FungREP 1.0: Online web-repository of microsatellite repeats from fungal genomes

Author Name(s): *Suresh B. Mudunuri, Ratna Prabha, Dhananjaya P Singh, Gopala Krishna Murthy Nookala
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Microsatellites are tandem repetitions of short DNA motifs found in genomes of all organisms. They have been significantly used in DNA fingerprinting, genome mapping, DNA forensics, linkage analysis, genetic disease studies, are known to be involved in gene regulation, bacterial adaptation  genome evolution and are extensively used as genetic markers. Microsatellites have been used as primers for genotyping of fungal strains, to study the evolution of fungal genomes as well as in the epidemiological studies of fungal pathogens. However, the distribution, frequency and abundance of microsatellites in several fungal genomes is not well studied. So, we have constructed an exclusive database of fungal microsatellites and a user-friendly web-interface to analyse the distribution and abundance of these repeats. FungREP currently hosts microsatellite data of 910 sequences of 44 different fungi that includes complete genome sequences, whole genome shotgun sequences and contigs. More than 10 million perfect and imperfect microsatellites and their corresponding information such as the repeat unit, position information, repeat statistics, protein information, etc., can be accessed from the first version of FungREP1.0. The database can be accessed for free from


Database, Microsatellite, Fungus, Genome, Tandem Repeat, web-interface


Microsatellites, also called Short Tandem Repeats or Simple Sequence Repeats, are tandem repetitions of DNA motifs of size 1 to 6 bp [1]. Microsatellites are unique elements of DNA that are ubiquitous in nature and are found to be highly polymorphic [2]. The intensity of undergoing mutations in these microsatellite regions is at the rate of 10-6 to 10-2 per generation which is considered extra ordinary when compared to the mutation rate in normal DNA sequences (10-12 to 10-10 per generation) [3][4]. The high mutation rates and the polymorphic nature of microsatellites favored them to be used as popular genetic markers and have been widely used in several areas including DNA fingerprinting, strain / species identification, DNA forensics, genome mapping, paternity and evolutionary studies [5]. Additionally, they are known to be responsible for causing certain genetic disorders and cancers, for bacterial / viral adaptation, gene regulation, etc. [6-10].


Microsatellites are widely being used in genotyping of fungal strains, in studies related to fungal pathogenesis and to understand their genome evolution. To provide a valuable resource for researchers working in fungal genomics, we have constructed an online fungal microsatellite database named FungREP that hosts microsatellite repeat information of various fungal genomes. This paper presents the details of FungREP database construction and the different modules integrated to the web interface for microsatellite data analysis and visualization. The database will be updated from time to time by including the repeat information from latest sequenced fungal genomes.

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