SpacerPlacer: ancestral reconstruction of CRISPR arrays reveals the evolutionary dynamics of spacer deletions.

ABSTRACT: Bacteria employ CRISPR-Cas systems for defense by integrating invader-derived sequences, termed spacers, into the CRISPR array, which constitutes an immunity memory. While spacer deletions occur randomly across the array, newly acquired spacers are predominantly integrated at the leader end. Consequently, spacer arrays can be used to derive the chronology of spacer insertions. Reconstruction of ancestral spacer acquisitions and deletions could help unravel the coevolution of phages and bacteria, the evolutionary dynamics in microbiomes, or track pathogens. However, standard reconstruction methods produce misleading results by overlooking insertion order and joint deletions of spacers. Here, we present SpacerPlacer, a maximum likelihood-based ancestral reconstruction approach for CRISPR arr

SUBMITTER: Fehrenbach A 

PROVIDER: S-EPMC11472070 | biostudies-literature | 2024 Oct

REPOSITORIES: biostudies-literature