Populus VariantDB v3.2 facilitates CRISPR and functional genomics research.

Area of Science:

• Genomics
• Bioinformatics
• Plant Science

Background:

• CRISPR genome editing success relies on precise guide RNA (gRNA) design.
• Sequence polymorphisms in heterozygous tree genomes complicate gRNA design and reduce CRISPR efficacy.
• Existing tree genome sequencing data is often not readily accessible for functional genomics.

Purpose of the Study:

• To develop a user-friendly tool, Populus VariantDB v3.2, for querying sequence polymorphisms in poplar genomes.
• To enhance the precision of gRNA and primer design for CRISPR applications in trees.
• To provide a versatile resource for functional genomics research in diverse tree species.

Main Methods:

• Implemented a search engine for querying sequence polymorphisms in heterozygous poplar genomes.
• Developed the database to accept short sequences (gRNAs, primers) as input.
• Enabled searching against multiple poplar genomes, including hybrids, with customizable parameters.

Main Results:

• Populus VariantDB v3.2 provides a searchable interface for poplar genome sequence variations.
• Demonstrated the utility of VariantDB in improving the accuracy of gRNA and primer design.
• Showcased the platform-agnostic nature of the probe search design.

Conclusions:

• Populus VariantDB v3.2 is a valuable tool for overcoming challenges in CRISPR genome editing design for trees.
• The database supports various sequence-sensitive functional genomics applications.
• The expandable schema allows for the incorporation of additional tree genomes, broadening its utility.