Major bacterial lineages are essentially devoid of CRISPR-Cas viral defence systems

[1]  Brian C. Thomas,et al.  Metagenomic analysis of a high carbon dioxide subsurface microbial community populated by chemolithoautotrophs and bacteria and archaea from candidate phyla. , 2016, Environmental microbiology.

[2]  R. Gardan,et al.  Costs of CRISPR-Cas-mediated resistance in Streptococcus thermophilus , 2015, Proceedings of the Royal Society B: Biological Sciences.

[3]  James C. Stegen,et al.  The reduced genomes of Parcubacteria (OD1) contain signatures of a symbiotic lifestyle , 2015, Front. Microbiol..

[4]  Brian C. Thomas,et al.  Unusual biology across a group comprising more than 15% of domain Bacteria , 2015, Nature.

[5]  Brian C. Thomas,et al.  CRISPR Immunity Drives Rapid Phage Genome Evolution in Streptococcus thermophilus , 2015, mBio.

[6]  Mike Boots,et al.  Parasite Exposure Drives Selective Evolution of Constitutive versus Inducible Defense , 2015, Current Biology.

[7]  Asaf Levy,et al.  CRISPR adaptation biases explain preference for acquisition of foreign DNA , 2015, Nature.

[8]  E. Koonin,et al.  Babela massiliensis, a representative of a widespread bacterial phylum with unusual adaptations to parasitism in amoebae , 2015, Biology Direct.

[9]  Kenneth H. Williams,et al.  Genomic Expansion of Domain Archaea Highlights Roles for Organisms from New Phyla in Anaerobic Carbon Cycling , 2015, Current Biology.

[10]  Brian C. Thomas,et al.  Diverse uncultivated ultra-small bacterial cells in groundwater , 2015, Nature Communications.

[11]  R. Sorek,et al.  BREX is a novel phage resistance system widespread in microbial genomes , 2015, The EMBO journal.

[12]  S. Yooseph,et al.  Cultivation of a human-associated TM7 phylotype reveals a reduced genome and epibiotic parasitic lifestyle , 2014, Proceedings of the National Academy of Sciences.

[13]  Richard J. Roberts,et al.  REBASE—a database for DNA restriction and modification: enzymes, genes and genomes , 2009, Nucleic Acids Res..

[14]  Kira S. Makarova,et al.  Classification and evolution of type II CRISPR-Cas systems , 2014, Nucleic acids research.

[15]  Matthew Fraser,et al.  InterProScan 5: genome-scale protein function classification , 2014, Bioinform..

[16]  Alexandros Stamatakis,et al.  RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies , 2014, Bioinform..

[17]  E. Birney,et al.  Pfam: the protein families database , 2013, Nucleic Acids Res..

[18]  I-Min A. Chen,et al.  IMG 4 version of the integrated microbial genomes comparative analysis system , 2013, Nucleic Acids Res..

[19]  Brian C. Thomas,et al.  Small Genomes and Sparse Metabolisms of Sediment-Associated Bacteria from Four Candidate Phyla , 2013, mBio.

[20]  Natalia N. Ivanova,et al.  Insights into the phylogeny and coding potential of microbial dark matter , 2013, Nature.

[21]  Eugene V. Koonin,et al.  Evolutionary Dynamics of the Prokaryotic Adaptive Immunity System CRISPR-Cas in an Explicit Ecological Context , 2013, Journal of bacteriology.

[22]  James E. DiCarlo,et al.  RNA-Guided Human Genome Engineering via Cas9 , 2013, Science.

[23]  Le Cong,et al.  Multiplex Genome Engineering Using CRISPR/Cas Systems , 2013, Science.

[24]  K. Katoh,et al.  MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability , 2013, Molecular biology and evolution.

[25]  Brian C. Thomas,et al.  Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization , 2013, Genome research.

[26]  Brian C. Thomas,et al.  Fermentation, Hydrogen, and Sulfur Metabolism in Multiple Uncultivated Bacterial Phyla , 2012, Science.

[27]  J. Doudna,et al.  A Programmable Dual-RNA–Guided DNA Endonuclease in Adaptive Bacterial Immunity , 2012, Science.

[28]  Siu-Ming Yiu,et al.  IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth , 2012, Bioinform..

[29]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[30]  Mart Krupovic,et al.  Genomics of Bacterial and Archaeal Viruses: Dynamics within the Prokaryotic Virosphere , 2011, Microbiology and Molecular Reviews.

[31]  Sean R. Eddy,et al.  Accelerated Profile HMM Searches , 2011, PLoS Comput. Biol..

[32]  Sagi Snir,et al.  Defense Islands in Bacterial and Archaeal Genomes and Prediction of Novel Defense Systems , 2011, Journal of bacteriology.

[33]  David S. Wishart,et al.  PHAST: A Fast Phage Search Tool , 2011, Nucleic Acids Res..

[34]  Stan J. J. Brouns,et al.  Evolution and classification of the CRISPR–Cas systems , 2011, Nature Reviews Microbiology.

[35]  Robert D. Finn,et al.  HMMER web server: interactive sequence similarity searching , 2011, Nucleic Acids Res..

[36]  Philippe Horvath,et al.  The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA , 2010, Nature.

[37]  Zixin Deng,et al.  TADB: a web-based resource for Type 2 toxin–antitoxin loci in bacteria and archaea , 2010, Nucleic Acids Res..

[38]  Robert C. Edgar,et al.  Search and clustering orders of magnitude faster than BLAST , 2010, Bioinform..

[39]  Adi Stern,et al.  Self-targeting by CRISPR: gene regulation or autoimmunity? , 2010, Trends in genetics : TIG.

[40]  Miriam L. Land,et al.  Trace: Tennessee Research and Creative Exchange Prodigal: Prokaryotic Gene Recognition and Translation Initiation Site Identification Recommended Citation Prodigal: Prokaryotic Gene Recognition and Translation Initiation Site Identification , 2022 .

[41]  Brian C. Thomas,et al.  Community-wide analysis of microbial genome sequence signatures , 2009, Genome Biology.

[42]  Philippe Horvath,et al.  Comparative analysis of CRISPR loci in lactic acid bacteria genomes. , 2009, International journal of food microbiology.

[43]  R. Kaul,et al.  Genome Sequence of the Fish Pathogen Renibacterium salmoninarum Suggests Reductive Evolution away from an Environmental Arthrobacter Ancestor , 2008, Journal of bacteriology.

[44]  V. Kunin,et al.  CRISPR — a widespread system that provides acquired resistance against phages in bacteria and archaea , 2008, Nature Reviews Microbiology.

[45]  J. Banfield,et al.  Rapidly evolving CRISPRs implicated in acquired resistance of microorganisms to viruses. , 2007, Environmental microbiology.

[46]  Ibtissem Grissa,et al.  CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats , 2007, Nucleic Acids Res..

[47]  Peter B. McGarvey,et al.  UniRef: comprehensive and non-redundant UniProt reference clusters , 2007, Bioinform..

[48]  R. Barrangou,et al.  CRISPR Provides Acquired Resistance Against Viruses in Prokaryotes , 2007, Science.

[49]  J. S. Godde,et al.  The Repetitive DNA Elements Called CRISPRs and Their Associated Genes: Evidence of Horizontal Transfer Among Prokaryotes , 2006, Journal of Molecular Evolution.

[50]  E. Bidnenko,et al.  Phage abortive infection in lactococci: variations on a theme. , 2005, Current opinion in microbiology.

[51]  Dmitrij Frishman,et al.  Illuminating the Evolutionary History of Chlamydiae , 2004, Science.

[52]  L. Schouls,et al.  Identification of genes that are associated with DNA repeats in prokaryotes , 2002, Molecular microbiology.

[53]  P. Wyrick.  Intracellular survival by Chlamydia , 2000, Cellular microbiology.

[54]  I. Longden,et al.  EMBOSS: the European Molecular Biology Open Software Suite. , 2000, Trends in genetics : TIG.

[55]  J. M. González,et al.  CRISPR elements in the Thermococcales: evidence for associated horizontal gene transfer inPyrococcus furiosus , 2010, Journal of Applied Genetics.

[56]  Hiroyuki Ogata,et al.  KEGG: Kyoto Encyclopedia of Genes and Genomes , 1999, Nucleic Acids Res..

[57]  N. Murray,et al.  Restriction and modification systems. , 1991, Annual review of genetics.

[58]  Supplemental Information 2: Kyoto Encyclopedia of genes and genomes. , 2022 .