons. The copy number of TAS49 varies widely in the genomes of 8 species analyzed being lowest in N. sylvestris, with 3300 copies per diploid genome. In N. tomentosiformis, TAS49 forms about 0.56% of the diploid genome, corresponding to 17 400 copies. TAS49 units are about 460 bp long and show about 90% of mutual homology, but no significant homology to DNA sequences deposited in GenBank and EMBL. Although genomic clones of TAS49 contain an open reading frame encoding a proline-rich protein similar to plant extensins, no mRNA transcript was detected. TAS49 is extensively methylated at CpG and CpNpG sites and its chromatin forms nucleosomes phased with a 170 ± 8 bp periodicity. Key words: repetitive DNA sequence, subtelomere, plant, Nicotiana.

Karyotype Evolution and Distinct Evolutionary History of the W Chromosomes in Swallows (Aves, Passeriformes)

2019 ◽  
Vol 158 (2) ◽  
pp. 98-105 ◽  
Author(s):  
Suziane A. Barcellos ◽  
Rafael Kretschmer ◽  
Marcelo S. de Souza ◽  
Alice L. Costa ◽  
Tiago M. Degrandi ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Evolutionary History ◽  
Karyotype Evolution ◽  
Sex Chromosome ◽  
Repetitive Sequences ◽  
Z Chromosome ◽  
W Chromosome ◽  
The Family ◽  
Agnor Staining ◽  
History Of

As in many other bird groups, data on karyotype organization and distribution of repetitive sequences are also lacking in species belonging to the family Hirundinidae. Thus, in the present study, we analyzed the karyotypes of 3 swallow species (Progne tapera, Progne chalybea, and Pygochelidon cyanoleuca) by Giemsa and AgNOR staining, C-banding, and FISH with 11 microsatellite sequences. The diploid chromosome number was 2n = 76 in all 3 species, and NORs were observed in 2 chromosome pairs each. The microsatellite distribution pattern was similar in both Progne species, whereas P. cyanoleuca presented a distinct organization. These repetitive DNA sequences were found in the centromeric, pericentromeric, and telomeric regions of the macrochromosomes, as well as in 2 interstitial blocks in the W chromosome. Most microchromosomes had mainly telomeric signals. The Z chromosome displayed 1 hybridization signal in P. tapera but none in the other species. In contrast, the W chromosome showed an accumulation of different microsatellite sequences. The swallow W chromosome is larger than that of most Passeriformes. The observed enlargement in chromosome size might be explained by these high amounts of repetitive sequences. In sum, our data highlight the significant role that microsatellite sequences may play in sex chromosome differentiation.

scholarly journals Characterization of the Plasmid Encoded Virulence Region pat-1 of Phytopathogenic Clavibacter michiganensis subsp. michiganensis

1997 ◽  
Vol 10 (2) ◽  
pp. 195-206 ◽  
Author(s):  
Jens Dreier ◽  
Dietmar Meletzus ◽  
Rudolf Eichenlaub
Keyword(s):  
Structural Gene ◽  
Dna Sequences ◽  
Repetitive Sequence ◽  
Transcription Initiation ◽  
Serine Proteases ◽  
Tandem Repeats ◽  
Sequence Motif ◽  
Clavibacter Michiganensis ◽  
Reading Frame ◽  
Clavibacter Michiganensis Subsp

The tomato pathogen Clavibacter michiganensis subsp. michiganensis NCPPB382, causing bacterial wilt and canker, harbors two plasmids, pCM1 (27.5 kb) and pCM2 (72 kb), carrying genes involved in virulence. The region of plasmid pCM2 encoding the pathogenicity locus pat-1 was mapped by deletion analysis and complementation studies to a 1.5-kb BglII/SmaI DNA fragment. Introduction of the pat-1 region into endophytic, plasmid-free isolates of C. michiganensis subsp. michiganensis converted these bacteria into virulent pathogens. Based on the nucleotide sequence of the pat-1 region, an open reading frame (ORF1) can be predicted, coding for a protein of 280 amino acids and 29.7 kDa with homology to serine proteases. Introduction of a frame-shift mutation in ORF1 leads to a loss of the pathogenic phenotype. Northern (RNA) hybridizations identified an 1.5-knt transcript of the pat-1 structural gene. The site of transcription initiation was mapped by primer extension and a typical -10/-35 region was located with significant homology to the consensus Escherichia coli σ70 and Bacillus subtilis σ43 promoters. Downstream of the pat-1 structural gene, a peculiar repetitive sequence motif (pat-1rep) is located, consisting of 20 direct tandem repeats preceded by a run of 14 guanosine residues. DNA sequences homologous to pat-1rep were isolated and characterized from four virulent C. michiganensis subsp. mich-iganensis strains exhibiting a high extent of structural conservation. The deletion of this repetitive sequence reduced virulence significantly but did not lead to a complete loss of the virulence phenotype.

Variations of two repetitive DNA sequences in several Triticeae genomes revealed by polymerase chain reaction and sequencing

Genome ◽  
1995 ◽  
Vol 38 (6) ◽  
pp. 1221-1229 ◽  
Author(s):  
Richard R.-C. Wang ◽  
Jun-Zhi Wei
Keyword(s):  
Repetitive Dna ◽  
Dna Sequences ◽  
Repetitive Sequence ◽  
Repetitive Sequences ◽  
Evolutionary Significance ◽  
Repetitive Dna Sequences ◽  
Chain Reaction ◽  
Pcr Product ◽  
Polymerase Chain ◽  
Thinopyrum Elongatum

Genomes of Triticeae were analyzed using PCR with synthesized primers that were based on two published repetitive DNA sequences, pLeUCD2 (pLe2) and l-E6hcII-l (L02368), which were originally isolated from Thinopyrum elongatum. The various genomes produced a 240 bp PCR product having high homology with the repetitive DNA pLe2. The PCR fragments produced from different genomes differed mainly in amplification quantity and in base composition at 89 variable sites. On the other hand, amplification products from the primer set for L02368 were of different sizes and nucleotide sequences. These results show that the two repetitive DNA sequences have different evolutionary significance. pLe2 is present in all genomes tested, although differences in copy number and nucleotide sequence are notable. L02368 is more genome specific, i.e., fewer genomes possess this family of repetitive sequences. It was concluded that the repetitive sequence pLe2 family is an ancient one that existed in the progenitor genome prior to divergence of annual and perennial genomes. In contrast, sequences similar to L02368 have only evolved following genome divergence.Key words: repetitive sequence, PCR, genome, evolution, Thinopyrum, Triticeae.

Genus-specific localization of the TaiI family of tandem-repetitive sequences in either the centromeric or subtelomeric regions in Triticeae species (Poaceae) and its evolution in wheat

Genome ◽  
2002 ◽  
Vol 45 (5) ◽  
pp. 946-955 ◽  
Author(s):  
Masahiro Kishii ◽  
Hisashi Tsujimoto
Keyword(s):  
Common Wheat ◽  
Dna Sequences ◽  
Repetitive Sequences ◽  
Chromosomal Distribution ◽  
B Genome ◽  
Triticeae Species ◽  
Copy Numbers ◽  
Specific Localization ◽  
Mixed Origin ◽  
Subtelomeric Regions

The TaiI family sequences are classified as tandem repetitive DNA sequences present in the genome of tribe Triticeae, and are localized in the centromeric regions of common wheat, but in the subtelomeric heterochromatic regions of Leymus racemosus and related species. In this study, we investigated the chromosomal distribution of TaiI family sequences in other Triticeae species. The results demonstrated a centromeric localization in genera Triticum and Aegilops and subtelomeric localization in other genera, thus showing a genus-dependent localization of TaiI family sequences in one or the other region. The copy numbers of TaiI family sequences in species in the same genus varied greatly, whether in the centromeric or subtelomeric regions (depending on genus). We also examined the evolution of TaiI family sequences during polyploidization of hexaploid common wheat. A comparison of chromosomal locations of the major TaiI family signals in common wheat and in its ancestral species suggested that the centromeric TaiI family sequences in common wheat were inherited from its ancestors with little modification, whereas a mixed origin for the B genome of common wheat was indicated.Key words: TaiI family, tandem repeat, centromere, subtelomere, Triticeae.

Species-diagnostic and species-specific DNA sequences evenly distributed throughout pine and spruce chromosomes

Genome ◽  
2010 ◽  
Vol 53 (10) ◽  
pp. 769-777 ◽  
Author(s):  
Melanie Mehes-Smith ◽  
Paul Michael ◽  
Kabwe Nkongolo
Keyword(s):  
Dna Sequences ◽  
Random Amplified Polymorphic Dna ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Pinus Monticola ◽  
The Family ◽  
Species Specific ◽  
Rapd And Issr ◽  
Specific Sequences

Genome organization in the family Pinaceae is complex and largely unknown. The main purpose of the present study was to develop and physically map species-diagnostic and species-specific molecular markers in pine and spruce. Five RAPD (random amplified polymorphic DNA) and one ISSR (inter-simple sequence repeat) species-diagnostic or species-specific markers for Picea mariana , Picea rubens , Pinus strobus , or Pinus monticola were identified, cloned, and sequenced. In situ hybridization of these sequences to spruce and pine chromosomes showed the sequences to be present in high copy number and evenly distributed throughout the genome. The analysis of centromeric and telomeric regions revealed the absence of significant clustering of species-diagnostic and species-specific sequences in all the chromosomes of the four species studied. Both RAPD and ISSR markers showed similar patterns.

scholarly journals IIMLP: integrated information-entropy-based method for LncRNA prediction

2021 ◽  
Vol 22 (S3) ◽  
Author(s):  
Junyi Li ◽  
Huinian Li ◽  
Xiao Ye ◽  
Li Zhang ◽  
Qingzhe Xu ◽  
...  
Keyword(s):  
Machine Learning ◽  
Dna Sequences ◽  
Information Entropy ◽  
Area Under The Curve ◽  
Prediction Method ◽  
Machine Learning Algorithms ◽  
Reading Frame ◽  
Non Coding Rna ◽  
The One ◽  
Long Non Coding Rna

Abstract Background The prediction of long non-coding RNA (lncRNA) has attracted great attention from researchers, as more and more evidence indicate that various complex human diseases are closely related to lncRNAs. In the era of bio-med big data, in addition to the prediction of lncRNAs by biological experimental methods, many computational methods based on machine learning have been proposed to make better use of the sequence resources of lncRNAs. Results We developed the lncRNA prediction method by integrating information-entropy-based features and machine learning algorithms. We calculate generalized topological entropy and generate 6 novel features for lncRNA sequences. By employing these 6 features and other features such as open reading frame, we apply supporting vector machine, XGBoost and random forest algorithms to distinguish human lncRNAs. We compare our method with the one which has more K-mer features and results show that our method has higher area under the curve up to 99.7905%. Conclusions We develop an accurate and efficient method which has novel information entropy features to analyze and classify lncRNAs. Our method is also extendable for research on the other functional elements in DNA sequences.

Comparative Cytogenetics in Four Leptodactylus Species (Amphibia, Anura, Leptodactylidae): Evidence of Inner Chromosomal Diversification in Highly Conserved Karyotypes

2021 ◽  
pp. 1-11
Author(s):  
David S. da Silva ◽  
Heriberto F. da Silva Filho ◽  
Marcelo B. Cioffi ◽  
Edivaldo H.C. de Oliveira ◽  
Anderson J.B. Gomes
Keyword(s):  
18S Rdna ◽  
Repetitive Sequences ◽  
Molecular Cytogenetics ◽  
Comparative Cytogenetics ◽  
The Family ◽  
Agnor Staining ◽  
Dna Elements ◽  
Conventional Cytogenetics ◽  
Species Specific ◽  
Repetitive Dna Elements

With 82 species currently described, the genus <i>Leptodactylus</i> is the most diverse and representative one in the family Leptodactylidae. Concerning chromosomal organization, this genus represents an interesting and underexplored group since data from molecular cytogenetics are incipient, and little is known about the organization and distribution of repetitive DNA elements in the karyotypes. In this sense, this study aimed at providing a comparative analysis in 4 <i>Leptodactylus</i> species (<i>L. macrosternum, L. pentadactylus, L. fuscus,</i> and <i>Leptodactylus</i> cf<i>. podicipinus</i>), combining conventional cytogenetics (Giemsa staining, C-banding, and AgNOR staining) and mapping of molecular markers (18S rDNA, telomeric and microsatellite probes), to investigate mechanisms underlying their karyotype differentiation process. The results showed that all species had karyotypes with 2n = 22 and FN = 44, except for <i>Leptodactylus</i> cf. <i>podicipinus</i> which presented FN = 36. The 18S rDNA was observed in pair 8 of all analyzed species (corresponding to pair 4 in <i>L. pentadactylus</i>), coinciding with the secondary constrictions and AgNOR staining. FISH with microsatellite DNA probes demonstrated species-specific patterns, as well as an association of these repetitive sequences with constitutive heterochromatin blocks and ribosomal DNA clusters, revealing the dynamics of microsatellites in the genome of the analyzed species. In summary, our data demonstrate an ongoing process of genomic divergence inside species with almost similar karyotype, driven most likely by a series of pericentric inversions, followed by differential accumulation of repetitive sequences.

An integrative redescription of Hypsibius dujardini (Doyère, 1840), the nominal taxon for Hypsibioidea (Tardigrada: Eutardigrada)

Zootaxa ◽  
2018 ◽  
Vol 4415 (1) ◽  
pp. 45 ◽  
Author(s):  
PIOTR GĄSIOREK ◽  
DANIEL STEC ◽  
WITOLD MOREK ◽  
ŁUKASZ MICHALCZYK
Keyword(s):  
Dna Sequences ◽  
Evolutionary Biology ◽  
Model Organism ◽  
Laboratory Strain ◽  
Sensu Stricto ◽  
Nominal Species ◽  
28S Rrna ◽  
The Family ◽  
The 19Th Century ◽  
Hypsibius Dujardini

A laboratory strain identified as “Hypsibius dujardini” is one of the best studied tardigrade strains: it is widely used as a model organism in a variety of research projects, ranging from developmental and evolutionary biology through physiology and anatomy to astrobiology. Hypsibius dujardini, originally described from the Île-de-France by Doyère in the first half of the 19th century, is now the nominal species for the superfamily Hypsibioidea. The species was traditionally considered cosmopolitan despite the fact that insufficient, old and sometimes contradictory descriptions and records prevented adequate delineations of similar Hypsibius species. As a consequence, H. dujardini appeared to occur globally, from Norway to Samoa. In this paper, we provide the first integrated taxonomic redescription of H. dujardini. In addition to classic imaging by light microscopy and a comprehensive morphometric dataset, we present scanning electron photomicrographs, and DNA sequences for three nuclear markers (18S rRNA, 28S rRNA, ITS-2) and one mitochondrial marker (COI) that are characterised by various mutation rates. The results of our study reveal that a commercially available strain that is maintained in many laboratories throughout the world, and assumed to represent H. dujardini sensu stricto, represents, in fact, a new species: H. exemplaris sp. nov. Redescribing the nominal taxon for Hypsibiidae, we also redefine the family and amend the definitions of the subfamily Hypsibiinae and the genus Hypsibius. Moreover, we transfer H. arcticus (Murray, 1907) and Hypsibius conifer Mihelčič, 1938 to the genus Ramazzottius since the species exhibit claws and eggs of the Ramazzottius type. Finally, we designate H. fuhrmanni as subjectively invalid because the extremely poor description precludes identifying neotype material. 

scholarly journals Two related ARID family proteins are alternative subunits of human SWI/SNF complexes

2004 ◽  
Vol 383 (2) ◽  
pp. 319-325 ◽  
Author(s):  
Xiaomei WANG ◽  
Norman G. NAGL ◽  
Deborah WILSKER ◽  
Michael VAN SCOY ◽  
Stephen PACCHIONE ◽  
...  
Keyword(s):  
Dna Binding ◽  
Direct Evidence ◽  
Potential Interaction ◽  
Atpase Subunit ◽  
Reading Frame ◽  
Atpase Subunits ◽  
A Subunit ◽  
Distinct Subunit ◽  
Binding Behaviour

p270 (ARID1A) is a member of the ARID family of DNA-binding proteins and a subunit of human SWI/SNF-related complexes, which use the energy generated by an integral ATPase subunit to remodel chromatin. ARID1B is an independent gene product with an open reading frame that is more than 60% identical with p270. We have generated monoclonal antibodies specific for either p270 or ARID1B to facilitate the investigation of ARID1B and its potential interaction with human SWI/SNF complexes in vivo. Immunocomplex analysis provides direct evidence that endogenous ARID1B is associated with SWI/SNF-related complexes and indicates that p270 and ARID1B, similar to the ATPase subunits BRG1 and hBRM, are alternative, mutually exclusive subunits of the complexes. The ARID-containing subunits are not specific to the ATPases. Each associates with both BRG1 and hBRM, thus increasing the number of distinct subunit combinations known to be present in cells. Analysis of the panels of cell lines indicates that ARID1B, similar to p270, has a broad tissue distribution. The ratio of p270/ARID1B in typical cells is approx. 3.5:1, and BRG1 is distributed proportionally between the two ARID subunits. Analysis of DNA-binding behaviour indicates that ARID1B binds DNA in a non-sequence-specific manner similar to p270.

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