Abstract
Simple sequence repeats (SSRs) are regions in DNA sequence that contain repeating motifs of length 1–6 nucleotides. These repeats are ubiquitously present and are found in both coding and non-coding regions of genome. A total of 534 complete chloroplast genome sequences (as on 18 September 2014) of Viridiplantae are available at NCBI organelle genome resource. It provides opportunity to mine these genomes for the detection of SSRs and store them in the form of a database. In an attempt to properly manage and retrieve chloroplastic SSRs, we designed ChloroSSRdb which is a relational database developed using SQL server 2008 and accessed through ASP.NET. It provides information of all the three types (perfect, imperfect and compound) of SSRs. At present, ChloroSSRdb contains 124 430 mined SSRs, with majority lying in non-coding region. Out of these, PCR primers were designed for 118 249 SSRs. Tetranucleotide repeats (47 079) were found to be the most frequent repeat type, whereas hexanucleotide repeats (6414) being the least abundant. Additionally, in each species statistical analyses were performed to calculate relative frequency, correlation coefficient and chi-square statistics of perfect and imperfect SSRs. In accordance with the growing interest in SSR studies, ChloroSSRdb will prove to be a useful resource in developing genetic markers, phylogenetic analysis, genetic mapping, etc. Moreover, it will serve as a ready reference for mined SSRs in available chloroplast genomes of green plants.Database URL: www.compubio.in/chlorossrdb/
Highlights
Chloroplasts are semiautonomous organelles having their own genome [1] and considered to be derived from cyanobacteria through endosymbiosis [2]
The front end of ChloroSSRdb provides a user-friendly browsing facility to look for the simple sequence repeats (SSRs) information in respective organism
The organism name is directly linked to the taxonomic page and its accession id to GenBank page at NCBI which enable user to fetch taxonomic and genomic DNA information, respectively
Summary
Chloroplasts are semiautonomous organelles having their own genome [1] and considered to be derived from cyanobacteria through endosymbiosis [2]. SSRs known as microsatellites are the specific portions of DNA sequence that contain clusters of tandem repeating motifs of length 1–6 nucleotides [10]. These repeats are supposed to be generated by slippage during replication [11] and are present in both coding as well as non-coding regions of DNA. Chloroplastic SSRs (cpSSRs) play an important role in population genetics and evolutionary studies of plants [18]
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