Abstract
BACKGROUND: CRISPR/Cas9 technology has become an important tool to generate targeted, highly specific genome mutations. The technology has great potential for crop improvement, as crop genomes are tailored to optimize specific traits over generations of breeding. Many crops have highly complex and polyploid genomes, particularly those used for bioenergy or bioproducts. The majority of tools currently available for designing and evaluating gRNAs for CRISPR experiments were developed based on mammalian genomes that do not share the characteristics or design criteria for crop genomes. RESULTS: We have developed an open source tool for genome-wide design and evaluation of gRNA sequences for CRISPR experiments, CROPSR. The genome-wide approach provides a significant decrease in the time required to design a CRISPR experiment, including validation through PCR, at the expense of an overhead compute time required once per genome, at the first run. To better cater to the needs of crop geneticists, restrictions imposed by other packages on design and evaluation of gRNA sequences were lifted. A new machine learning model was developed to provide scores while avoiding situations in which the currently available tools sometimes failed to provide guides for repetitive, A/T-rich genomic regions. We show that our gRNA scoring model provides a significant increase in prediction accuracy over existing tools, even in non-crop genomes. CONCLUSIONS: CROPSR provides the scientific community with new methods and a new workflow for performing CRISPR/Cas9 knockout experiments. CROPSR reduces the challenges of working in crops, and helps speed gRNA sequence design, evaluation and validation. We hope that the new software will accelerate discovery and reduce the number of failed experiments.
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Claims 4
Claim · model-written summary
CROPSR supplies genome-wide gRNA design and evaluation.
Verbatim
e0“We have developed an open source tool for genome-wide design and evaluation of gRNA sequences for CRISPR experiments, CROPSR.”
t0“CROPSR: an automated platform for complex genome-wide CRISPR gRNA design and validation”
t1“CROPSR: an automated platform for complex genome-wide CRISPR gRNA design and validation”
Claim · model-written summary
The genome-wide approach significantly reduced experiment design time, including PCR validation, with one-time computation overhead.
Verbatim
e0“The genome-wide approach provides a significant decrease in the time required to design a CRISPR experiment, including validation through PCR, at the expense of an overhead compute time required once per genome, at the first run.”
t0“crop”
t1“crop”
Claim · model-written summary
The scoring model can give scores in repetitive, A/T-rich regions where existing tools sometimes failed.
Verbatim
e0“A new machine learning model was developed to provide scores while avoiding situations in which the currently available tools sometimes failed to provide guides for repetitive, A/T-rich genomic regions.”
t0“crop”
t1“crop”
Claim · model-written summary
The gRNA scoring model significantly improved prediction accuracy over existing tools, even for non-crop genomes.
Verbatim
e0“our gRNA scoring model provides a significant increase in prediction accuracy over existing tools, even in non-crop genomes.”
t0“crop”
t1“crop”