SCRAMBLER: A Tool for de Novo CRISPR Array Reconstruction and Its Application for Analysis of the Structure of Prokaryotic Populations

Anton Rykachevsky, Alexander Stepakov, Polina Muzyukina, Sofia Medvedeva, Mark Dobrovolski, Evgeny Burnaev, Konstantin Severinov, Ekaterina Savitskaya

Research output: Contribution to journalArticlepeer-review

Abstract

CRISPR arrays are prokaryotic genomic loci consisting of repeat sequences alternating with unique spacers acquired from foreign nucleic acids. As one of the fastest-evolving parts of the genome, CRISPR arrays can be used to differentiate closely related prokaryotic lineages and track individual strains in prokaryotic communities. However, the assembly of full-length CRISPR arrays sequences remains a problem. Here, we developed SCRAMBLER, a tool that includes several pipelines for assembling CRISPR arrays from high-throughput short-read sequencing data. We assessed its performance with model data sets (Escherichia coli strains containing different CRISPR arrays and imitating prokaryotic communities of different complexities) and intestinal microbiomes of extant and extinct pachyderms. Evaluation of SCRAMBLER's performance using model data sets demonstrated its ability to assemble CRISPR arrays correctly from reads containing pairs of spacers, yielding a precision rate of >80% and a recall rate of 60-85% when checked against ground-truth data. Likewise, SCRAMBLER successfully assembled CRISPR arrays from the environmental samples, as attested by their matching with database entries. SCRAMBLER, an open-source software (github.com/biolab-tools/SCRAMBLER), can facilitate analysis of the composition and dynamics of CRISPR arrays in complex communities.

Original languageEnglish
Pages (from-to)673-685
Number of pages13
JournalCRISPR Journal
Volume4
Issue number5
DOIs
Publication statusPublished - Oct 2021

Fingerprint

Dive into the research topics of 'SCRAMBLER: A Tool for de Novo CRISPR Array Reconstruction and Its Application for Analysis of the Structure of Prokaryotic Populations'. Together they form a unique fingerprint.

Cite this