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DNA barcode is a very short, standardized DNA sequence in a well-known gene. It provides a way to
identify the species to which a plant, animal or fungus belongs. DNA barcoding is a new concept of
identifying unknown organisms based on species-specific DNA regions. fungi are a group of
eukaryotic organisms that includes microorganisms and these organisms are belongs to kingdom
Fungi, which is separated from plants, animals, protists, and bacteria. The nuclear ribosomal
Internal Transcribed Spacer ITS region is widely used as a DNA barcoding marker to characterize
the diversity and composition of fungal communities. Since the early 1990s, the ITS region has been
heavily used in both molecular methods and ecological studies of fungi, Due to its high degree of
interspecific variability, conserved primer sites and multiple copy nature in the genome. Primers
have long been available for the nuclear ITS (Internal transcribed spacer) rDNA region which are
now commonly used for fungal identification.COX1 gene is of limited use as a barcode for true
Fungi as the length of fungal COX1 is highly variable (1.6–22 kb). The ITS region of fungi varies in
length from 450bp to 750bp. Due to some limitations in COX1 gene ITS is introduced for barcoding
of fungal species identification. ITS is a piece of non-functional RNA situated between
structural ribosomal RNAs (rRNA) on a common precursor transcript. Most mycologists suggested
that the internal transcribed spacer (ITS) of the nuclear ribosomal RNA, the first barcode for the
kingdom Fungi. Approximately 172,000 full-length fungal ITS sequences are available in Genbank.
ITS marker exists in multiple copies in most fungal cells and is retrievable by relatively strong
primers with an established record of reliability. From some latest review papers on fungal
barcoding, it is observed that in ascomycetes, ITS had the most resolving power for species
discrimination. The International Sub-commission on Fungal barcoding has proposed the ITS region
as the prime fungal barcode or the default region for species identification.
Key words: DNA barcode, COX 1 gene, ITS rDNA, fungal identification, biodiversity.