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Open Access Highly Accessed Database

FishMicrosat: a microsatellite database of commercially important fishes and shellfishes of the Indian subcontinent

Naresh Sahebrao Nagpure1, Iliyas Rashid1, Rameshwar Pati1, Ajey Kumar Pathak2, Mahender Singh1*, Shri Prakash Singh2 and Uttam Kumar Sarkar2

Author Affiliations

1 Division of Molecular Biology and Biotechnology, National Bureau of Fish Genetic Resources, Lucknow 226002, India

2 Division of Fish Taxonomy and Resources, National Bureau of Fish Genetic Resources, Lucknow 226002, India

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BMC Genomics 2013, 14:630  doi:10.1186/1471-2164-14-630

Published: 18 September 2013

Abstract

Background

Microsatellite DNA is one of many powerful genetic markers used for the construction of genetic linkage maps and the study of population genetics. The biological databases in public domain hold vast numbers of microsatellite sequences for many organisms including fishes. The microsatellite data available in these data sources were extracted and managed into a database that facilitates sequences analysis and browsing relevant information. The system also helps to design primer sequences for flanking regions of repeat loci for PCR identification of polymorphism within populations.

Description

FishMicrosat is a database of microsatellite sequences of fishes and shellfishes that includes important aquaculture species such as Lates calcarifer, Ctenopharyngodon idella, Hypophthalmichthys molitrix, Penaeus monodon, Labeo rohita, Oreochromis niloticus, Fenneropenaeus indicus and Macrobrachium rosenbergii. The database contains 4398 microsatellite sequences of 41 species belonging to 15 families from the Indian subcontinent. GenBank of NCBI was used as a prime data source for developing the database. The database presents information about simple and compound microsatellites, their clusters and locus orientation within sequences. The database has been integrated with different tools in a web interface such as primer designing, locus finding, mapping repeats, detecting similarities among sequences across species, and searching using motifs and keywords. In addition, the database has the ability to browse information on the top 10 families and the top 10 species, through record overview.

Conclusions

FishMicrosat database is a useful resource for fish and shellfish microsatellite analyses and locus identification across species, which has important applications in population genetics, evolutionary studies and genetic relatedness among species. The database can be expanded further to include the microsatellite data of fishes and shellfishes from other regions and available information on genome sequencing project of species of aquaculture importance.

Keywords:
Microsatellite loci; Tandem repeats; Polymorphism; Primer; Flanking region; Fish