Solanaceae Information Resource (SoIR)

SoIR integrates genomic and transcriptomic data across Solanaceae species to enable comparative genomic, phylogenetic, evolutionary, and pan-genomic analyses.

Key Features:

• Multi-species data integration: SoIR incorporates genomic data from 81 species and transcriptomic data from 41 species, with 3,908,408 gene annotations derived from Gene Ontology, nonredundant protein, Pfam, Swiss-Prot and TrEMBL databases.
• Functional genomic annotations: The resource includes 3,437,115 CRISPR guide sequences, 212,395 transcription factors, and 19,086 genes associated with methylation modification.
• Comparative genomic analysis tools: SoIR provides Blast, Synteny and Sequence Alignment tools for cross-species comparative genomics.
• Phylogenetic and evolutionary analysis: The platform supports investigation of gene family evolution, phylogenetic relationships and karyotype reconstruction across 25 fully sequenced genomes.
• Pan-genomic resource: SoIR serves as a comprehensive pan-genomic resource for the entire Solanaceae family.

Scientific Applications:

• Plant evolution research: SoIR facilitates in-depth cross-species analysis supporting global research initiatives in plant evolution.
• Functional genomics: The resource enables functional genomic study through integrated gene annotations, transcription factor data and methylation modification information.
• Crop improvement: SoIR supports research initiatives aimed at crop improvement for economically important Solanaceae species including tomatoes, potatoes and peppers.
• Gene family evolution: Researchers can investigate gene family evolution across multiple Solanaceae species.
• Karyotype reconstruction: The tool enables karyotype reconstruction analysis across 25 fully sequenced genomes.

Methodology:

SoIR integrates genomic and transcriptomic data from multiple species, with gene annotations derived from Gene Ontology, nonredundant protein, Pfam, Swiss-Prot and TrEMBL databases; specific computational methods for data processing and integration are not explicitly detailed in the sources.