These are some of my favourite BRIG figures from recent Open Access publications. They are all really amazing and go far beyond what I thought was possible with the tool. I did not make these figures; all credit (and kudos) belong to the respective authors.

"Visualization of the reads selected for each strain mapped onto the S. pyogenes MGAS6180 reference genome. The innermost circles represent the GC content (black), GC skew (purple/green), and rRNA operons of MGAS6180 (pink boxes). BRIG (1) shows the distribution of the number of reads for each individual strain mapped onto the central reference using a window size of 500, arranged from inner to outer colored circles as follows: resequenced reference MGAS6180 (pink), PS001 (yellow), PS006 (orange), PS005 (red), PS007 (maroon), and PS008 (purple). Additional strain-specific regions of difference (RODs) (ϕPS008 and ICESpPS008) are represented as insertions. The outermost circle represents previously reported regions of difference in MGAS6180, namely, prophage elements 6180.1 and 6180.2, prophage remnants 6180.3 and 6180.4, and regions of difference 6180.RD1 and 6180.RD2 (15) (black)."

From Ben Zakour et al. (2012) 'Analysis of a Streptococcus pyogenes Puerperal Sepsis Cluster by Use of Whole-Genome Sequencing', J. Clin. Microbiol 50(7). doi: 10.1128/JCM.00675-12

"Distribution of CU fimbrial gene clusters among E. coli pathotypes. The inner ring represents the concatenated nucleotide sequences of the 38 fimbrial operons. Each segment is labelled in the outer ring according to the name and clade [3] of the corresponding fimbrial usher type with the intervening 36 rings displaying the presence of intact CU fimbrial gene clusters in each of the strains analysed. The legend on the right lists the colour of each strain that we included in our study, grouped according to pathogenicity class. Circular comparison was generated using BLAST ring image generator (BRIG) [69]. 1CFT073 contains two copies of the P fimbriae operon."

From Wurpel et al. (2013) 'Chaperone-Usher Fimbriae of Escherichia coli.', PLoS ONE 8(1): e52835. doi:10.1371/journal.pone.0052835

"BlastP comparison of the Janthinobacterium sp. HH01 genome compared against genomes of closely related species. The innermost rings indicate the GC content (black) and GC skew (purple/green). The outer rings represent the genomes of the following microbes in different colorings: Janthinobacterium sp. Marseille, blue; Janthinobacterium sp. PAMC 25724, red; Janthinobacterium sp. GC3, green; and C. violaceum ATCC 12472, black."

From Hornung et al. (2013) 'The Janthinobacterium sp. HH01 Genome Encodes a Homologue of the V. cholerae CqsA and L. pneumophila LqsA Autoinducer Synthases.', PLoS ONE 8(2): e55045. doi:10.1371/journal.pone.0055045

"Analysis of the Enterococcus faecium AUS0004 complete genome. (A) Circular map of AUS0004 by comparative BLASTN analysis against the contigs from the partially assembled genomes of 11 E. faecium strains, showing the locations of a large chromosomal inversion and Aus0004 accessory genome elements. Track identification, moving outwards, is as follows: G+C content, GC skew (G-C/G+C), IS elements, E. faecium isolates (next 11 tracks, as listed here and in Table 1), followed by regions (red arcs) potentially acquired by HGT revealed by AlienHunter, location of prophage, Aus004 unique regions revealed by read mapping against 23 E. faecium genomes (blue arcs), and finally the location of the eight MLST genes. Dotted lines indicate likely replication origin (dnaA) and terminus (dif) and highlight a replichore imbalance, caused by a phiEnfa001-mediated chromosomal inversion. (B) NcoI optical map of E. faecium AUS0004 compared with in silico-derived NcoI map demonstrating correct chromosome assembly. (C) Artemis linear view of Aus0004 chromosome and plasmids (appended), with vertical blue bars identifying the positions of accessory genome elements as determined by read mapping against 23 publicly available partially assembled genome sequences. Increasing height of vertical blue lines on this map indicates increasing specificity for Aus0004."

From Lam et al. (2012) 'Comparative Analysis of the First Complete Enterococcus faecium Genome', J. Bacteriol. 194(9). doi: 10.1128/JB.00259-12 N.B. Only Figure (A) was generated with BRIG.

"The inner circle represents the reference sequence, E. coli EC958, with scaffolds of the draft assembly displayed as alternating blue or red color in the inner-most ring. Outer rings show shared identity (according to BLASTn) with individual UPEC genomes and various other E. coli genomes. BLASTn matches between 80% and 100% nucleotide identity are colored from lightest to darkest shade, respectively, according to the graduated scale on the right of the circular BLAST image. Matches with less than 80% identity, or E. coli EC958 regions with no BLAST matches, appear as blank spaces in each ring. Rings indicate BLAST identity, from inside to out, between EC958 and: (1–5) individual UPEC genomes CFT073, 536, UTI89, IAI39, UMN026 (light to dark blue); (6) pooled ExPEC genomes: APEC O1, IHE3034, S88 (purple); (7) pooled EHEC/EPEC genomes: EC4115, Sakai, EDL933, E2348 (pink); (8) pooled EAEC/AIEC/ETEC genomes: 55989, O42, LF82, E24377A (yellow); (9) environmental E. coli genome: SMS_3_5 (lime green); (10) pooled commensal E. coli genomes: IAI1, SE11, SE15, HS, 8739, ED1a (teal); pooled E. coli K12 genomes: MG1655, W3110, DH10B (green). Black labels indicate regions that are known to be variable in E. coli genomes. Blue labels and arcs indicate RODs that appear to be prophage regions; red labels and arcs indicate known genomic islands (GI-pheV, GI-selC, GI-thrW, and GI-leuX) or potential new genomic islands (ROD1–3)."

From Totsika et al. (2011) 'Insights into a Multidrug Resistant Escherichia coli Pathogen of the Globally Disseminated ST131 Lineage: Genome Analysis and Virulence Mechanisms.', PLoS ONE 6(10): e26578. doi:10.1371/journal.pone.0026578

"BRIG for multiple genome comparison. BRIG is a free tool [42,43] that requires a local installation of BLAST (we used BRIG 0.95 on Mac OS X). The output is a static image. • Launch BRIG and set the reference sequence (EHEC EDL933 chromosome) and the location of other E. coli sequences for comparison. If you include reference sequences for the Stx2 phage and LEE pathogenicity island, it will be easy to see where these sequences are located. • Click ‘Next’ and specify the sequence data and colour for each ring to be displayed in comparison to the reference. • Click ‘Next’ and specify a title for the centre of the image and an output file, then click ‘Submit’ to run BRIG. • BRIG will create an output file containing a circular image like the one shown here. It is easy to see that the Stx2 phage is present in the EHEC chromosomes (purple) and the outbreak genome (black), but not the EAEC or EPEC chromosomes."

From Edwards & Holt (2013) 'Beginner's guide to comparative bacterial genome analysis using next-generation sequence data', Microbial Informatics and Experimentation 3(2). doi:10.1186/2042-5783-3-2


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