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CRISPR/Cas9 Genome Editing01:28

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The CRISPR-Cas system serves as a bacterial defense mechanism against invading genetic elements such as viruses and plasmids, forming the foundation for its adaptation as a powerful genome-editing tool. Originally discovered in prokaryotes, this system has been repurposed to revolutionize genetic engineering across a wide range of organisms, including plants, animals, and humans. The core component, Cas9, is an endonuclease derived from Streptococcus pyogenes, capable of introducing...
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Updated: Sep 16, 2025

High-throughput CRISPR Vector Construction and Characterization of DNA Modifications by Generation of Tomato Hairy Roots
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Populus VariantDB v3.2 facilitates CRISPR and functional genomics research.

Ran Zhou1,2,3, Sakshi R Seth1,4, Jacob Reeves1,4

  • 1Warnell School of Forestry and Natural Resources, University of Georgia, Athens, GA 30602, USA.

Tree Physiology
|July 11, 2025
PubMed
Summary

Designing precise CRISPR guide RNAs (gRNAs) for trees is challenging due to sequence variations. Populus VariantDB v3.2 offers a solution by searching poplar genomes for sequence polymorphisms, improving gRNA and primer design accuracy.

Keywords:
gene editingguide RNAheterozygosityprimersequence polymorphisms

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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.