Abstract
The CRISPR-Cas system biologically serves as an adaptive defense mechanism against phages. However, there is growing interest in exploiting the hypervariable nature of the CRISPR locus, often of viral origin, for microbial typing and tracking. Moreover, the spacer content of any given strain provides a phage resistance profile. Large-scale CRISPR typing studies require an efficient method for showcasing CRISPR array similarities across multiple isolates. Historically, CRISPR arrays found in microbes have been represented by colored shapes based on nucleotide sequence identity and, while this approach is now routinely used, only scarce computational resources are available to automate the process, making it very time-consuming for large datasets. To alleviate this tedious task, we introduce CRISPRStudio, a command-line tool developed to accelerate CRISPR analysis and standardize the preparation of CRISPR array figures. It first compares nucleotide spacer sequences present in a dataset and then clusters them based on sequence similarity to assign a meaningful representative color. CRISPRStudio offers versatility to suit different biological contexts by including options such as automatic sorting of CRISPR loci and highlighting of shared spacers, while remaining fast and user-friendly.
Highlights
Of all the applications and technologies developed around CRISPR-Cas systems, strain typing is arguably the oldest one, as it capitalizes on the ability of the system to acquire new DNA fragments [1]
Discovered as an unusual nucleotide arrangement in the Escherichia coli genome [2,3] and later as a defense mechanism [4], CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) loci, together with their cas (CRISPR-associated) genes, form the so-called CRISPR-Cas systems. These microbial systems provide resistance against invasion of foreign DNA elements, such as phage genomes and plasmids [4,5], by first incorporating short DNA sequences called spacers [6] which originate from the foreign DNA element, into the CRISPR array
In the case of phage infections, the CRISPR-Cas machinery will use these spacers of viral origin as a memory to produce crRNAs that will target subsequent infections by phage genomes carrying the exact spacer sequence
Summary
Of all the applications and technologies developed around CRISPR-Cas systems, strain typing is arguably the oldest one, as it capitalizes on the ability of the system to acquire new DNA fragments [1]. For reporting purposes, the CRISPR arrays are graphically represented with colored shapes, making it easy to visualize similarities and differences across microbial strains This representation is commonly used to facilitate comparison and analyses [17,18,19,20,21,22,23,24,25,26,27,28,29], the development of software to support such analyses remained unexplored until recently when the first automated visualization program, called CRISPRviz, was published [30]. The color-coded visualization is an intuitive method to identify strains with the same phage infection profile and conserved spacers among evolutionary distant microbial species, suggestive of infections by broad host range phages
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