OrchidBase 4.0

OrchidBase 4.0 provides integrated genomic and transcriptomic resources, including de novo assembled whole-genome sequences and expression data from Apostasia shenzhenica, Dendrobium catenatum, and Phalaenopsis equestris, to support comparative genomics, gene annotation, and stress-response analyses in orchids.

Key Features:

• Genomic Data: Whole-genome sequences and annotations from Apostasia shenzhenica, Dendrobium catenatum, and Phalaenopsis equestris obtained by de novo assembly.
• Transcriptomic Data: Transcriptomic datasets from various tissues and developmental stages of Phalaenopsis, including responses to biotic and abiotic stresses.
• Gene Annotation and Expression Analysis: Gene annotations with expression levels quantified as fragments per kilobase of transcript per million mapped reads (FPKM) and functional insights mapped to KEGG pathways.
• BLAST Search Capability: Sequence similarity searches against the orchid genomic and transcriptomic datasets via BLAST.
• Genome Browser Visualization: Genome browser tracks showing assembled genome sequences with annotated gene and microRNA (miRNA) locations.

Scientific Applications:

• Comparative Genomics: Comparative analyses across orchid species and subfamilies to investigate evolutionary relationships and diversification within Orchidaceae.
• Functional Genomics: Functional annotation and pathway mapping of genes using expression data and KEGG assignments.
• Stress-Response Studies: Investigation of genetic responses to biotic and abiotic stresses using transcriptomic profiles from Phalaenopsis.
• Molecular Biology and Breeding: Resource for gene discovery, candidate gene prioritization, and molecular studies relevant to orchid breeding programs.

Methodology:

De novo assembly of whole-genome sequences for three orchid species, followed by genome annotation; transcriptomic analyses from various developmental stages and stress conditions in Phalaenopsis with expression quantified as FPKM and mapped to KEGG pathways.