OrchidBase 5.0: updates of the orchid genome knowledgebase

Area of Science:

• Botany and Plant Science
• Genomics and Bioinformatics
• Evolutionary Biology

Background:

• The Orchidaceae family is diverse, offering insights into plant evolution and adaptation, and includes economically important ornamental species.
• Previous work established OrchidBase 4.0, providing access to genome and transcriptome data for three orchid species from two subfamilies.
• OrchidBase 4.0 facilitated comparative genomic studies and sequence retrieval for the plant science community.

Purpose of the Study:

• To develop an updated version of the OrchidBase resource, incorporating new genomic and transcriptomic data.
• To enhance comparative genomic analysis capabilities for orchid research.
• To provide advanced tools for characterizing microRNAs (miRNAs) in orchids.

Main Methods:

• De novo sequencing, assembly, and analysis of whole-genome and systemic transcriptome data from two Orchidoideae species (Platanthera zijinensis and Platanthera guangdongensis).
• Integration of newly generated datasets into the OrchidBase platform.
• Development and implementation of new analytical functions including synteny, gene order comparison, and miRNA analysis.

Main Results:

• OrchidBase 5.0 now encompasses genetic information from five orchid species spanning three subfamilies.
• New functionalities for synteny analysis, gene order comparison, and miRNA characterization have been successfully implemented.
• The updated database provides enhanced resources for comparative orchid genomics.

Conclusions:

• OrchidBase 5.0 significantly expands genetic resources for orchid research, covering more species and subfamilies.
• The new analytical tools empower researchers to conduct deeper comparative analyses of orchid genomes and transcriptomes.
• This updated platform serves as a valuable online resource for advancing orchid science and understanding plant evolution.