Fish and Shellfish Microsatellite Database

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  Top 10 FishMicrosat Families  
Family Species
Cyprinidae 39
Scombridae 11
Pomacentridae 9
Cichlidae 9
  Top 10 FishMicrosat Species  
Species Records
Cyprinus carpio42000
Lates calcarifer3681
Ctenopharyngodon idella3363
Oncorhynchus mykiss2674
Hypophthalmichthys molitrix1365
Carassius auratus717
Hypophthalmichthys nobilis640
Labeo rohita637
Penaeus monodon618
Pagrus major597
  About microsatellites

          Microsatellites, also known as simple sequence repeats (SSRs) or short tandem repeats (STRs) are repeat DNA sequence motifs consisting of 1-6 base pairs tandemly repeated several times at each locus. They are observed in almost all genomes with a significant percentage and suffer higher rates of mutation than the rest of the genome. A particular microsatellite locus can be identified by its flanking sequences that are generally conserved across individuals of the same species and sometimes of different species. Oligonucleotide primers can be designed to bind to the flanking region and amplification of a microsatellite locus. Individual allele at a locus differ in the number of tandem repeats of unit sequence owing to gain or loss of one or more repeats and can be differentiated  by high resolution gel electrophoresis according to their size.

          Based on the number and kind of nucleotides in a repeating unit, microsatellites are classified into four kinds namely perfect, imperfect,  compound, complex. Imperfect repeats (e.g. GCGCGCAGCGC) are more stable and are used in various genetic studies, including DNA fingerprinting and population genetics. Microsatellite can also be classified into mono-, di-, tri-, tetranucelotide repeat unit. Trinucleotide and tetranucleotide repeats are the most common choices for molecular genetic studies.

          Microsatellites are widely distributed in both coding and non-coding regions of fish genome. As the allele variants at microsatellite loci are co-dominant and inherited in Mendelian fashion, traditional approaches such as Hardy-Weinberg equilibrium can be used in initial data analysis. The variations in non-coding microsatellites are independent of natural selection, hence such microsatellites are widely used to assess the effective population size of stocks, genetic diversity, stock identification, levels of inbreeding, population structure and gene flow, parentage  and quantitative traits.

Accessing FishMicrosat
Keyword search: It takes valid keyword(s) (e.g. species name, family, author name, institute, accession id etc.) as an input and displays the relevant information.
Overview: The records pertaining to a particular species can be viewed by using species name instantiation index.
Analysis & Primer design: It helps to retrieve information pertaining to analysis of microsatellite repeats and designing of all the possible primers corresponding to each locus.
Motif search: It enables to search microsatellite sequences comprising of a motif of particular repeats based on selected parameters.
Locus finder: It enables the user to search for identical microsatellite locus/loci conserved among different species for their possible use in cross-species amplification.
Repeat similarity search: It uses a query microsatellite sequence as an input and retrieves all the microsatellite sequences that match with the query.
Statistics: It generates frequencies of different type of microsatellites repeats from the records available in FishMicrosat.
Current status
Species: 277 Family: 104 Order: 32 Specimen records: 66751 Sequences: 66751 Last update: 2024-02-20

How to cite FishMicrosat
Nagpure NS, Rashid I, Pati R, Pathak AK, Singh M, Singh SP, Sarkar UK. FishMicrosat: a microsatellite database of commercially important fishes and shellfishes of the Indian subcontinent. BMC Genomics. 2013, 14:630.
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