CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins

Couvin, David; Bernheim, Aude; Toffano‐Nioche, Claire; Touchon, Marie; Michálik, Juraj; Néron, Bertrand; Rocha, Eduardo P. C.; Vergnaud, Gilles; Gautheret, Daniel; Pourcel, Christine

doi:10.1093/nar/gky425

Cited by 967 publications

(842 citation statements)

References 27 publications

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“…CRISPR arrays were detected with CRISPRCasFinder (4.2.17, 73 ) and matched to a Type IV module if any predicted operon was within a 10kbp radius (distance to first gene in the operon, this cut-off was based on Supplementary Fig. 13).…”

Section: Spacer-protospacer Match Analysismentioning

confidence: 99%

Type IV CRISPR-Cas systems are highly diverse and involved in competition between plasmids

Pinilla‐Redondo

Mayo-Muñoz

Russel

et al. 2019

Preprint

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CRISPR-Cas systems provide prokaryotes with adaptive immune functions against viruses and other genetic parasites by leveraging small non-coding RNAs for nuclease-dependent degradation of their nucleic acid targets. In contrast to all other types of CRISPR-Cas systems, the mechanisms and biological roles of type IV systems have remained largely overlooked.Here, we describe a previously uncharted diversity of type IV gene cassettes, distributed across diverse prokaryotic genome backgrounds, and propose their classification into subtypes and variants. Congruent with recent findings, type IV modules were primarily found on plasmid-like elements. Remarkably, via a comprehensive analysis of their CRISPR spacer content, these systems were found to exhibit a strong bias towards the targeting of other plasmids. Our data indicate that the functions of type IV systems have diverged from those of other host-related CRISPR-Cas immune systems to adopt a yet unrecognised role in mediating conflicts between plasmids that compete to monopolize their hosts. Furthermore, we find evidence for cross-talk between certain type IV and type I CRISPR-Cas systems that co-exist intracellularly, thus providing an answer to the enigmatic absence of adaptation modules in these systems. Collectively, our results lead to the expansion and reclassification of type IV systems and provide novel insights into the biological function and evolution of these elusive systems.

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Section: Spacer-protospacer Match Analysismentioning

confidence: 99%

Type IV CRISPR-Cas systems are highly diverse and involved in competition between plasmids

Pinilla‐Redondo

Mayo-Muñoz

Russel

et al. 2019

Preprint

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“…B). Such speed is a sharp contrast to that of the other servers: CRISPRone, 15 min; CRISPRCasFin, 1–3 min; and CRISPRDetect, 2–20 min for a 5 Mb genome (refer to supplementary material 2 in ).…”

Section: Resultsmentioning

confidence: 91%

“…Continuous works from scientific communities can enrich the overall number of Acr entries in public resources depending on emerging CRISPR-Cas tools [36,37]. Web-based servers [21,23] and standalone programs have been, in recent years, made available for CRISPR-Cas identification [22,35], nevertheless the constructed service and the developed standalone program can be still as complementary tools mainly because of the following reasons: Compared to other methods, CasLocusAnno facilitates selection of more reasonable Cas profile, because it chooses profiles with minimum e-values in each cluster. CasLocusAnno can also identify fused Cas proteins, whereas neither MAC-SYFINDER nor CRISPRCasFinder can do so because they select only profiles with the highest score.…”

Section: Discussionmentioning

confidence: 99%

CasLocusAnno: a web‐based server for annotating cas loci and their corresponding (sub)types

Dong

Zeng

et al. 2019

FEBS Letters

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In prokaryotes, Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR‐associated protein (Cas) systems constitute adaptive immune systems against mobile genetic elements (MGEs). Here, we introduce the Markov cluster algorithm (MCL) to Makarova et al.'s method in order to select a more reasonable profile. Additionally, our new Maximum Continuous Cas Subcluster (MCCS) method helps identification of tightly clustered loci. The comparison with two other commonly used programs shows that the method could identify Cas proteins with higher accuracy and lower Additional Prediction Rate (APR). Moreover, we developed a web‐based server, CasLocusAnno (http://cefg.uestc.cn/CasLocusAnno), capable of annotating Cas proteins, cas loci and their (sub)types less than ~ 28 s following the whole proteome sequence submission. Its standalone version can be downloaded at https://github.com/RiversDong/CasLocusAnno.

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“…Protein-coding regions and gene annotations were derived from the NCBI prokaryotic genome annotation pipeline (Tatusova et al, 2016). Genomes were screened for the presence of mobile elements by identifying integrating and conjugative elements (ICEs) with the ICEberg database (Bi et al, 2011), prophage sequences using PhiSpy (Akhter et al, 2012), insertion sequences (IS) with ISfinder (Siguier et al, 2006), and CRISPR with CRISPRCasFinder (Couvin et al, 2018). Evolutionary History of the Core Genome.…”

Section: Methodsmentioning

confidence: 99%

Sympatric and allopatric differentiation delineates population structure in free-living terrestrial bacteria

Chase

Arevalo

Brodie

et al. 2019

Preprint

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In microorganisms, specifically free-living bacteria and archaea, the equivalent of the biological species concept does not exist, creating several barriers to the study of the fine-scale genetic structure of microbial populations and thus, the processes contributing to microbial diversification. More often than not, studies attempting to delineate microbial populations overestimate traditionally-defined eukaryotic populations, or groups of individuals with the potential for contemporary interactions and exchange of genetic material. Here, we investigate the abundant leaf litter bacterium, Curtobacterium, and asked whether population structure in a free-living soil bacterium was consistent with patterns of allopatric or sympatric speciation. By investigating the fine-scale genetic structure within a single bacterial ecotype, we concluded that the distributional patterns of the populations suggest that both isolation-by-distance and isolation-by-environment contribute to Curtobacterium population structure. FIG 2. Recombination network across all pairwise strains. Thicker edges represent increased recombination between strains. Nodes are colored by population designation and node size indicates number of clonal clusters (strains too closely-related to differentiate recombination). D = Desert, Sc = Scrubland, G/MMLR = Grassland, SS = Salton Sea, MCBA = Boston

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CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins

Cited by 967 publications

References 27 publications

Type IV CRISPR-Cas systems are highly diverse and involved in competition between plasmids

Type IV CRISPR-Cas systems are highly diverse and involved in competition between plasmids

CasLocusAnno: a web‐based server for annotating cas loci and their corresponding (sub)types

Sympatric and allopatric differentiation delineates population structure in free-living terrestrial bacteria

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