Structure and chromosomal localization of DNA sequences related to ribosomal subrepeats in Vicia faba

Maggini, F.; Cremonini, R.; Zolfino, C; Tucci, G. F.; D’Ovidio, R.; Delre, V.; DePace, C.; Mugnozza, G.T. Scarascia; Cionini, P. G.

doi:10.1007/bf00344156

Cited by 53 publications

(29 citation statements)

References 33 publications

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“…Such a difference could be explained by the fact that NOR regions could behave like mobile elements capable of spreading across the karyotype (Schubert and Wobus, 1985;Galetti et al, 1995). This mechanism could involve mobile elements associated with ribosomal genes or sequences dispersed throughout the genome, which could act as recombination spots for rDNA loci (Maggini et al, 1991;Jakubczak et al, 1992). In brown trout, the Bgl II element, a SINE-like sequence located in the IGS close to the 18S RNA gene, or the telomeric sequence (TTAGGG) n , which is scattered through rDNA, could be responsible for the origin of these multiple inactive NOR sites and the translocation of an active NOR site from chromosome No.…”

Section: Discussionmentioning

confidence: 99%

Chromosomal study of native and hatchery trouts from Italy (<i>Salmo trutta </i>complex, Salmonidae): conventional and FISH analysis

Caputo

Giovannotti

Cerioni

et al. 2009

Cytogenet Genome Res

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A cytogenetic analysis was carried out using conventional staining, banding techniques and fluorescence in situ hybridization (FISH) in Italian populations of brown trout (Salmo truttacomplex). All individuals analysed, belonging to the Atlantic (At), Marmoratus (Ma), Adriatic (Ad) and Mediterranean (Me) lineages, showed remarkable karyotype uniformity, with diploid complement of 2n = 80 chromosomes, arm number (NF) of 102 and invariable karyotype composition. Such uniformity was also observed with respect to the location of 5S rDNA and the active, i.e. silver-positive NOR sites. On the contrary, FISH with 28S ribosomal probe and fluorescent staining with CMA3 revealed that inactive NOR sites are more numerous in Ad and Me than in At and Ma lineages. A centromeric sequence was successfully isolated from Salmo trutta individuals by polymerase chain reaction (PCR)-based cloning, using primers designed from published Atlantic salmon (Salmo salar) satellite DNA sequences. This sequence had high AT content (65.3%) and short consensus motif (A/T)(G/C)AAA(T/C) similar to other centromeric satellite repeats. The isolated satellite DNA clones were localized with FISH in the centromeric regions of the brown trout chromosomes, showing lineage-specific patterns. Because it is well known that AT-rich sequences can induce a pronounced DNA curvature, which in turn would promote faster and higher chromatin spiralization, it may be hypothesised that the wide distribution of this satellite in the S. trutta genome may have played a role in its karyotype stability. The presence of this sequence in other salmonid species was also tested by Southern blot hybridization and used to analyze its evolution within salmonids.

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Section: Discussionmentioning

confidence: 99%

Chromosomal study of native and hatchery trouts from Italy (<i>Salmo trutta </i>complex, Salmonidae): conventional and FISH analysis

Caputo

Giovannotti

Cerioni

et al. 2009

Cytogenet Genome Res

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“…Supposing that the repeats originated from the IGS sequences, this phenomenon may represent one of the mechanisms of origin and amplification of satellite DNA in plants. On the other hand, there is also a possibility that the satellite sequences have transposed into rDNA spacers from other genomic regions, as proposed for V. faba (Maggini et al 1991). In any case, more information about these repeats and their genomic organization is needed to elucidate their evolutionary dynamics in the genome.…”

Section: Introductionmentioning

confidence: 94%

“…It has been established in all three species that these satellite sequences occur in blocks independent of the rRNA gene clusters (Maggini et al 1991;Unfried et al 1991;Falquet Communicated by B. McKee Accession numbers: GenBank AY234364-AY234374. The monomer sequences and additional information about the family of IGSlike repeat S12 will also appear in the PlantSat database (Macas et al 2002, http://w3lamc.umbr.cas.cz/PlantSat/) under Accession name Vicia_sativa_IGS-like et al 1997).…”

Section: Introductionmentioning

confidence: 99%

Sequence subfamilies of satellite repeats related to rDNA intergenic spacer are differentially amplified on Vicia sativa chromosomes

2003

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We cloned and sequenced the Vicia sativa 25S-18S rDNA intergenic spacer (IGS) and the satellite repeat S12, thought to be related to the spacer sequence. The spacer was shown to contain three types of subrepeats (A, B, and C) with monomers of 173 bp (A), 10 bp (B), and 66 bp (C), separated by unique or partially duplicated sequences. Two spacer variants were detected in V. sativa that differed in length (2990 and 3168 bp) owing to an extra copy of the subrepeat A. The A subrepeats were also shown to be highly homologous to the satellite repeat S12, which is located in large clusters on chromosomes 4, 5, and 6, and is not associated with the rDNA loci. Sequencing of additional S12 clones retrieved from a shotgun genomic library allowed definition of three subfamilies of this repeat based on minor differences in their nucleotide sequences. Two of these subfamilies could be discriminated from the rest of the S12 sequences as well as from the IGS A subrepeats using specific oligonucleotide primers that labeled only a subset of the S12 loci when used in the primed in situ DNA labeling (PRINS) reaction on mitotic chromosomes. These experiments showed that, in spite of the high overall similarity of the IGS A subrepeats and the S12 satellite repeats, there are S12 subfamilies that are divergent from the common consensus and are present at only some of the chromosomes containing the S12 loci. Thus, the subfamilies may have evolved at these loci following the spreading of the A subrepeats from the IGS to genomic regions outside the rDNA clusters.

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“…In V. faba, intraspecific alterations in the redundancy of tandemly repeated sequences have been demonstrated in the case of subrepeats in the intergenic spacer of the ribosomal DNA cistrons (cf. Maggini et al 1991) and of short DNA elements that can be isolated by digestion with FokI restriction endonuclease . Our present results show that dispersed repeats also can contribute to alterations in the amount of nuclear DNA.…”

Section: Discussionmentioning

confidence: 99%

A family of dispersed repeats in the genome of Vicia faba : structure, chromosomal organization, redundancy modulation, and evolution

et al. 1999

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A family of repeated DNA sequences of about 1200 bp in length and bordered by well-conserved, 18 bp inverted repeats (VfB family) was found in the nuclear genome of Vicia faba. The structure, chromosomal organization, redundancy modulation and evolution of these sequences were investigated. They are enriched in A+T base pairs (about 40% G+C) and lack any obvious internally repeated motif. A 64%-73% nucleotide sequence identity was found when pairwise comparisons between VfB sequences were carried out (average 69%). Direct repeats were not found to flank the inverted repeats that border these DNA sequences. The results obtained by hybridizing VfB repeats to Southern blots of V. faba genomic DNA digested with EcoRI indicated that these DNA elements are interspersed in the genome. The appearance of bands in these Southern blots and comparison of the structure of the sequences that flank different VfB elements showed that these repeats might be part of other, longer repeated DNA sequences. A high degree of dispersion throughout the genome was confirmed by cytological hybridization, which showed VfB sequences to be scattered along the length of all chromosomes and to be absent or rare only at heterochromatic chromosomal regions. These sequences contribute to intraspecific alterations of genomic size. Indeed, dot-blot hybridizations proved that their redundancy, which is positively correlated with the overall amount of nuclear DNA in each accession, varies between V. faba land races (27x10(3)-230x10(3) copies per 1C DNA). Southern blot hybridization of VfB repeats to restriction endonuclease-digested genomic DNAs of V. faba, V. narbonensis, V. sativa, Phaseolus coccineus, Populus deltoides, and Triticum durum revealed nucleotide sequence homology of these DNA elements, whatever the stringency conditions, only to the DNAs of Vicia species, and to a reduced extent to the DNAs of V. narbonensis and V. sativa compared with that of V. faba. It is concluded that VfB repeats might be descended from mobile DNA elements and contribute to change genomic size and organization during evolution.

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Structure and chromosomal localization of DNA sequences related to ribosomal subrepeats in Vicia faba

Cited by 53 publications

References 33 publications

Chromosomal study of native and hatchery trouts from Italy (<i>Salmo trutta </i>complex, Salmonidae): conventional and FISH analysis

Chromosomal study of native and hatchery trouts from Italy (<i>Salmo trutta </i>complex, Salmonidae): conventional and FISH analysis

Sequence subfamilies of satellite repeats related to rDNA intergenic spacer are differentially amplified on Vicia sativa chromosomes

A family of dispersed repeats in the genome of Vicia faba : structure, chromosomal organization, redundancy modulation, and evolution

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