CandiSSR

CandiSSR identifies candidate polymorphic simple sequence repeats (SSRs) from assembled genomic and transcriptomic sequences to enable marker development and genetic diversity analysis.

Key Features:

• Comprehensive Data Sources: CandiSSR processes assembled transcriptome datasets and multiple genome assemblies.
• Confidence Metrics: It calculates standard deviation and missing rate of SSR repeat counts to evaluate the feasibility of detected PolySSRs.
• Automated Primer Design: The pipeline designs primer pairs for each PolySSR and assesses primer binding regions using global sequence similarity checks.
• Validation and Accuracy: Experimental validation on rice genomes reported an accuracy exceeding 90% for identified PolySSRs.
• Broad Applicability: CandiSSR has been applied to identify PolySSRs in Arabidopsis genomes and Camellia transcriptomes.

Scientific Applications:

• Genetic studies: Rapid identification of polymorphic SSRs for population genetics and genetic diversity analyses.
• Breeding programs: Development of molecular markers and primer pairs for marker-assisted selection and cultivar characterization.
• Evolutionary biology: Comparative surveys of SSR polymorphism across genomes and transcriptomes to study neutral evolution and mutation rates.

Methodology:

CandiSSR leverages assembled sequences from next-generation sequencing outputs to identify candidate PolySSRs, assesses SSR polymorphism using standard deviation and missing rate of repeat counts, designs primer pairs, and evaluates primer-binding regions by global sequence similarity.