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

Abstract

BackgroundMicrosatellite 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.DescriptionFishMicrosat 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.ConclusionsFishMicrosat 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.

Characterization and Development of EST-SSR Markers Derived from Transcriptome of Yellow Catfish

“…In the di-nucleotide repeat SSRs, AC/GT (39,554, 73.3%) and AG/CT (11,460,21.2%) are the dominant types (Figure 2A). Similar to other fishes [19], (GC)n repeats are extremely rare in yellow catfish. Two most frequent repeats in the tri-nucleotide are AAT/ATT (3645, 45.0%) and ATC/GAT (1353, 16.7%) ( Figure 2B).…”

Genome-wide mapping and characterization of microsatellites in the swamp eel genome

“…In comparison with other genetic marker systems, such as restriction fragment length polymorphism, random amplified polymorphic DNA, amplified fragment length polymorphism, sequence-related amplified polymorphism, and target region amplification polymorphism, microsatellites are characterized by their high frequency of distribution, co-dominance, reproducibility, and high polymorphism 11, 12 . Efforts have been made worldwide to compile and develop microsatellite databases in eukaryotes 13–17 . In teleost fishes, valuable microsatellites and related genetic linkage maps have been characterized 18–21 .…”

FMiR: A Curated Resource of Mitochondrial DNA Information for Fish

“…'MISA' was used to investigate simple and compound SSRs in complete mitogenome and isolated subsequences files (gene, rRNA and D-loop) for determining occurrence, frequency and repeat types. SSRs with a minimum length of twelve nucleotides have been widely used in repeat finding studies [ 30 – 32 ]. During SSR finding, the input parameters for 'MISA' were set to twelve contiguous repeats for mononucleotides motifs, six repeating units for dinucleotide motifs, four repeating units for trinucleotide motifs and three contiguous repeats for tetra-, penta-, and hexanucleotide motifs.…”