What this entity is
CRISPR-Cas is a microbial defense-system gene category associated with clustered regularly interspaced short palindromic repeats and CRISPR-associated proteins. 1
- Canonical name: CRISPR-Cas. 1
- Known aliases: No additional aliases were reported in the source project. 1
- Stable external identifier: No stable external identifier was reported in the source project. 1
Acquisition and defense-arsenal evidence
CRISPR-Cas showed the strongest recent-to-ancient acquisition-depth contrast among the function classes reported in the atlas, with 58.7% of Sankoff gain events classified as recent and 2.4% classified as ancient. 1 The resulting recent-to-ancient acquisition ratio for CRISPR-Cas was 24.5×. 1 These acquisition-depth results support using gene-function-acquisition-depth to compare the evolutionary-age signatures of defense, regulatory, metabolic, and housekeeping functions. 1
The CRISPR-Cas acquisition signature is also relevant to environmental-resistome, where recent gene acquisition is used as a comparative signal across mobile and defense-associated functions. 1 In the pan-bacterial defense analysis, CRISPR-Cas was detected in 96.1% of species-level pangenomes, the highest reported prevalence among seven defense-system families. 2 This refines the acquisition-depth result by showing that a broadly distributed defense category can also carry a strong recent-acquisition signature. 2
The reported 96% prevalence is method-dependent: EggNOG description matching gave 96%, whereas the specific Cas1 Pfam marker PF01867 gave approximately 55% on the same pangenome, a difference of approximately 40 percentage points. 2 Thus, the new analysis qualifies cross-study comparisons of CRISPR-Cas prevalence, treating 96% as an upper bound rather than an unambiguous system-specific estimate. 2
CRISPR-Cas had 27.4% core and 47.2% singleton gene-cluster fractions in the defense pangenome analysis, compared with a background of 46.8% core and 37.9% singleton clusters. 2 This supports the existing interpretation of defense-associated functions as acquisition-relevant while indicating a weaker accessory-enrichment pattern for CRISPR-Cas than for several other systems. 2 CRISPR-Cas × CBASS was the only one of 28 defense-system pairs without significant positive co-occurrence, with z = 0.21 and p_emp = 0.98. 2
The project’s CRISPR-Cas result was generated within a GTDB-r214 atlas containing 18,989 species representatives and 17,073,194 Sankoff-parsimony gain events assigned to recipient-rank depth bins. 1
Source
The detailed acquisition-depth evidence is summarized in Gene Function Ecological Agora. 1 The pan-bacterial prevalence, detection-method comparison, and defense-syndrome evidence are summarized in Pan-Bacterial Anti-Phage Defense Arsenal. 2