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

Nagpure NS, Rashid I, Pati R, Pathak AK, Singh M, Singh SP, Sarkar UK - BMC Genomics (2013)

Bottom Line: GenBank of NCBI was used as a prime data source for developing the database.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Division of Molecular Biology and Biotechnology, National Bureau of Fish Genetic Resources, Lucknow 226002, India. mahender@scientist.com.

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.

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Related in: MedlinePlus

Flowchart of the locus finder algorithm.
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Figure 2: Flowchart of the locus finder algorithm.

Mentions: The microsatellite loci among the existing sequences were identified by implementing an algorithm into a program (locusfinder.pl) using Perl. In order to construct the algorithm, a microsatellite sequence of selected species was divided in parts (a) motif of repeats region (b) 25 bp flanking sequence upstream and (c) 25 bp flanking sequence downstream to the repeat region. The repeat region and motifs present in sequences of selected species were fetched from the ‘repeats’ table of the database sequentially for retrieving identical target motifs and its sequences. Further, the conserved flanking regions were checked in query as well as target sequences. The evolutionary conservation of the flanking region allows hetero specific identification of SSRs[34]. These conserved flanking regions have been used for designing PCR primers for microsatellite amplification and genotyping of individuals of the same species as well as across species[35,36]. Thus, to identify loci across species, an algorithm was designed by considering the approach for example ‘ABC’ as a repeat pattern and ‘L’ the number of repeat units in a selected query sequence. The same repeat pattern ‘ABC’ was used to check its availability and repeat frequency (denoted as P) in the target sequence (Figure 2). Here, because the repeat frequency may be polymorphic, the value of the repeat frequency in the selected query sequence (L) may or may not be equal to the repeat frequency in the target sequence (P) i.e. L = P or L! = P. The algorithm uses a 25 bp length of flanking region on either side, which is sufficient for amplification of a microsatellite locus in a PCR reaction for laboratory validation. The loci identification program supports the findings of the previous studies that microsatellite repeats vary within and between different genomes of organisms[37,38].


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

Nagpure NS, Rashid I, Pati R, Pathak AK, Singh M, Singh SP, Sarkar UK - BMC Genomics (2013)

Flowchart of the locus finder algorithm.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3852227&req=5

Figure 2: Flowchart of the locus finder algorithm.
Mentions: The microsatellite loci among the existing sequences were identified by implementing an algorithm into a program (locusfinder.pl) using Perl. In order to construct the algorithm, a microsatellite sequence of selected species was divided in parts (a) motif of repeats region (b) 25 bp flanking sequence upstream and (c) 25 bp flanking sequence downstream to the repeat region. The repeat region and motifs present in sequences of selected species were fetched from the ‘repeats’ table of the database sequentially for retrieving identical target motifs and its sequences. Further, the conserved flanking regions were checked in query as well as target sequences. The evolutionary conservation of the flanking region allows hetero specific identification of SSRs[34]. These conserved flanking regions have been used for designing PCR primers for microsatellite amplification and genotyping of individuals of the same species as well as across species[35,36]. Thus, to identify loci across species, an algorithm was designed by considering the approach for example ‘ABC’ as a repeat pattern and ‘L’ the number of repeat units in a selected query sequence. The same repeat pattern ‘ABC’ was used to check its availability and repeat frequency (denoted as P) in the target sequence (Figure 2). Here, because the repeat frequency may be polymorphic, the value of the repeat frequency in the selected query sequence (L) may or may not be equal to the repeat frequency in the target sequence (P) i.e. L = P or L! = P. The algorithm uses a 25 bp length of flanking region on either side, which is sufficient for amplification of a microsatellite locus in a PCR reaction for laboratory validation. The loci identification program supports the findings of the previous studies that microsatellite repeats vary within and between different genomes of organisms[37,38].

Bottom Line: GenBank of NCBI was used as a prime data source for developing the database.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Division of Molecular Biology and Biotechnology, National Bureau of Fish Genetic Resources, Lucknow 226002, India. mahender@scientist.com.

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.

Show MeSH
Related in: MedlinePlus