PSMD: An extensive database for pan-species microsatellite investigation and marker development

Area of Science:

• Genomics
• Bioinformatics
• Molecular Biology

Background:

• Microsatellites are highly polymorphic genetic markers found in genomes.
• Length variations in microsatellites are linked to gene regulation, genetic diseases, and cancers.
• Existing microsatellite databases have limitations including restricted species coverage, poor export formats, and lack of gene annotation.

Purpose of the Study:

• To develop a comprehensive, web-based database (PSMD) to address limitations of existing microsatellite resources.
• To facilitate easy identification and exploitation of microsatellites as reliable molecular markers.
• To enable genome-wide comparison of microsatellite distribution patterns.

Main Methods:

• Developed PSMD as a web-based platform.
• Integrated a large dataset of perfect and compound microsatellites from numerous organisms.
• Implemented interactive browsing, flexible filtering, and data export functionalities (GFF3, CSV).
• Embedded Primer3 for primer design and an online tool for microsatellite occurrence analysis.

Main Results:

• PSMD contains over 678 million perfect and 43 million compound microsatellites from 18,408 species.
• The database covers nearly all species with available genomic data.
• Offers user-friendly tools for data retrieval, analysis, and primer design.

Conclusions:

• PSMD is the most extensive microsatellite resource available to date.
• It overcomes previous limitations, supporting downstream analysis in biological, medical, environmental, and agricultural research.
• Facilitates efficient microsatellite identification, marker development, and comparative genomics.