Chromosomal Mapping of Ribosomal rRNA Genes in the Small Rock Oyster, Saccostrea mordax (Gould 1850)

2011 ◽  
Author(s):  
Wang Yan
Keyword(s):  
Chromosomal Mapping ◽  
Rrna Genes ◽  
Rock Oyster ◽  
Ribosomal Rrna Genes ◽  
Ribosomal Rrna

scholarly journals Use of 16S ribosomal (rRNA) genes and immunofluorescence microscopy to detect prosthetic hip infection

1998 ◽  
Vol 50 (S9) ◽  
pp. 37-37 ◽  
Author(s):  
M. M. Tunney ◽  
G. Ramage ◽  
S. Patrick ◽  
M. Curran ◽  
J. R. Nixon ◽  
...  
Keyword(s):  
Immunofluorescence Microscopy ◽  
Rrna Genes ◽  
Hip Infection ◽  
Ribosomal Rrna Genes ◽  
Ribosomal Rrna

scholarly journals Long-read DNA metabarcoding of ribosomal rRNA in the analysis of fungi from aquatic environments

2018 ◽  
Author(s):  
Felix Heeger ◽  
Elizabeth C. Bourne ◽  
Christiane Baschien ◽  
Andrey Yurkov ◽  
Boyke Bunk ◽  
...  
Keyword(s):  
De Novo ◽  
Error Rates ◽  
Rrna Genes ◽  
Taxonomic Resolution ◽  
Sequencing Error ◽  
Rrna Gene ◽  
Dna Metabarcoding ◽  
Long Read ◽  
Reference Sequences ◽  
Ribosomal Rrna

ABSTRACTDNA metabarcoding is now widely used to study prokaryotic and eukaryotic microbial diversity. Technological constraints have limited most studies to marker lengths of ca. 300-600 bp. Longer sequencing reads of several 5 thousand bp are now possible with third-generation sequencing. The increased marker lengths provide greater taxonomic resolution and enable the use of phylogenetic methods of classifcation, but longer reads may be subject to higher rates of sequencing error and chimera formation. In addition, most well-established bioinformatics tools for DNA metabarcoding were originally 10 designed for short reads and are therefore not suitable. Here we used Pacifc Biosciences circular consensus sequencing (CCS) to DNA-metabarcode environmental samples using a ca. 4,500 bp marker that included most of the eukaryote ribosomal SSU and LSU rRNA genes and the ITS spacer region. We developed a long-read analysis pipeline that reduced error rates to levels 15 comparable to short-read platforms. Validation using fungal isolates and a mock community indicated that our pipeline detected 98% of chimeras de novo i.e., even in the absence of reference sequences. We recovered 947 OTUs from water and sediment samples in a natural lake, 848 of which could be classifed to phylum, 486 to family, 397 to genus and 330 to species. By 20 allowing for the simultaneous use of three global databases (Unite, SILVA, RDP LSU), long-read DNA metabarcoding provided better taxonomic resolution than any single marker. We foresee the use of long reads enabling the cross-validation of reference sequences and the synthesis of ribosomal rRNA gene databases. The universal nature of the rRNA operon and our recovery of >100 25 non-fungal OTUs indicate that long-read DNA metabarcoding holds promise for the study of eukaryotic diversity more broadly.

scholarly journals Chromosomal mapping of rRNA genes, core histone genes and telomeric sequences in Brachidontes puniceus and Brachidontes rodriguezi (Bivalvia, Mytilidae)

BMC Genetics ◽  
2010 ◽  
Vol 11 (1) ◽  
pp. 109 ◽  
Author(s):  
Concepción Pérez-García ◽  
Jorge Guerra-Varela ◽  
Paloma Morán ◽  
Juan J Pasantes
Keyword(s):  
Chromosomal Mapping ◽  
Core Histone ◽  
Rrna Genes ◽  
Histone Genes ◽  
Telomeric Sequences

Chromosomal mapping of mouse 5S rRNA genes by direct R-banding fluorescence in situ hybridization

1994 ◽  
Vol 66 (4) ◽  
pp. 246-249 ◽  
Author(s):  
Y. Matsuda ◽  
K. Moriwaki ◽  
V.M. Chapman ◽  
Y. Hoi-Sen ◽  
J. Akbarzadeh ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Fluorescence In Situ Hybridization ◽  
5S Rrna ◽  
Chromosomal Mapping ◽  
Rrna Genes ◽  
5S Rrna Genes

Chromosomal mapping of 18S–28S and 5S rRNA genes by two-colour fluorescent in situ hybridization in six sturgeon species

Genome ◽  
2003 ◽  
Vol 46 (3) ◽  
pp. 473-477 ◽  
Author(s):  
Francesco Fontana ◽  
Massimo Lanfredi ◽  
Leonardo Congiu ◽  
Marilena Leis ◽  
Milvia Chicca ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Close Association ◽  
5S Rdna ◽  
28S Rdna ◽  
5S Rrna ◽  
Chromosomal Mapping ◽  
Rrna Genes ◽  
Acipenser Baerii ◽  
Sturgeon Species

The number and distribution of the 18S–28S and 5S rRNA (rDNA) gene sequences were examined on mitotic chromosomes of six sturgeon species by two-colour in situ hybridization. Four of the six species, Huso huso, Acipenser stellatus, Acipenser sturio, and Acipenser ruthenus, with about 120 chromosomes, showed from six to eight 18S–28S rDNA signals, while 5S rDNA signals were on only one chromosome pair. The two species with 250–270 chromosomes, Acipenser baerii and Acipenser transmontanus, showed from 10 to 12 18S–28S sites and two chromosome pairs bearing 5S rDNA signals. In all examined species, the rather intense 5S rDNA signals apparently overlapped those of 18S–28S rDNA. These data support the diploid–tetraploid relationships between the two chromosome groups of sturgeons. The close association between the two rDNA families in species belonging to an ancestral fish order, such as Acipenseriformes, supports the hypothesis that the association represents a primitive condition.Key words: Acipenseriformes, FISH, fish cytogenetics, ribosomal genes.

Chromosomal Mapping of Repeat DNA in Bergiaria westermanni (Pimelodidae, Siluriformes): Localization of 45S rDNA in B Chromosomes

2018 ◽  
Vol 154 (2) ◽  
pp. 99-106 ◽  
Author(s):  
Geovana C. Malimpensa ◽  
Josiane B. Traldi ◽  
Danyelle Toyama ◽  
Flávio Henrique-Silva ◽  
Marcelo R. Vicari ◽  
...  
Keyword(s):  
Chromosomal Rearrangements ◽  
Indirect Evidence ◽  
5S Rdna ◽  
B Chromosomes ◽  
Chromosomal Mapping ◽  
Interindividual Variation ◽  
Rrna Genes ◽  
45S Rdna ◽  
Rdna Sites ◽  
Repeat Dna

The occurrence of repetitive DNA in autosomes and B chromosomes of Bergiaria westermanni was examined using conventional and molecular cytogenetic techniques. This species exhibited 2n = 56 chromosomes, with intra- and interindividual variation in the number of heterochromatic B chromosomes (from 0 to 4). The 5S rDNA was localized in pairs 1 and 5, and histone probes (H1, H3, and H4) and U2 small nuclear RNA were syntenic with 5S rDNA in pair 5. Histone sequences were also located in chromosome pair 14. The (GATA)n sequence was dispersed throughout the autosomes and B chromosomes, with clusters (microsatellite accumulation) in some chromosome regions. The telomeric probe revealed no signs of chromosomal rearrangements in the genome of B. westermanni. The 45S rDNA sites were detected in the terminal region of pair 27; these sites corresponded to a GC-rich heterochromatin block. In addition, 3 of the 4 B chromosomes also contained 45S rDNA copies. Silver nitrate staining in interphase nuclei provided indirect evidence of the expression of these rRNA genes in B chromosomes, indicating the probable origin of these elements. This report shows plasticity in the chromosomal localization of repeat DNA in B. westermanni and features a discussion of genomic diversification.

scholarly journals Cost-efficient high throughput capture of museum arthropod specimen DNA using PCR-generated baits

2018 ◽  
Author(s):  
Alexander Knyshov ◽  
Eric R.L. Gordon ◽  
Christiane Weirauch
Keyword(s):  
A Priori ◽  
Rrna Genes ◽  
Model Organisms ◽  
List Type ◽  
Data Generation ◽  
Reduced Representation ◽  
Cost Efficient ◽  
The Cost ◽  
Ribosomal Rrna Genes ◽  
Complete Mitochondrial Genomes

AbstractGathering genetic data for rare species is one of the biggest remaining obstacles in modern phylogenetics, particularly for megadiverse groups such as arthropods. Next generation sequencing techniques allow for sequencing of short DNA fragments contained in preserved specimens >20 years old, but approaches such as whole genome sequencing are often too expensive for projects including many taxa. Several methods of reduced representation sequencing have been proposed that lower the cost of sequencing per specimen, but many remain costly because they involve synthesizing nucleotide probes and target hundreds of loci. These datasets are also frequently unique for each project and thus generally incompatible with other similar datasets.Here, we explore utilization of in-house generated DNA baits to capture commonly utilized mitochondrial and ribosomal DNA loci from insect museum specimens of various age and preservation types without the a priori need to know the sequence of the target loci. Both within species and cross-species capture are explored, on preserved specimens ranging in age from one to 54 years old.We found most samples produced sufficient amounts of data to assemble the nuclear ribosomal rRNA genes and near complete mitochondrial genomes and produce well-resolved phylogenies in line with expected results. The dataset obtained can be straightforwardly combined with the large cache of existing Sanger-sequencing-generated data built up over the past 30 years and targeted loci can be easily modified to those commonly used in different taxa. Furthermore, the protocol we describe allows for inexpensive data generation (as low as ∼$35/sample), of at least 20 kilobases per specimen, for specimens at least as old as ∼1965, and can be easily conducted in most laboratories.If widely applied, this technique will accelerate the accurate resolution of the Tree of Life especially on non-model organisms with limited existing genomic resources.

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