TIGRdisco: a tool for the discovery of TIGR arrays and TIGR-associated Tas proteins from nucleotide sequences

Abstract

Tandem Interspaced Guide RNA (TIGR)-TIGR-associated protein (Tas) systems mediate DNA targeting through a hypercompact Tas effector, guided by dual spacers within a tigRNA that is processed from TIGR arrays. TIGR-Tas loci are composed of a Tas coding sequence associated with TIGR arrays of short units in either dual-repeat or stem-loop architecture. Unlike CRISPR (Clustered regularly interspaced short palindromic repeats) arrays that comprise units of direct repeats interspersed with unique spacers, units within the two distinct TIGR architectures only conform through extremely short box motifs, complicating detection. Here, we present TIGRdisco, an integrated tool capable of discovering both the Tas protein and its associated TIGR arrays directly from unannotated nucleotide sequences. TIGRdisco implements independent engines to detect the two array architectures through a motif-agnostic approach. We benchmarked TIGRdisco against a reference dataset of TIGR-Tas loci, recovering more than 80% of array units within its search window. Furthermore, TIGRdisco recovered arrays for loci within entire clades of Tas where associated arrays were unannotated in the reference. We found that these arrays largely contain non-canonical box motifs or unit lengths. Lastly, as a case study, we utilized TIGRdisco and successfully uncovered TIGR-Tas loci across metagenomic and genomic datasets.