PSSRdt

PSSRdt identifies polymorphic simple sequence repeat (SSR) loci directly from transcriptome and RNA-seq data to support development of SSR markers for population genetics and genetic diversity analyses.

Key Features:

• Transcriptome-based SSR mining: Mines SSR loci from transcriptome and RNA-seq datasets, including expressed sequence tag (EST) collections, without requiring a reference genome.
• Polymorphism detection: Obtains detailed polymorphism information of SSR loci through analysis of diverse transcriptome datasets.
• Three-step workflow: Implements a workflow of raw data processing, application of PSSRdt software, and subsequent extraction and verification of loci.
• Large-scale discovery: Applied to a combined dataset of 44 pea aphid transcriptomes, identifying 1,940 potential polymorphic SSRs.
• Experimental validation results: Genotyping of 52 selected SSR loci showed over 92% polymorphism and 73.1% of loci classified as highly polymorphic.

Scientific Applications:

• Microsatellite development: Generation of candidate polymorphic SSR markers from RNA-seq and transcriptome data for marker development.
• Population genetics: Discovery of SSR markers suitable for population structure and genetic diversity analyses.
• Reference-free marker discovery: Identification of polymorphic loci in species lacking reference genomes using ESTs or transcriptome assemblies.
• Genotyping assay development: Selection of candidate loci for downstream genotyping and validation experiments.

Methodology:

The computational workflow comprises three explicit steps: raw data processing, application of the PSSRdt software to detect SSRs and polymorphisms, and extraction and verification of candidate loci.