Ribosomal RNA and their Applications in Species Identification

By : Ranjithkumar K , Utsa Roy , Madhusudhana Rao B , Sudhan C

Page No: 91-99

Abstract
The rRNA genes are one of the most conserved genes in the living world. The core function of the ribosome is basically the same across different groups of organisms. However, the actual sequence of the nucleotides in rRNAs does vary between species and this enables its use as a molecular marker for species identification. Prokaryotes have three different types of rRNAs which include 23S, 16S and 5S rRNA. Of these, 16S rRNA has the most favorable characters due to which it is widely accepted for prokaryotic species identification. Eukaryotes consist of four different types of nuclear rRNA (18S, 28S, 5.8S & 5S) and two types of mitochondrial rRNA (12S and 16S). The eukaryotic 18S rRNA is similar to the prokaryotic 16S rRNA and it has less evolution rate compared to the cytochrome oxidase gene. The 18S rRNA is commonly used for identification of marine nematodes. Biparental inheritance of the 28S rRNA enables the identification of hybrid species. The 5.8S rRNA is located in the internal transcribed spacer regions (ITS), and its conserved nature provides PCR primer sites for amplification of ITS regions that are most commonly used for identification of fungus species. Apart from 5S rRNA gene that is transcribed by RNA Pol III, all the others are transcribed by RNA Pol I in the nucleolus which is the site for ribosome assembly. The nucleotide variation in both the mitochondrial 16S and 12S sequences is suitable for identifying the majority of fish specimens at genus level, but less useful for the explicit differentiation of certain congeneric fish species.

Authors :
Ranjithkumar K, Utsa Roy and Madhusudhana Rao B
ICAR-Central Institute of Fisheries Education, Mumbai, Maharashtra.

Sudhan C
TNJFU-Fisheries College and Research Institute, Thoothukudi, Tamil Nadu.