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CRISPRdisco: An Automated Pipeline for the Discovery and Analysis of CRISPR-Cas Systems - PubMed Skip to main page content
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. 2018 Apr;1(2):171-181.
doi: 10.1089/crispr.2017.0022. Epub 2018 Apr 9.

CRISPRdisco: An Automated Pipeline for the Discovery and Analysis of CRISPR-Cas Systems

Alexandra B Crawley  1 , James R Henriksen  2 , Rodolphe Barrangou  1
Affiliations

CRISPRdisco: An Automated Pipeline for the Discovery and Analysis of CRISPR-Cas Systems

Alexandra B Crawley et al. CRISPR J. 2018 Apr.

Abstract

CRISPR-Cas adaptive immune systems of bacteria and archaea have catapulted into the scientific spotlight as genome editing tools. To aid researchers in the field, we have developed an automated pipeline, named CRISPRdisco (CRISPR discovery), to identify CRISPR repeats and cas genes in genome assemblies, determine type and subtype, and describe system completeness. All six major types and 23 currently recognized subtypes and novel putative V-U types are detected. Here, we use the pipeline to identify and classify putative CRISPR-Cas systems in 2,777 complete genomes from the NCBI RefSeq database. This allows comparison to previous publications and investigation of the occurrence and size of CRISPR-Cas systems. Software available at http://github.com/crisprlab/CRISPRdisco provides reproducible, standardized, accessible, transparent, and high-throughput analysis methods available to all researchers in and beyond the CRISPR-Cas research community. This tool opens new avenues to enable classification within a complex nomenclature and provides analytical methods in a field that has evolved rapidly.

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Conflict of interest statement

A.B.C. and R.B. are inventors on several patents related to CRISPR technology and derived applications. R.B. is a shareholder of Caribou Biosciences, a co-founder and SAB member of Intellia Therapeutics, and co-founder and chairman of the SAB for Locus Biosciences. R.B. is the Editor-in-Chief of The CRISPR Journal and has been excluded from all editorial proceedings with this manuscript. This work was funded by AgBiome/LifeEDIT.

Figures

<b>FIG. 1.</b>
FIG. 1.
Overview of bioinformatic pipeline. The bioinformatic pipeline uses nucleotide and coding sequence information to annotate both CRISPR repeats and Cas proteins. This information is combined to determine type, subtype and completeness of CRISPR-Cas systems in archaeal and bacterial genomes.
<b>FIG. 2.</b>
FIG. 2.
Distribution of type of CRISPR-Cas system. The outer ring demonstrates the total distribution of CRISPR-Cas systems detected in archaea and bacteria. The inner ring shows the same distribution with a correction for sampling bias in the data set used. The inner ring is normalized to the number of replicons in each taxonomic class used for this analysis.
<b>FIG. 3.</b>
FIG. 3.
Size of CRISPR loci. The total number of repeats from genomes where repeats co-occur with cas genes broken down by type. *Average size is statistically different based on Tukey's HSD (alpha 0.05).
<b>FIG. 4.</b>
FIG. 4.
Length of CRISPR repeats by CRISPR subtype. The distribution of CRISPR repeat length by subtype is shown. The bar height is scaled by CRISPR-Cas type. Relative abundance of each subtype within a type can be determined by bar height on the x-axis.
<b>FIG. 5.</b>
FIG. 5.
Occurrence of CRISPR‐Cas systems in archaea and bacteria. The total number of complete CRISPR‐Cas systems where proteins co‐occur with repeats in chromosomes is depicted in the left heat map. The taxonomic class level was used to group the genomes. Total counts for archaea and bacteria appear at the top of each kingdom. The classes are ranked by total number of genomes included in the search. The column titled “Does Not Contain CRISPR” includes all genomes without a single cas gene or CRISPR repeat detected, while the “Contains CRISPR features” column denotes that a protein coding sequence with homology to known Cas proteins or CRISPR repeats were detected in the chromosome. The right heat map displays the percent of genomes containing CRISPR‐Cas systems when normalized for total number of genomes included in this analysis.
<b>FIG. 5.</b>
FIG. 5.
Occurrence of CRISPR‐Cas systems in archaea and bacteria. The total number of complete CRISPR‐Cas systems where proteins co‐occur with repeats in chromosomes is depicted in the left heat map. The taxonomic class level was used to group the genomes. Total counts for archaea and bacteria appear at the top of each kingdom. The classes are ranked by total number of genomes included in the search. The column titled “Does Not Contain CRISPR” includes all genomes without a single cas gene or CRISPR repeat detected, while the “Contains CRISPR features” column denotes that a protein coding sequence with homology to known Cas proteins or CRISPR repeats were detected in the chromosome. The right heat map displays the percent of genomes containing CRISPR‐Cas systems when normalized for total number of genomes included in this analysis.
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