A novel species-specific tandem repeat DNA family from Sinapis arvensis: detection of telomere-like sequences

Genome ◽  
1996 ◽  
Vol 39 (4) ◽  
pp. 758-766 ◽  
Author(s):  
Ritu Kapila ◽  
Sandip Das ◽  
Malathi Lakshmikumaran ◽  
P. S. Srivastava
Keyword(s):  
Tandem Repeat ◽  
Dna Sequences ◽  
Tandem Repeats ◽  
Consensus Sequence ◽  
Repeat Element ◽  
Matrix Analysis ◽  
Repetitive Region ◽  
Repeat Family ◽  
Sinapis Arvensis ◽  
Species Specific

DNA sequences representing a tandemly repeated DNA family of the Sinapis arvensis genome were cloned and characterized. The 700-bp tandem repeat family is represented by two clones, pSA35 and pSA52, which are 697 and 709 bp in length, respectively. Dot matrix analysis of the sequences indicates the presence of repeated elements within each monomeric unit. Sequence analysis of the repetitive region of clones pSA35 and pSA52 shows that there are several copies of a 7-bp repeat element organized in tandem. The consensus sequence of this repeat element is 5′-TTTAGGG-3′. These elements are highly mutated and the difference in length between the two clones is due to different copy numbers of these elements. The repetitive region of clone pSA35 has 26 copies of the element TTTAGGG, whereas clone pSA52 has 28 copies. The repetitive region in both clones is flanked on either side by inverted repeats that may be footprints of a transposition event. Sequence comparison indicates that the element TTTAGGG is identical to telomeric repeats present in Arabidopsis, maize, tomato, and other plants. However, Bal31digestion kinetics indicates non-telomeric localization of the 700-bp tandem repeats. The clones represent a novel repeat family as (i) they contain telomere-like motifs as subrepeats within each unit; and (ii) they do not hybridize to related crucifers and are species-specific in nature. Key words : Brassica species, Sinapis arvensis, tandem repeats, telomeres.

A species-specific satellite DNA from the entomopathogenic nematode Heterorhabditis indicus

Genome ◽  
1998 ◽  
Vol 41 (2) ◽  
pp. 148-153 ◽  
Author(s):  
Monique Abadon ◽  
Eric Grenier ◽  
Christian Laumond ◽  
Pierre Abad
Keyword(s):  
Dna Sequence ◽  
Satellite Dna ◽  
Tandem Repeats ◽  
Sequence Data ◽  
Entomopathogenic Nematode ◽  
Consensus Sequence ◽  
Repeated Sequence ◽  
Nucleotide Sequence Analysis ◽  
Specific Sequence ◽  
Species Specific

An AluI satellite DNA family has been cloned from the entomopathogenic nematode Heterorhabditis indicus. This repeated sequence appears to be an unusually abundant satellite DNA, since it constitutes about 45% of the H. indicus genome. The consensus sequence is 174 nucleotides long and has an A + T content of 56%, with the presence of direct and inverted repeat clusters. DNA sequence data reveal that monomers are quite homogeneous. Such homogeneity suggests that some mechanism is acting to maintain the homogeneity of this satellite DNA, despite its abundance, or that this repeated sequence could have appeared recently in the genome of H. indicus. Hybridization analysis of genomic DNAs from different Heterorhabditis species shows that this satellite DNA sequence is specific to the H. indicus genome. Considering the species specificity and the high copy number of this AluI satellite DNA sequence, it could provide a rapid and powerful tool for identifying H. indicus strains.Key words: AluI repeated DNA, tandem repeats, species-specific sequence, nucleotide sequence analysis.

scholarly journals HYPERCOMPLEX CROSS-CORRELATION OF DNA SEQUENCES

2010 ◽  
Vol 18 (04) ◽  
pp. 711-725 ◽  
Author(s):  
JIAN-JUN SHU ◽  
YAJING LI
Keyword(s):  
Dynamic Programming ◽  
Dna Sequences ◽  
Cross Correlation ◽  
Consensus Sequence ◽  
Correlation Method ◽  
Matrix Analysis ◽  
Analysis Method ◽  
Number Representation ◽  
Hypercomplex Number ◽  
New Scoring

A hypercomplex representation of DNA is proposed to facilitate comparing DNA sequences with fuzzy composition. With the hypercomplex number representation, the conventional sequence analysis method, such as, dot matrix analysis, dynamic programming, and cross-correlation method have been extended and improved to align DNA sequences with fuzzy composition. The hypercomplex dot matrix analysis can provide more control over the degree of alignment desired. A new scoring system has been proposed to accommodate the hypercomplex number representation of DNA and integrated with dynamic programming alignment method. By using hypercomplex cross-correlation, the match and mismatch alignment information between two aligned DNA sequences are separately stored in the resultant real part and imaginary parts respectively. The mismatch alignment information is very useful to refine consensus sequence based motif scanning.

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 Tyrosine-Phosphorylated Ehrlichia chaffeensis and Ehrlichia canis Tandem Repeat Orthologs Contain a Major Continuous Cross-Reactive Antibody Epitope in Lysine-Rich Repeats

2011 ◽  
Vol 79 (8) ◽  
pp. 3178-3187 ◽  
Author(s):  
Jere W. McBride ◽  
Xiaofeng Zhang ◽  
Abdul Wakeel ◽  
Jeeba A. Kuriakose
Keyword(s):  
Amino Acids ◽  
Tandem Repeat ◽  
Tandem Repeats ◽  
Ehrlichia Canis ◽  
Small Subset ◽  
Ehrlichia Chaffeensis ◽  
Whole Cell ◽  
Content Type ◽  
Cell Lysates ◽  
Species Specific

ABSTRACTA small subset of major immunoreactive proteins have been identified inEhrlichia chaffeensisandEhrlichia canis, including three molecularly and immunologically characterized pairs of immunoreactive tandem repeat protein (TRP) orthologs with major continuous species-specific epitopes within acidic tandem repeats (TR) that stimulate strong antibody responses during infection. In this study, we identified a fourth major immunoreactive TR-containing ortholog pair and defined a major cross-reactive epitope in homologous nonidentical 24-amino-acid lysine-rich TRs. Antibodies from patients and dogs with ehrlichiosis reacted strongly with recombinant TR regions, and epitopes were mapped to the N-terminal TR region (18 amino acids) inE. chaffeensisand the complete TR (24 amino acids) inE. canis. Two less-dominant epitopes were mapped to adjacent glutamate/aspartate-rich and aspartate/tyrosine-rich regions in the acidic C terminus ofE. canisTRP95 but not inE. chaffeensisTRP75. Major immunoreactive proteins inE. chaffeensis(75-kDa) andE. canis(95-kD) whole-cell lysates and supernatants were identified with TR-specific antibodies. Consistent with other ehrlichial TRPs, the TRPs identified in ehrlichial whole-cell lysates and the recombinant proteins migrated abnormally slow electrophoretically a characteristic that was demonstrated with the positively charged TR and negatively charged C-terminal domains.E. chaffeensisTRP75 andE. canisTRP95 were immunoprecipitated with anti-pTyr antibody, demonstrating that they are tyrosine phosphorylated during infection of the host cell.

Molecular characterization and distribution of a 145-bp tandem repeat family in the genus Populus

Genome ◽  
1999 ◽  
Vol 42 (5) ◽  
pp. 909-918 ◽  
Author(s):  
J Rajagopal ◽  
S Das ◽  
D K Khurana ◽  
P S Srivastava ◽  
M Lakshmikumaran
Keyword(s):  
Molecular Characterization ◽  
Tandem Repeat ◽  
Tandem Repeats ◽  
Populus Deltoides ◽  
Point Mutations ◽  
Sequence Divergence ◽  
Methylation Pattern ◽  
Dot Blot ◽  
Repeat Family ◽  
Sequence Comparisons

This report aims to describe the identification and molecular characterization of a 145-bp tandem repeat family that accounts for nearly 1.5% of the Populus genome. Three members of this repeat family were cloned and sequenced from Populus deltoides and P. ciliata. The dimers of the repeat were sequenced in order to confirm the head-to-tail organization of the repeat. Hybridization-based analysis using the 145-bp tandem repeat as a probe on genomic DNA gave rise to ladder patterns which were identified to be a result of methylation and (or) sequence heterogeneity. Analysis of the methylation pattern of the repeat family using methylation-sensitive isoschizomers revealed variable methylation of the C residues and lack of methylation of the A residues. Sequence comparisons between the monomers revealed a high degree of sequence divergence that ranged between 6% and 11% in P. deltoides and between 4.2% and 8.3% in P. ciliata. This indicated the presence of sub-families within the 145-bp tandem family of repeats. Divergence was mainly due to the accumulation of point mutations and was concentrated in the central region of the repeat. The 145-bp tandem repeat family did not show significant homology to known tandem repeats from plants. A short stretch of 36 bp was found to show homology of 66.7% to a centromeric repeat from Chironomus plumosus. Dot-blot analysis and Southern hybridization data revealed the presence of the repeat family in 13 of the 14 Populus species examined. The absence of the 145-bp repeat from P. euphratica suggested that this species is relatively distant from other members of the genus, which correlates with taxonomic classifications. The widespread occurrence of the tandem family in the genus indicated that this family may be of ancient origin.Key words: Satellite DNA, centromeric DNA, genome organization, phylogeny.

scholarly journals Differentially Amplified Repetitive Sequences Among Aegilops tauschii Subspecies and Genotypes

2021 ◽  
Vol 12 ◽  
Author(s):  
Rahman Ebrahimzadegan ◽  
Fatemeh Orooji ◽  
Pengtao Ma ◽  
Ghader Mirzaghaderi
Keyword(s):  
Dna Sequences ◽  
Tandem Repeats ◽  
Repetitive Sequences ◽  
Aegilops Tauschii ◽  
Distribution Patterns ◽  
Snp Analysis ◽  
Specific Sequence ◽  
Factors Affecting ◽  
Illumina Sequence ◽  
Species Specific

Genomic repetitive sequences commonly show species-specific sequence type, abundance, and distribution patterns, however, their intraspecific characteristics have been poorly described. We quantified the genomic repetitive sequences and performed single nucleotide polymorphism (SNP) analysis between 29 Ae. tauschii genotypes and subspecies using publicly available raw genomic Illumina sequence reads and used fluorescence in situ hybridization (FISH) to experimentally analyze some repeats. The majority of the identified repetitive sequences had similar contents and proportions between anathera, meyeri, and strangulata subspecies. However, two Ty3/gypsy retrotransposons (CL62 and CL87) showed significantly higher abundances, and CL1, CL119, CL213, CL217 tandem repeats, and CL142 retrotransposon (Ty1/copia type) showed significantly lower abundances in subspecies strangulata compared with the subspecies anathera and meyeri. One tandem repeat and 45S ribosomal DNA (45S rDNA) abundances showed a high variation between genotypes but their abundances were not subspecies specific. Phylogenetic analysis using the repeat abundances of the aforementioned clusters placed the strangulata subsp. in a distinct clade but could not discriminate anathera and meyeri. A near complete differentiation of anathera and strangulata subspecies was observed using SNP analysis; however, var. meyeri showed higher genetic diversity. FISH using major tandem repeats couldn’t detect differences between subspecies, although (GAA)10 signal patterns generated two different karyotype groups. Taken together, the different classes of repetitive DNA sequences have differentially accumulated between strangulata and the other two subspecies of Ae. tauschii that is generally in agreement with spike morphology, implying that factors affecting repeatome evolution are variable even among highly closely related lineages.

scholarly journals Tandem Repeat Hypothesis in Imprinting: Deletion of a Conserved Direct Repeat Element Upstream of H19 Has No Effect on Imprinting in the Igf2-H19 Region

2004 ◽  
Vol 24 (13) ◽  
pp. 5650-5656 ◽  
Author(s):  
Annabelle Lewis ◽  
Kohzoh Mitsuya ◽  
Miguel Constancia ◽  
Wolf Reik
Keyword(s):  
Tandem Repeat ◽  
Tandem Repeats ◽  
Direct Repeat ◽  
Regulatory Elements ◽  
Repeat Element ◽  
Allelic Expression ◽  
Differentially Methylated Region ◽  
Paternal Allele ◽  
Imprinted Genes ◽  
Allele Specific

ABSTRACT Igf2 and H19 are reciprocally imprinted genes on mouse distal chromosome 7. They share several regulatory elements, including a differentially methylated region (DMR) upstream of H19 that is paternally methylated throughout development. The cis-acting sequence requirements for targeting DNA methylation to the DMR remain unknown; however, it has been suggested that direct tandem repeats near DMRs could be involved. Previous studies of the imprinted Rasgrf1 locus demonstrate indeed that a direct repeat element adjacent to a DMR is responsible for establishing paternal allele-specific methylation at the DMR and therefore allelic expression of the Rasgrf1 transcript. We identified a prominent and conserved direct tandem repeat 1 kb upstream of the H19 DMR and proposed that it played a similar role in imprinted regulation of H19. To test our hypothesis, we generated mice harboring a 1.7-kb targeted deletion of the direct repeat element and analyzed fetal growth, allelic expression, and methylation within the Igf2-H19 region. Surprisingly the deletion had no effect on imprinting. These results together with deletions of other repeats close to imprinted genes suggest that direct repeats may not be important for the targeting of methylation at the majority of imprinted loci and that the Rasgrf1 locus may be an exception to this rule.

Self-amplification of satellite DNA in vitro

Genome ◽  
1998 ◽  
Vol 41 (3) ◽  
pp. 429-434 ◽  
Author(s):  
J B Buntjer ◽  
J A Lenstra
Keyword(s):  
Tandem Repeat ◽  
Satellite Dna ◽  
Genomic Dna ◽  
Tandem Repeats ◽  
Repeat Unit ◽  
Dna Amplification ◽  
Repeat Units ◽  
Rapid Amplification ◽  
Species Specific

We describe a PCR-like reaction in which genomic DNA acts as a template as well as a primer. Interaction between genomic tandem repeat units leads to self-amplification of satellite DNA. This genomic self-priming PCR (GSP-PCR) allowed the rapid amplification of species-specific tandem repeats of horse, cattle, dolphin, and chicken. A novel specific satellite of ostrich with a repeat unit of 60 bp was isolated using this method.Key words: satellite DNA, amplification, isolation, species-specific probes.

scholarly journals Discovery of Hyperactive Antifreeze Protein from Phylogenetically Distant Beetles Questions Its Evolutionary Origin

2021 ◽  
Vol 22 (7) ◽  
pp. 3637
Author(s):  
Tatsuya Arai ◽  
Akari Yamauchi ◽  
Ai Miura ◽  
Hidemasa Kondo ◽  
Yoshiyuki Nishimiya ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Tandem Repeats ◽  
Freezing Point ◽  
Consensus Sequence ◽  
Antifreeze Protein ◽  
Ice Crystal ◽  
Freezing Point Depression ◽  
Entire Surface ◽  
Chilled Storage ◽  
Peptide Region

Beetle hyperactive antifreeze protein (AFP) has a unique ability to maintain a supercooling state of its body fluids, however, less is known about its origination. Here, we found that a popular stag beetle Dorcus hopei binodulosus (Dhb) synthesizes at least 6 isoforms of hyperactive AFP (DhbAFP). Cold-acclimated Dhb larvae tolerated −5 °C chilled storage for 24 h and fully recovered after warming, suggesting that DhbAFP facilitates overwintering of this beetle. A DhbAFP isoform (~10 kDa) appeared to consist of 6−8 tandem repeats of a 12-residue consensus sequence (TCTxSxNCxxAx), which exhibited 3 °C of high freezing point depression and the ability of binding to an entire surface of a single ice crystal. Significantly, these properties as well as DNA sequences including the untranslated region, signal peptide region, and an AFP-encoding region of Dhb are highly similar to those identified for a known hyperactive AFP (TmAFP) from the beetle Tenebrio molitor (Tm). Progenitor of Dhb and Tm was branched off approximately 300 million years ago, so no known evolution mechanism hardly explains the retainment of the DNA sequence for such a lo­ng divergence period. Existence of unrevealed gene transfer mechanism will be hypothesized between these two phylogenetically distant beetles to acquire this type of hyperactive AFP.

scholarly journals Sequence, Chromatin and Evolution of Satellite DNA

2021 ◽  
Vol 22 (9) ◽  
pp. 4309
Author(s):  
Jitendra Thakur ◽  
Jenika Packiaraj ◽  
Steven Henikoff
Keyword(s):  
Dna Sequences ◽  
Satellite Dna ◽  
Tandem Repeats ◽  
Large Fraction ◽  
Dna Curvature ◽  
Sequence Motifs ◽  
Specific Sequence ◽  
Satellite Dnas ◽  
Dna Repeat ◽  
Species Specific

Satellite DNA consists of abundant tandem repeats that play important roles in cellular processes, including chromosome segregation, genome organization and chromosome end protection. Most satellite DNA repeat units are either of nucleosomal length or 5–10 bp long and occupy centromeric, pericentromeric or telomeric regions. Due to high repetitiveness, satellite DNA sequences have largely been absent from genome assemblies. Although few conserved satellite-specific sequence motifs have been identified, DNA curvature, dyad symmetries and inverted repeats are features of various satellite DNAs in several organisms. Satellite DNA sequences are either embedded in highly compact gene-poor heterochromatin or specialized chromatin that is distinct from euchromatin. Nevertheless, some satellite DNAs are transcribed into non-coding RNAs that may play important roles in satellite DNA function. Intriguingly, satellite DNAs are among the most rapidly evolving genomic elements, such that a large fraction is species-specific in most organisms. Here we describe the different classes of satellite DNA sequences, their satellite-specific chromatin features, and how these features may contribute to satellite DNA biology and evolution. We also discuss how the evolution of functional satellite DNA classes may contribute to speciation in plants and animals.

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