Comparative Genomic Analysis of Mycobacteriaceae Reveals Horizontal Gene Transfer-Mediated Evolution of the CRISPR-Cas System in the Mycobacterium tuberculosis Complex

A sister lineage of the Mycobacterium tuberculosis complex discovered in the African Great Lakes region

(2020) Jean Claude Semuto Ngabonziza et al.   Nature Communications

Higher genome mutation rates of Beijing lineage of Mycobacterium tuberculosis during human infection

(2020) Mariko Hakamata et al.   Scientific Reports

Unexpected diversity of CRISPR unveils some evolutionary patterns of repeated sequences in Mycobacterium tuberculosis

(2020) Guislaine Refrégier et al.   BMC GENOMICS

RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference

(2019) Alexey M Kozlov et al.   BIOINFORMATICS

Simple assay to detect Central Asia Outbreak clade of Mycobacterium tuberculosis Beijing genotype

(2019) Egor Shitikov et al.   JOURNAL OF CLINICAL MICROBIOLOGY

The Mycobacterium tuberculosis CRISPR-Associated Cas1 Involves Persistence and Tolerance to Anti-Tubercular Drugs

(2019) Jiawei Wei et al.   Biomed Research International

Genomic determinants of speciation and spread of the Mycobacterium tuberculosis complex

(2019) Á. Chiner-Oms et al.   Science Advances

Cyclic oligoadenylate signalling mediates Mycobacterium tuberculosis CRISPR defence

(2019) Sabine Grüschow et al.   NUCLEIC ACIDS RESEARCH

Evolutionary classification of CRISPR–Cas systems: a burst of class 2 and derived variants

(2019) Kira S. Makarova et al.   NATURE REVIEWS MICROBIOLOGY

Mycobacterium tuberculosis type III-A CRISPR/Cas system crRNA and its maturation have atypical features

(2018) Wenjing Wei et al.   FASEB JOURNAL

Phylogenomic analysis of the species of the Mycobacterium tuberculosis complex demonstrates that Mycobacterium africanum, Mycobacterium bovis, Mycobacterium caprae, Mycobacterium microti and Mycobacterium pinnipedii are later heterotypic synonyms of Mycobacterium tuberculosis

(2018) Marco A. Riojas et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

History of CRISPR-Cas from Encounter with a Mysterious Repeated Sequence to Genome Editing Technology

(2018) Yoshizumi Ishino et al.   JOURNAL OF BACTERIOLOGY

Ecology and evolution of Mycobacterium tuberculosis

(2018) Sebastien Gagneux   NATURE REVIEWS MICROBIOLOGY

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

(2018) David Couvin et al.   NUCLEIC ACIDS RESEARCH

Methylation in Mycobacterium tuberculosis is lineage specific with associated mutations present globally

(2018) Jody Phelan et al.   Scientific Reports

New insights into the transposition mechanisms of IS6110 and its dynamic distribution between Mycobacterium tuberculosis Complex lineages

(2018) Jesús Gonzalo-Asensio et al.   PLoS Genetics

Phylogenomics and Comparative Genomic Studies Robustly Support Division of the Genus Mycobacterium into an Emended Genus Mycobacterium and Four Novel Genera

(2018) Radhey S. Gupta et al.   Frontiers in Microbiology

CRISPRStudio: A User-Friendly Software for Rapid CRISPR Array Visualization

(2018) Moïra Dion et al.   Viruses-Basel

A New Phylogenetic Framework for the Animal-Adapted Mycobacterium tuberculosis Complex

(2018) Daniela Brites et al.   Frontiers in Microbiology

IslandViewer 4: expanded prediction of genomic islands for larger-scale datasets

(2017) Claire Bertelli et al.   NUCLEIC ACIDS RESEARCH

CRISPRDetect: A flexible algorithm to define CRISPR arrays

(2016) Ambarish Biswas et al.   BMC GENOMICS

Roary: rapid large-scale prokaryote pan genome analysis

(2015) Andrew J. Page et al.   BIOINFORMATICS

Role of the horizontal gene exchange in evolution of pathogenic Mycobacteria

(2015) Oleg Reva et al.   BMC EVOLUTIONARY BIOLOGY

An updated evolutionary classification of CRISPR–Cas systems

(2015) Kira S. Makarova et al.   NATURE REVIEWS MICROBIOLOGY

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Inter-phylum HGT has shaped the metabolism of many mesophilic and anaerobic bacteria

(2014) Alejandro Caro-Quintero et al.   ISME Journal

Mycobacterium tuberculosis Strains of the Modern Sublineage of the Beijing Family Are More Likely To Display Increased Virulence than Strains of the Ancient Sublineage

(2014) S. C. M. Ribeiro et al.   JOURNAL OF CLINICAL MICROBIOLOGY

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

CRISPR–Cas systems: beyond adaptive immunity

(2014) Edze R. Westra et al.   NATURE REVIEWS MICROBIOLOGY

Consequences of genomic diversity in Mycobacterium tuberculosis

(2014) Mireia Coscolla et al.   SEMINARS IN IMMUNOLOGY

A robust SNP barcode for typing Mycobacterium tuberculosis complex strains

(2014) Francesc Coll et al.   Nature Communications

CRISPRs: Molecular Signatures Used for Pathogen Subtyping

(2013) Nikki Shariat et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Genomic analysis of smooth tubercle bacilli provides insights into ancestry and pathoadaptation of Mycobacterium tuberculosis

(2013) Philip Supply et al.   NATURE GENETICS

CRISPRmap: an automated classification of repeat conservation in prokaryotic adaptive immune systems

(2013) Sita J. Lange et al.   NUCLEIC ACIDS RESEARCH

Comparative genomic structures of Mycobacterium CRISPR-Cas

(2012) Liming He et al.   JOURNAL OF CELLULAR BIOCHEMISTRY

LocARNA-P: Accurate boundary prediction and improved detection of structural RNAs

(2012) S. Will et al.   RNA

Easyfig: a genome comparison visualizer

(2011) M. J. Sullivan et al.   BIOINFORMATICS

HMMER web server: interactive sequence similarity searching

(2011) R. D. Finn et al.   NUCLEIC ACIDS RESEARCH

A dual function of the CRISPR-Cas system in bacterial antivirus immunity and DNA repair

(2010) Mohan Babu et al.   MOLECULAR MICROBIOLOGY

Detecting genomic islands using bioinformatics approaches

(2010) Morgan G. I. Langille et al.   NATURE REVIEWS MICROBIOLOGY

CRISPR-based adaptive and heritable immunity in prokaryotes

(2009) John van der Oost et al.   TRENDS IN BIOCHEMICAL SCIENCES