Investigations of 5S rDNA of Vitis vinifera L.: sequence analysis and physical mapping

Genome ◽  
2007 ◽  
Vol 50 (10) ◽  
pp. 927-938 ◽  
Author(s):  
E. Falistocco ◽  
V. Passeri ◽  
G. Marconi
Keyword(s):  
Vitis Vinifera ◽  
Repeat Unit ◽  
5S Rdna ◽  
Nucleotide Composition ◽  
Large Deletion ◽  
Rrna Genes ◽  
Vitis Vinifera L ◽  
Fish Analysis ◽  
Rdna Sequences ◽  
Short Repeat

Here we report the first results of a study of 5S rDNA of Vitis vinifera . 5S rDNA sequences from seven genotypes were amplified by PCR, cloned, and sequenced. Three types of repeats were found. Two variants, denominated long repeat and short repeat, appeared to be the main components of the 5S rDNA of this species, since they were found in all genotypes analyzed. They differed markedly from each other in both the length and the nucleotide composition of the spacers. The third variant, classified as DEL short repeat, differs from the short repeat owing to a large deletion in the spacer region. It appears to be the most recent repeat type, since it was identified in only one genotype. The organization of the 5S rDNA repeat unit variants was investigated by amplifying the genomic DNA with primers designed on the sequence of the long and short spacers. The PCR-amplified fragments showed that the long repeat is associated with the other two repeats, indicating that in V. vinifera different repeat units coexist within the same tandem array. FISH analysis demonstrated that 5S rRNA genes are localized at a single locus. The variability of 5S rDNA repeats is discussed in relation to the putative allopolyploid origin of V. vinifera.

Novel variants of the 5S rRNA genes in Eruca sativa

Genome ◽  
1994 ◽  
Vol 37 (1) ◽  
pp. 121-128 ◽  
Author(s):  
Kapil Singh ◽  
Sabhyata Bhatia ◽  
Malathi Lakshmikumaran
Keyword(s):  
Repeat Unit ◽  
5S Rdna ◽  
5S Rrna ◽  
Rrna Genes ◽  
Gene Variants ◽  
Eruca Sativa ◽  
Coding Region ◽  
Coding Regions ◽  
Rdna Sequences ◽  
5S Rrna Genes

The 5S ribosomal RNA (rRNA) genes of Eruca sativa were cloned and characterized. They are organized into clusters of tandemly repeated units. Each repeat unit consists of a 119-bp coding region followed by a noncoding spacer region that separates it from the coding region of the next repeat unit. Our study reports novel gene variants of the 5S rRNA genes in plants. Two families of the 5S rDNA, the 0.5-kb size family and the l-kb size family, coexist in the E. sativa genome. The 0.5-kb size family consists of the 5S rRNA genes (S4) that have coding regions similar to those of other reported plant 5S rDNA sequences, whereas the 1-kb size family consists of the 5S rRNA gene variants (S1) that exist as 1-kb BamHI tandem repeats. S1 is made up of two variant units (V1 and V2) of 5S rDNA where the BamHI site between the two units is mutated. Sequence heterogeneity among S4, V1, and V2 units exists throughout the sequence and is not limited to the noncoding spacer region only. The coding regions of V1 and V2 show approximately 20% dissimilarity to the coding regions of S4 and other reported plant 5S rDNA sequences. Such a large variation in the coding regions of the 5S rDNA units within the same plant species has been observed for the first time. Restriction site variation is observed between the two size classes of 5S rDNA in E. sativa. The noncoding spacers of the variants V1 and V2 that make up the 1-kb family lack the EcoRI site that is present in the 0.5-kb family. The sequence analysis indicates that V1 and V2 sequences are probably pseudogenes derived from functional 5S rRNA genes. The results also suggest that the two families exist as independent clusters at different locations in the E. sativa genome.Key words: 5S rRNA genes, crucifers, Eruca sativa, organization, sequence analysis.

The 5S rRNA gene units in ancestral two-rowed barley (Hordeum spontaneum C. Koch) and bulbous barley (H. bulbosum L.): sequence analysis and phylogenetic relationships with the 5S rDNA units of cultivated barley (H. vulgare L.)

Genome ◽  
1996 ◽  
Vol 39 (1) ◽  
pp. 140-149 ◽  
Author(s):  
Bernard R. Baum ◽  
Douglas A. Johnson
Keyword(s):  
Phylogenetic Analysis ◽  
5S Rdna ◽  
Hordeum Spontaneum ◽  
Wild Relatives ◽  
5S Rrna ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Sequence Comparisons ◽  
Rdna Sequences ◽  
Cultivated Barley

5S rRNA genes from several accessions of Hordeum spontaneum and Hordeum bulbosum, wild relatives of cultivated barley, Hordeum vulgare, have been amplified by the polymerase chain reaction, cloned, and sequenced. Evaluation of aligned sequences along with principal coordinate analysis demonstrates that the two classes of 5S rDNA sequences found in cultivated barley, and subclasses (groups) of these sequences, can also be found in its closest wild relatives. The two classes of units, formerly categorized as containing short or long 5S rDNA repeats, are distinguishable by the presence or absence of a TAG repeating unit. Sequence comparisons of individual clones (units) isolated from different species have allowed us to confirm that orthology exists for several groups. This demonstration of orthologous groups suggests that the 5S rDNA sequence may be useful for further phylogenetic analysis in the genus Hordeum and possibly in the Triticeae. Key words : 5S rDNA, barley, sequence diversity, phylogenetic analysis.

Structure of the 5S rRNA genes in birch (Betula papyrifera) and alder (Alnus incana)

Genome ◽  
1992 ◽  
Vol 35 (2) ◽  
pp. 337-341 ◽  
Author(s):  
D. A. Johnson ◽  
C. C-Y. Chan ◽  
S. G. Gottlob-McHugh ◽  
K. Mackenzie ◽  
L. Marengère ◽  
...  
Keyword(s):  
Repeat Unit ◽  
Evolutionary Relationship ◽  
5S Rdna ◽  
Repeat Sequence ◽  
Rrna Genes ◽  
Alnus Incana ◽  
Betula Papyrifera ◽  
Repeat Units ◽  
5S Rrna Genes ◽  
Triple Band

Hybridization of a 5S rDNA probe to Southern transfers of birch (Betula papyrifera) or alder (Alnus incana) DNA digested with BamH1 reveals similar triple-band "ladder-like" patterns. The sizes of sequenced 5S repeat units from both plants ranges only from 471 to 490 base pairs, suggesting that the complexity detected by Southern analysis is not due to different size classes of 5S repeats as found in other species. Within the intercistronic spacer region, conservation of large blocks of sequence between birch and alder 5S is observed implying a close evolutionary relationship between these two species. In both species, a duplication of part of the coding sequence including a restriction site for BamH1 introduces a second BamH1 site into the repeat unit. Differential methylation of the two BamH1 restriction sites can account for the observed triple-band pattern.Key words: 5S rDNA repeat, sequence, methylation, birch, alder.

5S rRNA genes in tribe Phaseoleae: array size, number, and dynamics

Genome ◽  
1996 ◽  
Vol 39 (2) ◽  
pp. 445-455 ◽  
Author(s):  
Kathleen J. Danna ◽  
Rachel Workman ◽  
Virginia Coryell ◽  
Paul Keim
Keyword(s):  
Gel Electrophoresis ◽  
Copy Number ◽  
Glycine Soja ◽  
Repeat Unit ◽  
Diploid Species ◽  
5S Rdna ◽  
5S Rrna ◽  
Array Size ◽  
Rrna Genes ◽  
5S Rrna Genes

The organization of 5S rRNA genes in plants belonging to tribe Phaseoleae was investigated by clamped homogeneous electric field gel electrophoresis and Southern blot hybridization. Representatives of subtribe Glycininae included the diploid species Neonotonia wightii and Teramnus labialis, as well as three soybean accessions: an elite Glycine max (L.) Merr. cultivar (BSR101), an unadapted G. max introduction (PI 437.654), and a wild Glycine soja (PI 468.916). A cultivar of Phaseolus vulgaris (kidney bean), a member of subtribe Phaseolinae, was also examined. We determined the number of 5S rDNA arrays and estimated the size and copy number of the repeat unit for each array. The three soybean accessions all have a single 5S locus, with a repeat unit size of ~345 bp and a copy number ranging from about 600 in 'BSR101' to about 4600 in the unadapted soybean introduction. The size of the 5S gene cluster in 'BSR101' is the same in roots, shoots, and trifoliate leaves. Given that the genus Glycine probably has an allotetraploid origin, our data strongly suggest that one of the two progenitor 5S loci has been lost during diploidization of soybean. Neonotonia wightii, the diploid species most closely related to soybean, also has a single locus but has a repeat unit of 520 bp and a copy number of about 1300. The more distantly related species T. labialis and P. vulgaris exhibited a more complex arrangement of 5S rRNA genes, having at least three arrays, each comprising a few hundred copies of a distinct repeat unit. Although each array in P. vulgaris exhibits a high degree of homogeneity with regard to the sequence of the repeat unit, heterogeneity in array size (copy number) was evident when individual plants were compared. A cis-dependent molecular drive process, such as unequal crossing-over, could account for both the homogenization of repeat units within individual arrays and the observed variation in copy number among individuals. Key words : pulsed-field gel electrophoresis, rRNA genes, soybean, tandem arrays.

FISH-mapping of rDNAs and Arabidopsis BACs on pachytene complements of selected Brassicas

Genome ◽  
2002 ◽  
Vol 45 (1) ◽  
pp. 189-197 ◽  
Author(s):  
Piotr A Ziolkowski ◽  
Jan Sadowski
Keyword(s):  
In Situ Hybridization ◽  
Physical Mapping ◽  
5S Rdna ◽  
Artificial Chromosome ◽  
Rdna Locus ◽  
Fish Analysis ◽  
45S Rdna ◽  
Fish Mapping ◽  
Rdna Sequences

To improve resolution of physical mapping on Brassica chromosomes, we have chosen the pachytene stage of meiosis where incompletely condensed bivalents are much longer than their counterparts at mitotic metaphase. Mapping with 5S and 45S rDNA sequences demonstrated the advantage of pachytene chromosomes in efficient physical mapping and confirmed the presence of a novel 5S rDNA locus in Brassica oleracea, initially identified by genetic mapping using restriction fragment length polymorphism (RFLP). Fluorescence in situ hybridization (FISH) analysis visualized the presence of the third 5S rDNA locus on the long arm of chromosome C2 and confirmed the earlier reports of two 45S rDNA loci in the B. oleracea genome. FISH mapping of low-copy sequences from the Arabidopsis thaliana bacterial artificial chromosome (BAC) clones on the B. oleracea chromosomes confirmed the expectation of efficient and precise physical mapping of meiotic bivalents based on data available from A. thaliana and indicated conserved organization of these two BAC sequences on two B. oleracea chromosomes. Based on the heterologous in situ hybridization with BACs and their mapping applied to long pachytene bivalents, a new approach in comparative analysis of Brassica and A. thaliana genomes is discussed.Key words: Brassicaceae, pachytene chromosomes, FISH, rDNA, BACs.

scholarly journals Chromosomal mapping of H3 histone and 5S rRNA genes in eight species of Astyanax (Pisces, Characiformes) with different diploid numbers: syntenic conservation of repetitive genes

Genome ◽  
2016 ◽  
Vol 59 (3) ◽  
pp. 167-172 ◽  
Author(s):  
Diovani Piscor ◽  
Patricia Pasquali Parise-Maltempi
Keyword(s):  
Genomic Organization ◽  
5S Rdna ◽  
Gene Families ◽  
5S Rrna ◽  
Chromosomal Mapping ◽  
Rrna Genes ◽  
Rdna Sequences ◽  
Cytogenetic Studies ◽  
5S Rrna Genes ◽  
Syntenic Conservation

The genus Astyanax is widely distributed from the southern United States to northern Patagonia, Argentina. While cytogenetic studies have been performed for this genus, little is known about the histone gene families. The aim of this study was to examine the chromosomal relationships among the different species of Astyanax. The chromosomal locations of the 5S rRNA and H3 histone genes were determined in A. abramis, A. asuncionensis, A. altiparanae, A. bockmanni, A. eigenmanniorum, A. mexicanus (all 2n = 50), A. fasciatus (2n = 46), and A. schubarti (2n = 36). All eight species exhibited H3 histone clusters on two chromosome pairs. In six species (A. abramis, A. asuncionensis, A. altiparanae, A. bockmanni, A. eigenmanniorum, and A. fasciatus), syntenic clusters of H3 histone and 5S rDNA were observed on metacentric (m) or submetacentric (sm) chromosomes. In seven species, clusters of 5S rDNA sequences were located on one or two chromosome pairs. In A. mexicanus, 5S rDNA clusters were located on four chromosome pairs. This study demonstrates that H3 histone clusters are conserved on two chromosome pairs in the genus Astyanax, and specific chromosomal features may contribute to the genomic organization of the H3 histone and 5S rRNA genes.

Resveratrol oligomers from Vitis Vinifera L. stems

Planta Medica ◽  
2007 ◽  
Vol 73 (09) ◽  
Author(s):  
H Amira-Guebailia ◽  
T Richard ◽  
S Rouaiguia ◽  
P Waffo Tueguo ◽  
JC Delaunay ◽  
...  
Keyword(s):  
Vitis Vinifera ◽  
Vitis Vinifera L

Biotransformation of 4-hydroxybenzoic acid in the rhizosphere of grapevine (Vitis vinifera L.)

2017 ◽  
Vol 40 (1) ◽  
pp. 95-102 ◽  
Author(s):  
B. Wang ◽  
T. Zhou1 ◽  
K. Li ◽  
X.W. Guo ◽  
Y.S. Guo ◽  
...  
Keyword(s):  
Vitis Vinifera ◽  
Vitis Vinifera L ◽  
Hydroxybenzoic Acid

Isolation and characterization of cell walls from the mesocarp of mature grape berries (Vitis vinifera)

2020 ◽  
Author(s):  
KJ Nunan ◽  
Ian Sims ◽  
A Bacic ◽  
SP Robinson ◽  
GB Fincher
Keyword(s):  
Vitis Vinifera ◽  
Cell Walls ◽  
Vascular Tissue ◽  
Compositional Analysis ◽  
Water Soluble ◽  
Vitis Vinifera L ◽  
Nylon Mesh ◽  
Cytoplasmic Material ◽  
Isolation And Characterization ◽  
Tissue Homogenates

Cell walls have been isolated from the mesocarp of mature grape (Vitis vinifera L.) berries. Tissue homogenates were suspended in 80% (v/v) ethanol to minimise the loss of water-soluble wall components and wet-sieved on nylon mesh to remove cytoplasmic material. The cell wall fragments retained on the sieve were subsequently treated with buffered phenol at pH 7.0, to inactivate any wall-bound enzymes and to dislodge small amounts of cytoplasmic proteins that adhered to the walls. Finally, the wall preparation was washed with chloroform/methanol (1:1, v/v) to remove lipids and dried by solvent exchange. Scanning electron microscopy showed that the wall preparation was essentially free of vascular tissue and adventitious protein of cytoplasmic origin. Compositional analysis showed that the walls consisted of approximately 90% by weight of polysaccharide and less than 10% protein. The protein component of the walls was shown to be rich in arginine and hydroxyproline residues. Cellulose and polygalacturonans were the major constituents, and each accounted for 30-40% by weight of the polysaccharide component of the walls. Substantial varietal differences were observed in the relative abundance of these two polysaccharides. Xyloglucans constituted approximately 10% of the polysaccharide fraction and the remainder was made up of smaller amounts of mannans, heteroxylans, arabinans and galactans.

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