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PMDBase: a database for studying microsatellite DNA and marker development in plants.

Jingyin Yu1, Komivi Dossa1,2, Linhai Wang1

  • 1Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture; Oil Crops Research Institute, the Chinese Academy of Agricultural Sciences, Wuhan 430062, China.

Nucleic Acids Research
|October 14, 2016
PubMed
Summary

A new database, PMDBase, offers a comprehensive resource for plant microsatellite DNAs (SSRs) and primer development. It provides integrated data and web tools for SSR identification and analysis across 110 plant species.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Plant Science

Background:

  • Microsatellite DNAs (SSRs) are crucial genomic elements with diverse biological functions.
  • SSRs are widely used as molecular markers for genetic diversity, mapping, and evolutionary studies.
  • A centralized database and web service for plant SSRs and marker development were previously lacking.

Purpose of the Study:

  • To develop PMDBase, a comprehensive database and web service for plant microsatellite DNAs.
  • To facilitate SSR identification and marker development in plant genomics research.

Main Methods:

  • Integrated large-scale microsatellite DNA data from sequenced plant genomes.
  • Developed a user-friendly web interface with browsing, searching, and downloading functionalities.
  • Embedded MISAweb and Primer3web for online SSR identification and primer design.

Main Results:

  • Identified 26,230,099 SSRs across 110 plant species.
  • Provided up to three primer pairs for each SSR.
  • Included genomic features (genic/non-genic) for SSRs in 81 species, linked to public gene/transcript data.

Conclusions:

  • PMDBase offers a valuable, freely accessible resource for plant SSR research.
  • The integrated tools streamline SSR discovery and primer design for researchers.
  • Regular updates with new genomic data will ensure PMDBase remains a vital platform.