PSSRdb: a relational database of polymorphic simple sequence repeats extracted from prokaryotic genomes

Area of Science:

• Microbiology
• Genomics
• Bioinformatics

Background:

• Simple Sequence Repeats (SSRs) are tandem repeats of nucleotide motifs (1-6 bp) known for high polymorphism.
• SSR mutations can influence gene transcription and translation, driving phase and antigenic variations in bacteria.
• While studied in some bacteria, SSRs in many prokaryotes remain underexplored for adaptive and evolutionary roles.

Purpose of the Study:

• To create a comprehensive database of polymorphic SSRs (PSSRs) in prokaryotes.
• To facilitate research on SSR-mediated variations and their evolutionary significance in a wide range of prokaryotic species.

Main Methods:

• Genome sequences from 85 prokaryotic species were analyzed.
• Polymorphic Simple Sequence Repeats (PSSRs) exhibiting length variations were identified and extracted.
• A relational database, PSSRdb, was constructed to store and present PSSR information.

Main Results:

• PSSRdb contains data on PSSRs from 85 prokaryotic species.
• The database provides critical information including PSSR locations within genomes and length variations across different strains.
• Details on the genomic regions harboring PSSRs are also included.

Conclusions:

• PSSRdb serves as a valuable resource for studying SSR polymorphism in prokaryotes.
• The database supports further research into the adaptive and evolutionary implications of SSRs in diverse prokaryotic organisms.