DOI: 10.5061/dryad.t76hdr87m
title: Data for: CRISPR spacers acquired from plasmids primarily target backbone genes, making them valuable for predicting potential hosts and host range

description: Here we provide the full data which is described and discussed in CRISPR
 Spacers Acquired from Plasmids Primarily Target Backbone Genes, Making
 Them Valuable for Predicting Potential Hosts and Host Range, submitted to
 Microbiology Spectrum. Abstract of the main manuscript: In recent years,
 there has been a surge in metagenomic studies focused on identifying
 plasmids in environmental samples. While these studies have unearthed
 numerous novel plasmids, enriching our understanding of their
 environmental roles, a significant gap remains: the scarcity of
 information regarding the bacterial hosts of these newly discovered
 plasmids. Furthermore, even when plasmids are identified within bacterial
 isolates, the reported host is typically limited to the original isolate,
 with no insight into alternative hosts or the plasmid’s potential host
 range. Given that plasmids depend on hosts for their existence,
 investigating plasmids without knowledge of potential hosts offers only a
 partial perspective. This study introduces a method for identifying
 potential hosts and host ranges for plasmids through alignment with CRISPR
 spacers. To validate the method, we compared the PLSDB plasmids database
 with the CRISPR spacers database, yielding host predictions for 46% of the
 plasmids. When compared to reported hosts, our predictions achieved an 84%
 concordance at the family level and 99% concordance at the phylum level.
 Moreover, the method frequently identified multiple potential hosts for a
 plasmid, thereby enabling predictions of alternative hosts and the host
 range. Notably, we found that CRISPR spacers predominantly target plasmid
 backbone genes while sparing functional genes, such as those linked to
 antibiotic resistance, aligning with our hypothesis that CRISPR spacers
 are acquired from plasmid-specific regions rather than insertion elements
 from diverse sources. Lastly, we illustrate the network of connections
 among different bacterial taxa through plasmids, revealing potential
 pathways for horizontal gene transfer. IMPORTANCE: Plasmids are notorious
 for their role in distributing antibiotic resistance genes, but they may
 also carry and distribute other environmentally important genes. Since
 plasmids are not free-living entities and rely on host bacteria for
 survival and propagation, predicting their hosts is essential. This study
 presents a method for predicting potential hosts for plasmids and offers
 insights into the potential paths for spreading functional genes between
 different bacteria. Understanding plasmid-host relationships is crucial
 for comprehending the ecological and clinical impact of plasmids and
 implications for various biological processes.
description: # Data for: CRISPR Spacers Acquired from Plasmids Primarily Target
 Backbone Genes, Making Them Valuable for Predicting Potential Hosts and
 Host Range
 [https://doi.org/10.5061/dryad.t76hdr87m](https://doi.org/10.5061/dryad.t76hdr87m) ## Description of the data and file structure Supplementary Table A: The full list of the alignment of all the entries of the plasmid database (PLSDB, version 2021_06_23) with all the entries of the spacers database from CRISPRCasdb (version 20210121). Each line represents a match between a plasmid from PLSDB and a spacer from CRISPRCasdb. Each line lists the NCBI Accession number of the plasmid (Column A), NCBI Accession number of the source of the spacer (Column B), length of match (Column C), the region of match on the plasmid (Start - Column D; End - Column E), plasmid taxonomic lineage (from species, Column F, to Phylum, Column K), predicted host taxonomic lineage (from species, Column L, to Phylum, Column Q), the lowest taxonomic level in which the reported host and the predicted host match (Column R) and the matched sequence (Column S).  Further analysis of the results, as well as detailed description of the methods, can be found in the main manuscript. ## Sharing/Access information Data was derived from the following sources: * PLSDB, version 2021_06_23; [PLSDB (uni-saarland.de)](https://ccb-microbe.cs.uni-saarland.de/plsdb/) * CRISPRCasdb version 20210121; [CRISPR-CAS++ (paris-saclay.fr)](https://crisprcas.i2bc.paris-saclay.fr/) ## Code/Software All codes used for the production and analysis of the data are available on GitHub: [https://github.com/Tal-Lab/crispr_plasmidome](https://github.com/Tal-Lab/crispr_plasmidome)