Related Experiment Video
Updated: Aug 11, 2026
16:17
The ITS2 Database
Published on: March 12, 2012
A 5.8S nuclear ribosomal RNA gene sequence database: applications to ecology and evolution
1NASA-Ames Research Center, Moffett Field, California 94035-1000, USA. kcullings@mail.arc.nasa.gov
Molecular Ecology
|August 6, 1998
Summary
A new 5.8S ribosomal gene database aids in verifying sequenced organisms, identifying fungal placements, and recognizing ectomycorrhizal fungi. This tool supports ecological and evolutionary research by ensuring data accuracy and taxonomic resolution.
Area of Science:
- Molecular Biology
- Mycology
- Ecology
Background:
- Accurate species identification is crucial for ecological and evolutionary studies.
- Nuclear ribosomal gene sequences are widely used for taxonomic classification.
- A comprehensive database is needed for reliable identification of diverse organisms, including fungi.
Purpose of the Study:
- To create a 5.8S nuclear ribosomal gene sequence database for animals, plants, and fungi.
- To demonstrate the database's utility for quality control in sequencing.
- To provide a diagnostic tool for fungal taxonomy and ectomycorrhizal identification.
Main Methods:
- Compilation of newly generated and existing sequences from GenBank.
- Database construction focused on the 5.8S nuclear ribosomal gene.
- Application of the database for organism verification and taxonomic placement.
Main Results:
- A functional 5.8S nuclear ribosomal gene sequence database was successfully compiled.
- The database serves as an effective internal control against sequencing contaminants.
- The database aids in determining the taxonomic placement of asexual fungi and identifying ectomycorrhizal fungi.
Conclusions:
- The 5.8S ribosomal gene database is a valuable resource for molecular ecology and evolutionary biology.
- It enhances the reliability of sequence data by enabling contaminant checks.
- The database facilitates advancements in fungal taxonomy and the study of symbiotic relationships.
Related Concept Videos
02:05Gene Evolution - Fast or Slow?
The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...
In contrast, regions which code...
00:43Bacterial RNA Polymerase
Unlike eukaryotes, bacteria use a single RNA Polymerase (RNAP) to transcribe all genes. The different subunits of bacterial RNAPhave distinct functions. The multisubunit structure of the bacterial RNAP helps the enzyme to maintain catalytic function, facilitate assembly, interact with DNA and RNA, and self-regulate its activity.
In most genes, the transcription site is a single base present upstream of the coding sequence. Though RNAP is a catalytically efficient enzyme, it does not recognize...
In most genes, the transcription site is a single base present upstream of the coding sequence. Though RNAP is a catalytically efficient enzyme, it does not recognize...
02:54Evolutionary Relationships through Genome Comparisons
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
02:24Ribosome Profiling
Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique helps...
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique helps...
02:05Gene Evolution - Fast or Slow?
The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...
In contrast, regions which code...
01:20Applications of Molecular Taxonomy
Molecular taxonomy has revolutionized the understanding and classification of bacteria, providing precise insights into their diversity, evolutionary relationships, and ecological roles. By utilizing molecular techniques such as DNA sequencing and fingerprinting, researchers have made significant strides in various fields related to bacterial studies.Resolving Taxonomic AmbiguitiesMolecular taxonomy has been instrumental in distinguishing closely related bacterial species initially thought to...