ChloroMitoSSRDB 2.00: more genomes, more repeats, unifying SSRs search patterns and on-the-fly repeat detection

Area of Science:

• Genomics
• Bioinformatics
• Evolutionary Biology

Background:

• Organelle genomes evolve rapidly and are valuable for phylogenomic analyses using simple sequence repeats (SSRs).
• The ChloroMitoSSRDB previously provided access to a substantial repository of organelle SSRs from 2161 genomes.
• Continuous updates are crucial for maintaining comprehensive genomic databases.

Purpose of the Study:

• To update and expand the ChloroMitoSSRDB with new organelle genome data.
• To enhance the database's utility for in silico SSR mining and evolutionary genomics research.
• To provide users with advanced tools for SSR analysis and primer pair identification.

Main Methods:

• Systematic analysis and addition of 191 chloroplast and 2102 mitochondrial genomes to the existing database.
• Integration of in silico SSR mining tools for assembled genomes and next-generation sequencing reads.
• Implementation of multiple SSR search functionalities and browsing options using two repeat algorithms.

Main Results:

• ChloroMitoSSRDB 2.00 now hosts 4454 organelle genomes.
• The updated database contains over 40,000 IMEx Perfect SSRs and over 275,000 IMEx Imperfect SSRs.
• Includes MISA Perfect and Compound SSRs, along with detailed repeat information and primer pairs.

Conclusions:

• ChloroMitoSSRDB 2.00 is a significantly expanded resource for organelle SSRs.
• The integrated tools facilitate efficient in silico SSR mining and analysis for evolutionary genomics.
• The database serves as a valuable platform for phylogenomic studies utilizing organelle SSR markers.