RPGD

RPGD provides centralized storage and integrated analysis of genomic and transcriptomic data for Rhododendron species to support genome assembly, annotation, expression profiling, and comparative genomics.

Key Features:

• Genome assemblies: Complete genome sequence assemblies for R. delavayi, R. williamsianum, and R. simsii.
• Gene expression profiles: Integrated gene expression profiles derived from public RNA-Seq datasets.
• Functional annotation: Extensive functional annotations of genes.
• Gene families and transcription factors: Identification and cataloging of gene families and transcription factors.
• Gene homology and Orthologous Groups: Gene homology information and Orthologous Groups for evolutionary analysis.
• Simple sequence repeats (SSRs): Identification of simple sequence repeats (SSRs).
• Chloroplast genomes: Inclusion of chloroplast genome sequences and related data.
• BLAST: BLAST for sequence alignment and similarity searches.
• JBrowse: JBrowse for genome visualization.
• Genome Synteny Browser: Genome Synteny Browser to explore chromosomal rearrangements.
• Flanking Sequence Finder: Flanking Sequence Finder to locate adjacent genomic regions.
• Expression Heatmap: Expression Heatmap for visualization of gene expression data.
• Batch Download: Batch Download for bulk retrieval of datasets.
• Data integration: Integration of genomics and transcriptomics datasets from public sources.

Scientific Applications:

• Genome-based gene discovery: Discovery and annotation of genes in Rhododendron genomes.
• Transcriptome analysis: Transcriptome profiling and visualization using RNA-Seq-derived expression data.
• Comparative genomics: Comparative genomics and synteny analysis across Rhododendron species.
• Evolutionary and orthology studies: Evolutionary analysis using orthologous groups and gene homology information.

Methodology:

Integration of complete genome sequence assemblies and public RNA-Seq datasets for gene expression profiles, functional annotation, identification of gene families and transcription factors, detection of gene homology, simple sequence repeats and chloroplast genomes; supported computational tools and components include BLAST, JBrowse, Orthologous Groups, Genome Synteny Browser, Flanking Sequence Finder, Expression Heatmap, and Batch Download.