Characterization of two families of tandem repeated DNA sequences in Potamogeton pectinatus L.

Genome ◽  
2008 ◽  
Vol 51 (11) ◽  
pp. 871-877 ◽  
Author(s):  
Marilena Ceccarelli ◽  
Vania Sarri ◽  
Stefania Minelli ◽  
Maria Teresa Gelati
Keyword(s):  
Dna Sequences ◽  
Tandem Repeats ◽  
Sequence Similarity ◽  
Evolutionary Relationship ◽  
Potamogeton Pectinatus ◽  
Target Sequence ◽  
Entire Genome ◽  
Diploid Parent

DNA sequences belonging to two families of tandem repeats, PpeRsa1 (362–364 bp in length, 62% A+T residues) and PpeRsa2 (355–359 bp in length, 59% A+T residues), have been isolated from the Potamogeton pectinatus L. genome. The two sequence families do not share significant nucleotide sequence similarity, even if an evolutionary relationship between them could be assumed. The comparison of the cleaving activity of isoschizomeres that are either sensitive or insensitive to methylation of cytosine residues in the target sequence revealed high methylation in both sequence families. The copy number per 1C DNA of PpeRsa1- and PpeRsa2-related sequences is estimated to be 4.92 × 104 and 7.96 × 104, respectively. Taken together, these sequences account for about 7.5% of the entire genome of P. pectinatus. The chromosomal organization of these sequences was investigated by fluorescent in situ hybridization. PpeRsa1 and PpeRsa2 repeats found related sequences in 52 chromosomes of the P. pectinatus complement (2n = 78). The related sequences were localized around the centromeres and at the chromosome ends in three pairs of chromosomes, while they were found only at the chromosome ends in the remaining pairs. Twenty-six chromosomes did not show any hybridization signal. The hypothesis that the species is a hybrid between a diploid parent and an allotetraploid parent is put forward.

Characterization of genes encoding Starch Branching Enzyme I from Triticum monococcum and its diploid wheat relatives

Biologia ◽  
2015 ◽  
Vol 70 (9) ◽  
pp. 1193-1200
Author(s):  
Xiu-Ying Wang ◽  
Chang-Shui Wang ◽  
Jian Ma ◽  
Ji-Rui Wang ◽  
Ya-Xi Liu ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Sequence Similarity ◽  
Expression Patterns ◽  
Evolutionary Relationship ◽  
Amino Acid Sequences ◽  
Triticum Monococcum ◽  
Branching Enzyme ◽  
Starch Branching Enzyme ◽  
Enzyme I

Abstract The Starch Branching Enzyme I (SBEI) gene plays an important role in amylopectin synthesis. Here, we isolated and characterized the full-length cDNA and DNA sequences of SBEI gene from diploid Triticeae species, Triticum monococcum, T. urartu, Aegilopsspeltoides, and Ae. tauschii. Then we predicted its protein structure, analyzed its evolutionary relationship with other species, and explored its expression patterns using real-time quantitative PCR. The SBEI cDNA includes a 2,490-bp open reading frame (ORF) encoding 829 amino acids. The genomic DNA of SBEI is 5,526-bp in length, containes fourteen exons and thirteen introns, and shares a similar structure with its homologous genes from other cereal plants. Sequence similarity ranging from 70.50% to 98.02% in exons and from 15.50% to 83.63% in introns was detected. Results of phylogenetic tree based on the deduced amino acid sequences from T. monococcum and other plants indicated that T. monococcum SBEI is more closely related to T. boeoticum and T. urartu. Expression analysis revealed that T. monococcum SBEI and AGPase genes were highly expressed in the seeds at middle developmental stage. This is the first report on characterization of the SBEI gene in T. monococcum. These results could be used to explore the roles of this enzyme in amylopectin synthesis.

scholarly journals Molecular Characterization of a Family of Tandemly Repeated DNA Sequences, TR-1, in Heterochromatic Knobs of Maize and Its Relatives

Genetics ◽  
2003 ◽  
Vol 164 (3) ◽  
pp. 1087-1097 ◽  
Author(s):  
F C Hsu ◽  
C J Wang ◽  
C M Chen ◽  
H Y Hu ◽  
C C Chen
Keyword(s):  
Dna Sequences ◽  
Tandem Repeats ◽  
B Chromosome ◽  
Repeated Dna ◽  
Sequence Comparisons ◽  
Repeat Units ◽  
Entire Sequence ◽  
Single Sequence

Abstract Two families of tandem repeats, 180-bp and TR-1, have been found in the knobs of maize. In this study, we isolated 59 clones belonging to the TR-1 family from maize and teosinte. Southern hybridization and sequence analysis revealed that members of this family are composed of three basic sequences, A (67 bp); B (184 bp) or its variants B′ (184 bp), 2/3B (115 bp), 2/3B′ (115 bp); and C (108 bp), which are arranged in various combinations to produce repeat units that are multiples of ∼180 bp. The molecular structure of TR-1 elements suggests that: (1) the B component may evolve from the 180-bp knob repeat as a result of mutations during evolution; (2) B′ may originate from B through lateral amplification accompanied by base-pair changes; (3) C plus A may be a single sequence that is added to B and B′, probably via nonhomologous recombination; and (4) 69 bp at the 3′ end of B or B′, and the entire sequence of C can be removed from the elements by an unknown mechanism. Sequence comparisons showed partial homologies between TR-1 elements and two centromeric sequences (B repeats) of the supernumerary B chromosome. This result, together with the finding of other investigators that the B repeat is also fragmentarily homologous to the 180-bp repeat, suggests that the B repeat is derived from knob repeats in A chromosomes, which subsequently become structurally modified. Fluorescence in situ hybridization localized the B repeat to the B centromere and the 180-bp and TR-1 repeats to the proximal heterochromatin knob on the B chromosome.

scholarly journals Karyotype Characterization of Nine Periwinkle Species (Gastropoda, Littorinidae)

Genes ◽  
2018 ◽  
Vol 9 (11) ◽  
pp. 517 ◽  
Author(s):  
Daniel García-Souto ◽  
Sandra Alonso-Rubido ◽  
Diana Costa ◽  
José Eirín-López ◽  
Emilio Rolán-Álvarez ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Chromosome Numbers ◽  
Gene Clusters ◽  
Chromosomal Mapping ◽  
Closely Related Species ◽  
Submetacentric Chromosome ◽  
The Family ◽  
Littorina Arcana

Periwinkles of the family Littorinidae (Children, 1834) are common members of seashore littoral communities worldwide. Although the family is composed of more than 200 species belonging to 18 genera, chromosome numbers have been described in only eleven of them. A molecular cytogenetic analysis of nine periwinkle species, the rough periwinkles Littorina arcana, L. saxatilis, and L. compressa, the flat periwinkles L. obtusata and L. fabalis, the common periwinkle L. littorea, the mangrove periwinkle Littoraria angulifera, the beaded periwinkle Cenchritis muricatus, and the small periwinkle Melarhaphe neritoides was performed. All species showed diploid chromosome numbers of 2n = 34, and karyotypes were mostly composed of metacentric and submetacentric chromosome pairs. None of the periwinkle species showed chromosomal differences between male and female specimens. The chromosomal mapping of major and minor rDNA and H3 histone gene clusters by fluorescent in situ hybridization demonstrated that the patterns of distribution of these DNA sequences were conserved among closely related species and differed among less related ones. All signals occupied separated loci on different chromosome pairs without any evidence of co-localization in any of the species.

scholarly journals Conversion of DNA Sequences: From a Transposable Element to a Tandem Repeat or to a Gene

Genes ◽  
2019 ◽  
Vol 10 (12) ◽  
pp. 1014 ◽  
Author(s):  
Ana Paço ◽  
Renata Freitas ◽  
Ana Vieira-da-Silva
Keyword(s):  
Repetitive Dna ◽  
Dna Sequences ◽  
Tandem Repeats ◽  
Evolutionary Relationship ◽  
Repetitive Dna Sequences ◽  
Dna Remodeling ◽  
Eukaryotic Genomes ◽  
Similar Organization ◽  
Dispersed Repeats

Eukaryotic genomes are rich in repetitive DNA sequences grouped in two classes regarding their genomic organization: tandem repeats and dispersed repeats. In tandem repeats, copies of a short DNA sequence are positioned one after another within the genome, while in dispersed repeats, these copies are randomly distributed. In this review we provide evidence that both tandem and dispersed repeats can have a similar organization, which leads us to suggest an update to their classification based on the sequence features, concretely regarding the presence or absence of retrotransposons/transposon specific domains. In addition, we analyze several studies that show that a repetitive element can be remodeled into repetitive non-coding or coding sequences, suggesting (1) an evolutionary relationship among DNA sequences, and (2) that the evolution of the genomes involved frequent repetitive sequence reshuffling, a process that we have designated as a “DNA remodeling mechanism”. The alternative classification of the repetitive DNA sequences here proposed will provide a novel theoretical framework that recognizes the importance of DNA remodeling for the evolution and plasticity of eukaryotic genomes.

Variation in highly repetitive DNA composition of heterochromatin in rye studied by fluorescence in situ hybridization

Genome ◽  
1995 ◽  
Vol 38 (6) ◽  
pp. 1061-1069 ◽  
Author(s):  
A. Cuadrado ◽  
N. Jouve ◽  
C. Ceoloni
Keyword(s):  
In Situ Hybridization ◽  
Fluorescence In Situ Hybridization ◽  
Repetitive Dna ◽  
Dna Sequences ◽  
5S Rdna ◽  
Individual Identification ◽  
Highly Repetitive Dna ◽  
The Individual

The molecular characterization of heterochromatin in six lines of rye has been performed using fluorescence in situ hybridization (FISH). The highly repetitive rye DNA sequences pSc 119.2, pSc74, and pSc34, and the probes pTa71 and pSc794 containing the 25S–5.8S–18S rDNA (NOR) and the 5S rDNA multigene families, respectively, were used. This allowed the individual identification of all seven rye chromosomes and most chromosome arms in all lines. All varieties showed similar but not identical patterns. A standard in situ hybridization map was constructed following the nomenclature system recommended for C-bands. All FISH sites observed appeared to correspond well with C-band locations, but not all C-banding sites coincided with hybridization sites of the repetitive DNA probes used. Quantitative and qualitative differences between different varieties were found for in situ hybridization response at corresponding sites. Variation between plants and even between homologous chromosomes of the same plant was found in open-pollinated lines. In inbred lines, the in situ pattern of the homologues was practically identical and no variation between plants was detected. The observed quantitative and qualitative differences are consistent with a corresponding variation for C-bands detected both within and between cultivars.Key words: fluorescence in situ hybridization, repetitive DNA, rye, Secale cereale, polymorphism.

Molecular cytogenetic analysis of durum wheat × tritordeum hybrids

Genome ◽  
1997 ◽  
Vol 40 (3) ◽  
pp. 362-369 ◽  
Author(s):  
J. Lima-Brito ◽  
H. Guedes-Pinto ◽  
G. E. Harrison ◽  
J. S. Heslop-Harrison
Keyword(s):  
In Situ Hybridization ◽  
Plant Breeding ◽  
Durum Wheat ◽  
Dna Sequences ◽  
Genomic Dna ◽  
Tandem Repeats ◽  
Nuclear Architecture ◽  
Molecular Cytogenetics ◽  
Hordeum Chilense

Southern and in situ hybridization were used to examine the chromosome constitution, genomic relationships, repetitive DNA sequences, and nuclear architecture in durum wheat × tritordeum hybrids (2n = 5x = 35), where tritordeum is the fertile amphiploid (2n = 6x = 42) between Hordeum chilense and durum wheat. Using in situ hybridization, H. chilense total genomic DNA hybridized strongly to the H. chilense chromosomes and weakly to the wheat chromosomes, which showed some strongly labelled bands. pHcKB6, a cloned repetitive sequence isolated from H. chilense, enabled the unequivocal identification of each H. chilense chromosome at metaphase. Analysis of chromosome disposition in prophase nuclei, using the same probes, showed that the chromosomes of H. chilense origin were in individual domains with only limited intermixing with chromosomes of wheat origin. Six major sites of 18S–26S rDNA genes were detected on the chromosomes of the hybrids. Hybridization to Southern transfers of restriction enzyme digests using genomic DNA showed some variants of tandem repeats, perhaps owing to methylation. Both techniques gave complementary information, extending that available from phenotypic, chromosome morphology, or isozyme analysis, and perhaps are useful for following chromosomes or chromosome segments during further crossing of the lines in plant breeding programs.Key words: In situ hybridization, molecular cytogenetics, plant breeding, Hordeum chilense, Southern hybridization, durum wheat, hybrids.

Characterization and chromosomal organization of satellite DNA sequences in Picea abies

Genome ◽  
2008 ◽  
Vol 51 (9) ◽  
pp. 705-713 ◽  
Author(s):  
V. Sarri ◽  
S. Minelli ◽  
F. Panara ◽  
M. Morgante ◽  
I. Jurman ◽  
...  
Keyword(s):  
Picea Abies ◽  
Dna Sequences ◽  
Satellite Dna ◽  
Sequence Similarity ◽  
Intergenic Spacer ◽  
Structural Diversity ◽  
Dna Library ◽  
Genomic Dna Library ◽  
Chromosome Regions

Three clones containing satellite DNA sequences were selected from a randomly sheared genomic DNA library of Picea abies (clones PAF1, PAG004P22F (2F), and PAG004E03C (3C)). PAF1 contained 7 repeats that were 37–55 bp in length and had 68.9%–91.9% nucleotide sequence similarity. Two 2F repeats were 305–306 bp in length and had 83% sequence similarity. Two 3C repeats were 193–226 bp in length and had a sequence similarity of 78.6%. The copy number per 1C DNA of PAF1, 2F, and 3C repeats was 2.7 × 106, 2.9 × 105, and 2.9 × 104, respectively. In situ hybridization showed centromeric localization of these sequences in two chromosome pairs with PAF1, all pairs but one with 2F, and three pairs with 3C. Moreover, PAF1 sequences hybridized at secondary constrictions in six pairs, while 2F-related sequences were found at these chromosome regions only in four pairs. These hybridization patterns allow all chromosome pairs to be distinguished. PAF1-related repeats were contained in the intergenic spacer (IGS) of ribosomal cistrons in all six nucleolar organizers of the complement, while sequences related to 2F were found on only one side of the rDNA arrays in four pairs, showing structural diversity between rDNA regions of different chromosomes.

scholarly journals Characterization of a Maize Chromosome 4 Centromeric Sequence: Evidence for an Evolutionary Relationship With the B Chromosome Centromere

Genetics ◽  
2001 ◽  
Vol 159 (1) ◽  
pp. 291-302 ◽  
Author(s):  
Brent T Page ◽  
Michael K Wanous ◽  
James A Birchler
Keyword(s):  
Evolutionary Relationship ◽  
Bac Library ◽  
B Chromosome ◽  
B Chromosomes ◽  
Chromosome 4 ◽  
Centromeric Sequence ◽  
Unit Repeat ◽  
Specific Sequences

Abstract Previous work has identified sequences specific to the B chromosome that are a major component of the B centromere. To address the issue of the origin of the B and the evolution of centromere-localized sequences, DNA prepared from plants without B chromosomes was probed to seek evidence for related sequences. Clones were isolated from maize line B73 without B chromosomes by screening DNA at reduced stringency with a B centromeric probe. These clones were localized to maize centromere 4 using fluorescence in situ hybridization. They showed homology to a maize centromere-mapped sequence, to maize B chromosome centromere sequences, and to a portion of the unit repeat of knobs, which act as neocentromeres in maize. A representative copy was used to screen a BAC library to obtain these sequences in a larger context. Each of the six positive BACs obtained was analyzed to determine the nature of centromere 4-specific sequences present. Fifteen subclones of one BAC were sequenced and the organization of this chromosome 4-specific repeat was examined.

scholarly journals Identification and characterization of satellite DNAs in two-toed sloths of the genus Choloepus (Megalonychidae, Xenarthra)

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Radarane Santos Sena ◽  
Pedro Heringer ◽  
Mirela Pelizaro Valeri ◽  
Valéria Socorro Pereira ◽  
Gustavo C. S. Kuhn ◽  
...  
Keyword(s):  
Tandem Repeats ◽  
Satellite Dnas ◽  
Phylogenetic Studies ◽  
Tandem Repeat Sequences ◽  
Mammalian Genomes ◽  
Living Species ◽  
Bradypus Variegatus ◽  
Identification And Characterization

Abstract Choloepus, the only extant genus of the Megalonychidae family, is composed of two living species of two-toed sloths: Choloepus didactylus and C. hoffmanni. In this work, we identified and characterized the main satellite DNAs (satDNAs) in the sequenced genomes of these two species. SATCHO1, the most abundant satDNA in both species, is composed of 117 bp tandem repeat sequences. The second most abundant satDNA, SATCHO2, is composed of ~ 2292 bp tandem repeats. Fluorescence in situ hybridization in C. hoffmanni revealed that both satDNAs are located in the centromeric regions of all chromosomes, except the X. In fact, these satDNAs present some centromeric characteristics in their sequences, such as dyad symmetries predicted to form secondary structures. PCR experiments indicated the presence of SATCHO1 sequences in two other Xenarthra species: the tree-toed sloth Bradypus variegatus and the anteater Myrmecophaga tridactyla. Nevertheless, SATCHO1 is present as large tandem arrays only in Choloepus species, thus likely representing a satDNA exclusively in this genus. Our results reveal interesting features of the satDNA landscape in Choloepus species with the potential to aid future phylogenetic studies in Xenarthra and mammalian genomes in general.

scholarly journals Molecular genetics of the Posterior sex combs/Suppressor 2 of zeste region of Drosophila: aberrant expression of the Suppressor 2 of zeste gene results in abnormal bristle development.

Genetics ◽  
1991 ◽  
Vol 128 (1) ◽  
pp. 119-132
Author(s):  
B P Brunk ◽  
E C Martin ◽  
P N Adler
Keyword(s):  
Dna Sequences ◽  
Polycomb Group ◽  
Loss Of Function ◽  
Distal Breakpoint ◽  
Gain Of Function ◽  
Aberrant Expression ◽  
Sex Combs ◽  
Foreign Dna

Abstract We report the molecular characterization of the Posterior sex combs-Suppressor 2 of zeste region of Drosophila melanogaster. The distal breakpoint of the Aristapedioid inversion divides the region into two parts. We have molecularly mapped the lesions associated with several loss of function mutations in the Polycomb group gene Posterior sex combs (Psc) proximal to this breakpoint. In addition, we have found that lesions associated with several loss of function mutations in the Suppressor 2 of zeste [Su(z)2] gene lie distal to this breakpoint. Since the breakpoint does not cause a loss of function in either gene, no essential sequences are shared by these two neighboring genes. There are three dominant gain of function mutations in the region that result in abnormal bristle development. We find that all three juxtapose foreign DNA sequences upstream of the Su(z)2 gene, and that at least two of these mutations (Arp1 and vgD) behave genetically as gain of function mutations in Su(z)2. Northern and in situ hybridization analyses show that the mutations result in increased accumulation of the Su(z)2 mRNA, which we argue is responsible for the bristle loss phenotype.

Sign in / Sign up

Export Citation Format

Share Document