SpinachBase: a central portal for spinach genomics.

Area of Science:

• Plant genomics
• Bioinformatics
• Agricultural science

Background:

• Spinach (Spinacia oleracea L.) is a nutrient-rich vegetable with increasing genomic resources.
• The recent release of a reference spinach genome necessitates a centralized data repository.
• Existing spinach genomic data requires integration and accessible analytical tools for research and breeding.

Purpose of the Study:

• To develop SpinachBase, a centralized database for spinach genomic data.
• To provide public access to spinach genome sequences, gene annotations, and expression profiles.
• To offer analytical tools for spinach research and breeding.

Main Methods:

• Developed SpinachBase (http://spinachbase.org) for data storage and querying.
• Integrated reference genome sequence and predicted protein-coding genes with functional annotations.
• Incorporated RNA-Seq derived gene expression profiles and genetic variants from 120 Spinacia accessions.
• Included a pathway database (SpinachCyc) with predicted biochemical pathways.

Main Results:

• SpinachBase provides centralized access to the spinach reference genome and gene annotations.
• The database includes gene expression data and genetic variants from diverse Spinacia accessions.
• SpinachBase offers a genome browser, BLAST searches, and functional analysis tools.

Conclusions:

• SpinachBase serves as a crucial resource for spinach genomic research and breeding.
• The database facilitates data integration, analysis, and discovery in spinach.
• SpinachBase empowers researchers with comprehensive genomic information and analytical capabilities.