Repetitive DNA: A Versatile Tool for Karyotyping in Festuca pratensis Huds.

2017 ◽  
Vol 151 (2) ◽  
pp. 96-105 ◽  
Author(s):  
Anna Křivánková ◽  
David Kopecký ◽  
Štěpán Stočes ◽  
Jaroslav Doležel ◽  
Eva Hřibová
Keyword(s):  
Structural Changes ◽  
Tandem Repeats ◽  
Molecular Organization ◽  
Rrna Genes ◽  
Grass Species ◽  
Similar Distribution ◽  
Festuca Pratensis ◽  
Dna Repeats ◽  
Meadow Fescue ◽  
Molecular Karyotype

FISH is a useful method to identify individual chromosomes in a karyotype and to discover their structural changes accompanying genome evolution and speciation. DNA probes for FISH should be chromosome specific and/or exhibit specific patterns of distribution along each chromosome. Such probes are not available in many plants including meadow fescue (Festuca pratensis Huds.), an important forage grass species. In the present study, various DNA repeats identified in Illumina shotgun sequences specific to chromosome 4F of F. pratensis were used as probes for FISH to develop the molecular karyotype of meadow fescue and to reveal a long-range molecular organization of its chromosomes. Five tandem repeats produced specific patterns on individual chromosomes. Their use in combination with probes for rRNA genes enabled the establishment of the molecular karyotype of meadow fescue. Most of the mobile genetic elements were dispersed along all the chromosomes except for the DNA transposon CACTA, which was localized preferentially to telomeric and subtelomeric regions, and a putative LTR element, which was localized to (peri)centromeric regions. Cytogenetic mapping of the 5 tandem repeats in other accessions of meadow fescue showed a highly similar distribution and confirmed the versatility and robustness of these probes.

Growth and Nutrient Uptake of Orchardgrass (Dactylis glomerata L.) and Meadow Fescue (Festuca pratensis Huds.) as Affected by Rhizobacteria

2016 ◽  
Vol 44 (1) ◽  
pp. 296-301 ◽  
Author(s):  
Olivera STAJKOVIĆ-SRBINOVIĆ ◽  
Dušica DELIĆ ◽  
Djordje KUZMANOVIĆ ◽  
Biljana SIKIRIĆ ◽  
Nataša RASULIĆ ◽  
...  
Keyword(s):  
Plant Growth ◽  
Dactylis Glomerata ◽  
Grass Species ◽  
Festuca Pratensis ◽  
Meadow Fescue ◽  
Total N ◽  
Plant Growth Promoting ◽  
Uninoculated Control ◽  
Growth Promoting ◽  
Dactylis Glomerata L

A diverse group of soil bacteria found in the rhizosphere which can colonize plant roots and improve plant growth are designated as plant growth promoting rhizobacteria. The aim of this study was isolation and screening of different rhizobacterial strains for plant growth promoting characteristics and their ability to improve growth of two grass species, orchardgrass (Dactylis glomerata L.) and meadow fescue (Festuca pratensis Huds.). The strains investigated, belonging to the genera Azotobacter, Bacillus, Pseudomonas and rhizobial bacteria, showed various plant growth promoting traits, such as phosphate solubilisation, siderophore production, and indole-3-acetic acid (IAA) production. Co-inoculation of meadow fescue with Azotobacter chroococcum A2 and Sinorhizobium meliloti or Pseudomonas sp., and A. chroococcum A5 with S. meliloti, significantly increased shoot dry weight (SDW)(25-33%), as well as total N (26-33%), P (24-31%) and K (26-28%) contents in plants (mg pot-1), compared to uninoculated control. In addition, inoculation of orchardgrass with A. chroococcum strain A1, as well as co-inoculation with B. megaterium and A. chroococcum A1 or A31, significantly increased SDW (51-59%) and total N (54-59%), P (51-74%) and K (49-55%) contents, compared to uninoculated control. Nitrogen percentage in SDW was slightly higher than sufficiency ranges, while K percentage was optimal in all treatments in both species. Phosphorous percentage was lower than sufficiency ranges as a consequence of very low soil P content. The results emphasize the potential of particular rhizobacteria to improve the growth of forage grasses.

scholarly journals ForageGrassBase: molecular resource for the forage grass meadow fescue (Festuca pratensis Huds.)

Database ◽  
2020 ◽  
Vol 2020 ◽  
Author(s):  
Jeevan Karloss Antony Samy ◽  
Odd Arne Rognli ◽  
Mallikarjuna Rao Kovi
Keyword(s):  
Draft Genome ◽  
Grass Species ◽  
Comparative Genomic ◽  
Festuca Pratensis ◽  
Forage Grass ◽  
Forage Grasses ◽  
Meadow Fescue ◽  
Crop Species ◽  
Genome Database ◽  
Genomic Resources

Abstract Meadow fescue (Festuca pratensis Huds.) is one of the most important forage grasses in temperate regions. It is a diploid (2n = 14) outbreeding species that belongs to the genus Festuca. Together with Lolium perenne, they are the most important genera of forage grasses. Meadow fescue has very high quality of yield with good winter survival and persistency. However, extensive genomic resources for meadow fescue have not become available so far. To address this lack of comprehensive publicly available datasets, we have developed functionally annotated draft genome sequences of two meadow fescue genotypes, ‘HF7/2’ and ‘B14/16’, and constructed the platform ForageGrassBase, available at http://foragegrass.org/, for data visualization, download and querying. This is the first open-access platform that provides extensive genomic resources related to this forage grass species. The current database provides the most up-to-date draft genome sequence along with structural and functional annotations for genes that can be accessed using Genome Browser (GBrowse), along with comparative genomic alignments to Arabidopsis, L. perenne, barley, rice, Brachypodium and maize genomes. We have integrated homologous search tool BLAST also for the users to analyze their data. Combined, GBrowse, BLAST and downloadable data gives a user-friendly access to meadow fescue genomic resources. To our knowledge, ForageGrassBase is the first genome database dedicated to forage grasses. The current forage grass database provides valuable resources for a range of research fields related to meadow fescue and other forage crop species, as well as for plant research communities in general. The genome database can be accessed at http://foragegrass.org.

Comparison of meadow fescue and meadow bromegrass in monoculture and in association with white clover

2009 ◽  
Vol 89 (6) ◽  
pp. 1059-1063 ◽  
Author(s):  
R Drapeau ◽  
G Bélanger
Keyword(s):  
Key Words ◽  
White Clover ◽  
Trifolium Repens ◽  
Grass Species ◽  
Growing Degree Days ◽  
Festuca Pratensis ◽  
Degree Days ◽  
Meadow Fescue ◽  
Bromus Riparius ◽  
Meadow Bromegrass

Meadow fescue and meadow bromegrass alone or with white clover were compared in a four cut system in a region with less than 1400 growing degree days. Cultivars of the two grass species did not affect yield. The annual yields of two grass species, alone or with white clover, were similar in the first production year, but in second and third production years, meadow bromegrass yielded more than meadow fescue. The persistence of white clover, alone or with a grass, was limited. Key words: Festuca pratensis, Bromus riparius, Trifolium repens, yield

scholarly journals Non-Coding, RNAPII-Dependent Transcription at the Promoters of rRNA Genes Regulates Their Chromatin State in S. cerevisiae

2021 ◽  
Vol 7 (3) ◽  
pp. 41
Author(s):  
Emma Lesage ◽  
Jorge Perez-Fernandez ◽  
Sophie Queille ◽  
Christophe Dez ◽  
Olivier Gadal ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Tandem Repeats ◽  
Chromatin State ◽  
Rrna Genes ◽  
Rdna Genes ◽  
Regulatory Pathways ◽  
Chromatin States ◽  
Non Coding Rnas ◽  
Pervasive Transcription

Pervasive transcription is widespread in eukaryotes, generating large families of non-coding RNAs. Such pervasive transcription is a key player in the regulatory pathways controlling chromatin state and gene expression. Here, we describe long non-coding RNAs generated from the ribosomal RNA gene promoter called UPStream-initiating transcripts (UPS). In yeast, rDNA genes are organized in tandem repeats in at least two different chromatin states, either transcribed and largely depleted of nucleosomes (open) or assembled in regular arrays of nucleosomes (closed). The production of UPS transcripts by RNA Polymerase II from endogenous rDNA genes was initially documented in mutants defective for rRNA production by RNA polymerase I. We show here that UPS are produced in wild-type cells from closed rDNA genes but are hidden within the enormous production of rRNA. UPS levels are increased when rDNA chromatin states are modified at high temperatures or entering/leaving quiescence. We discuss their role in the regulation of rDNA chromatin states and rRNA production.

A Demonstration of a 1:1 Correspondence Between Chiasma Frequency and Recombination Using a Lolium perenne/Festuca pratensis Substitution

Genetics ◽  
2002 ◽  
Vol 161 (1) ◽  
pp. 307-314 ◽  
Author(s):  
J King ◽  
L A Roberts ◽  
M J Kearsey ◽  
H M Thomas ◽  
R N Jones ◽  
...  
Keyword(s):  
Lolium Perenne ◽  
Chiasma Frequency ◽  
Chiasma Formation ◽  
Grass Species ◽  
Festuca Pratensis ◽  
Single Chromosome ◽  
Length Polymorphisms ◽  
Amplified Fragment Length Polymorphisms ◽  
Frequency Counts

Abstract A single chromosome of the grass species Festuca pratensis has been introgressed into Lolium perenne to produce a diploid monosomic substitution line (2n = 2x = 14). The chromatin of F. pratensis and L. perenne can be distinguished by genomic in situ hybridization (GISH), and it is therefore possible to visualize the substituted F. pratensis chromosome in the L. perenne background and to study chiasma formation in a single marked bivalent. Recombination occurs freely in the F. pratensis/L. perenne bivalent, and chiasma frequency counts give a predicted map length for this bivalent of 76 cM. The substituted F. pratensis chromosome was also mapped with 104 EcoRI/Tru91 and HindIII/Tru91 amplified fragment length polymorphisms (AFLPs), generating a marker map of 81 cM. This map length is almost identical to the map length of 76 cM predicted from the chiasma frequency data. The work demonstrates a 1:1 correspondence between chiasma frequency and recombination and, in addition, the absence of chromatid interference across the Festuca and Lolium centromeres.

Highly Condensed Potato Pericentromeric Heterochromatin Contains rDNA-Related Tandem Repeats

Genetics ◽  
2002 ◽  
Vol 162 (3) ◽  
pp. 1435-1444 ◽  
Author(s):  
Robert M Stupar ◽  
Junqi Song ◽  
Ahmet L Tek ◽  
Zhukuan Cheng ◽  
Fenggao Dong ◽  
...  
Keyword(s):  
Repetitive Dna ◽  
Dna Sequences ◽  
Tandem Repeats ◽  
Intergenic Spacer ◽  
Pericentromeric Heterochromatin ◽  
Dna Repeats ◽  
Solanum Bulbocastanum ◽  
Origin And Evolution ◽  
Potato Genome ◽  
Dna Elements

Abstract The heterochromatin in eukaryotic genomes represents gene-poor regions and contains highly repetitive DNA sequences. The origin and evolution of DNA sequences in the heterochromatic regions are poorly understood. Here we report a unique class of pericentromeric heterochromatin consisting of DNA sequences highly homologous to the intergenic spacer (IGS) of the 18S•25S ribosomal RNA genes in potato. A 5.9-kb tandem repeat, named 2D8, was isolated from a diploid potato species Solanum bulbocastanum. Sequence analysis indicates that the 2D8 repeat is related to the IGS of potato rDNA. This repeat is associated with highly condensed pericentromeric heterochromatin at several hemizygous loci. The 2D8 repeat is highly variable in structure and copy number throughout the Solanum genus, suggesting that it is evolutionarily dynamic. Additional IGS-related repetitive DNA elements were also identified in the potato genome. The possible mechanism of the origin and evolution of the IGS-related repeats is discussed. We demonstrate that potato serves as an interesting model for studying repetitive DNA families because it is propagated vegetatively, thus minimizing the meiotic mechanisms that can remove novel DNA repeats.

Regular arrangement of nucleosomes on 5S rRNA genes in Xenopus laevis

1983 ◽  
Vol 3 (4) ◽  
pp. 720-730
Author(s):  
D Young ◽  
D Carroll
Keyword(s):  
Xenopus Laevis ◽  
Chromatin Structure ◽  
Micrococcal Nuclease ◽  
Rrna Genes ◽  
Dna Repeats ◽  
5S Rna ◽  
5S Dna ◽  
Regular Arrangement ◽  
5S Rna Genes ◽  
Rna Genes

The chromatin structure of the oocyte-type 5S RNA genes in Xenopus laevis was investigated. Blot hybridization analysis of DNA from micrococcal nuclease digests of erythrocyte nuclei showed that 5S DNA has the same average nucleosome repeat length, 192 +/- 4 base pairs, as two Xenopus satellite DNAs and bulk erythrocyte chromatin. The positions of nuclease-sensitive regions in the 5S DNA repeats of purified DNA and chromatin from erythrocytes were mapped by using an indirect end-labeling technique. Although most of the sites cleaved in purified DNA were also cleaved in chromatin, the patterns of intensities were strikingly different in the two cases. In 5S chromatin, three nuclease-sensitive regions were spaced approximately a nucleosome length apart, suggesting a single, regular arrangement of nucleosomes on most of the 5S DNA repeats. The observed nucleosome locations are discussed with respect to nucleotide sequences known to be important for expression of 5S RNA. Because the preferred locations appear to be reestablished in each repeating unit, despite spacer length heterogeneity, we suggest that the regular chromatin structure reflects the presence of a sequence-specific DNA-binding component on inactive 5S RNA genes.

scholarly journals Application of SCoT markers for accessing of genetic diversity of gramineous forage grass species

2021 ◽  
Vol 901 (1) ◽  
pp. 012038
Author(s):  
Yu M Mavlyutov ◽  
A O Shamustakimova ◽  
I A Klimenko
Keyword(s):  
Lolium Multiflorum ◽  
Molecular Genetic ◽  
Grass Species ◽  
Festuca Rubra ◽  
Festuca Pratensis ◽  
Forage Grass ◽  
Marker System ◽  
Scot Marker ◽  
Dna Profiles ◽  
Subsequent Identification

Abstract Using the SCoT marker system, 8 varieties of cereal grasses belonging to 5 species were analyzed: Festuca pratensis, Lolium perenne, Lolium multiflorum, Festuca rubra, Festulolium. Of the 10 tested SCoT markers, 7 informative markers were selected that reveal interspecies genetic polymorphism. According to the results of the analysis, DNA profiles characteristic of each studied species were obtained, and primers allowing to detect intervarietal differences for subsequent identification and molecular genetic passportization were selected.

scholarly journals Mapping-based all-RNA-information sequencing analysis (ARIseq) pipeline simultaneously revealed taxonomic composition, gene expression, and their correlation in an acidic stream ecosystem

2017 ◽  
Author(s):  
Arisa Tsuboi ◽  
Misao Itoga ◽  
Yuichi Hongoh ◽  
Shigeharu Moriya
Keyword(s):  
Gene Expression ◽  
Expression Patterns ◽  
Taxonomic Composition ◽  
Rrna Genes ◽  
Reference Database ◽  
Similar Distribution ◽  
Sequencing Analysis ◽  
Protein Coding ◽  
Microbial Ecosystems ◽  
Sulfur Oxidizing

AbstractWe developed a new pipeline for simultaneous analyses of both rRNA profile as a taxonomic marker and mRNA profile as a functional marker, to understand microbial ecosystems in natural environments. Our pipeline, named All-RNA-Information sequencing (ARIseq), comprises a high-throughput sequencing of reverse transcribed total RNA and several widely used computational tools, and generates quantitatively reliable information on both community structures and gene expression patterns, which were verified by quantitative PCR analyses in this study. Particularly, correlation network analysis in the pipeline can reveal microbial taxa and expressed genes that share patterns of dynamics among different time and/or geographical points. The pipeline is primarily mapping-based, using a public database for small subunit rRNA genes and obtained contigs as the reference database for protein-coding genes. We applied this pipeline to biofilm samples, as examples, collected from an acidic spring water stream in the Chyatsubomi-goke Park in Gunma prefecture, Japan. Our analyses revealed the predominance of iron and sulfur-oxidizing bacteria and Pinnularia diatoms, and also indicated that the distributions of the iron-sulfur-oxidizing bacterial consortium and the Pinnularia diatoms largely overlapped but showed distinct patterns. In addition, our analyses showed that the iron-oxidizing bacterial genus Acidithiobacillus and co-occurring Acidiphilium shared similar distribution pattern whereas another iron-oxidizing genus Leptospirillum exhibited a distinct pattern. Our pipeline enables researchers to more easily capture the outline of microbial ecosystems based on the taxonomic composition, protein-coding gene expression, and their correlations.

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