Ribosomal DNA
Ribosomal DNA codes for ribosomal RNA
Ribosomal RNA
Ribosomal ribonucleic acid is the RNA component of the ribosome, the enzyme that is the site of protein synthesis in all living cells. Ribosomal RNA provides a mechanism for decoding mRNA into amino acids and interacts with tRNAs during translation by providing peptidyl transferase activity...

. The ribosome
A ribosome is a component of cells that assembles the twenty specific amino acid molecules to form the particular protein molecule determined by the nucleotide sequence of an RNA molecule....

 is an intracellular macromolecule that produces proteins or polypeptide chains. The ribosome itself consists of a composite of proteins and RNA. As shown in the figure, rDNA consists of a tandem repeat of a unit segment, an operon, composed of NTS, ETS, 18S, ITS1, 5.8S, ITS2, and 28S tracts. rDNA has another gene, coding for 5S rRNA, located in the genome in most eukaryotes. 5S rDNA is also present in tandem repeats as in Drosophila. In the nucleus, the rDNA region of the chromosome is visualized as a nucleolus
The nucleolus is a non-membrane bound structure composed of proteins and nucleic acids found within the nucleus. Ribosomal RNA is transcribed and assembled within the nucleolus...

 which forms expanded chromosomal loops with rDNA. These rDNA regions are also called nucleolus organizer region
Nucleolus organizer region
The nucleolus organizer region or nucleolar organizer is a chromosomal region around which the nucleolus forms. This region is the particular part of a chromosome that is associated with a nucleolus after the nucleus divides. The region contains several tandem copies of ribosomal RNA genes...

s, as they give rise to the nucleolus. In the human genome
Human genome
The human genome is the genome of Homo sapiens, which is stored on 23 chromosome pairs plus the small mitochondrial DNA. 22 of the 23 chromosomes are autosomal chromosome pairs, while the remaining pair is sex-determining...

there are 5 chromosomes with nucleolus organizer regions: chromosomes 13,14,15,21 and 22.

Sequence homogeneity of the repeat unit

In the large rDNA array, polymorphisms between rDNA repeat units are very low, indicating that rDNA tandem arrays are evolving through concerted evolution. 5S tandem repeat sequences in several Drosophila were compared with each other; the result revealed that insertions and deletions occurred frequently between species and often flanked by conserved sequences. They could occur by slippage of the newly synthesized strand during DNA replication or by gene conversion.

Sequence divergence to clarify phylogeny

The rDNA transcription tracts have low rate of polymorphism among species, which allows interspecific comparison to elucidate phylogenetic relationship using only a few specimens. Coding regions of rDNA are highly conserved among species but ITS regions are variable due to insertions, deletions, and point mutations. Between remote species as human and frog comparison of sequences at ITS tracts is not appropriate. Conserved sequences at coding regions of rDNA allow comparisons of remote species, even between yeast and human. Human 5.8S rRNA has 75% identity with yeast 5.8S rRNA.
In cases for sibling species, comparison of the rDNA segment including ITS tracts among species and phylogenetic analysis are made satisfactorily.
The different coding regions of the rDNA repeats usually show distinct evolutionary rates. As a result, this DNA can provide phylogenetic information of species belonging to wide systematic levels.
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