Figure 1.
Schematic location of CRISPR loci on Syn OS-A OS-B genomes.
Bars indicate the relative positions of the Type I (red), Type II (green) and Type III (blue) CRISPR loci on the genomes of Syn OS-A (top) and Syn OS-B′ (bottom). Asterisks indicate CRISPRs with an associated cas operon. CRISPRs within syntenic genome blocks are connected with lines. Approximate location and direction of the mapped clone-mates of CRISPR containing clones are show as triangles colored by the repeat type (as above). Two clones that mapped to a location on a reference genome that lacks a CRISPR array are shown within the genome box. Line below shows genome size (large ticks at 1 Mbp; small ticks at 0.5 Mbp).
Table 1.
CRISPR repeats in Synechococcus OS-A and OS-B′.
Figure 2.
A) CRISPR-IA region from Syn OS-A (top) and Syn OS-B′ (bottom). The cas gene cluster is indicated by a grey bracket. B) CRISPR-IB region. Gene identifiers are shown above or below each gene, excluding the GenBank locus tag prefix ‘CYA_’ (for Syn OS-A) or ‘CYB_’ (for Syn OS-B′). Genes are color-coded following the COG-based IMG convention (http://img.jgi.doe.gov), (described in Figure 4), except that genes annotated as “hypothetical protein” are in grey, genes with no putative ortholog in the other genome are in red, and genes annotated as transposases are in black. Orthologous genes are indicated by yellow blocks. Detailed information on each gene is available in Table S3.
Figure 3.
Homologous regions from Syn OS-A and Syn OS-B′ where one or both genomes has a Type II CRISPR locus are displayed. The CRISPR displayed is indicated by the panel letter (e.g. panel ‘A’ shows CRISPR-IIA, panel ‘B’ shows CRISPR-IIB, etc.) Figure conventions are as described in Figure 2. FS indicates a frameshift in the CDS. Additional details can be found in Table S3.
Figure 4.
Comparison of Type III CRISPR locus to Roseiflexus RS-1 and Symbiobacterium.
Homologous regions from Syn OS-A, Syn-OS-B′, Roseiflexus RS-1 and Symbiobacterium are displayed. Gene identifiers are shown above or below each gene, excluding the GenBank locus tag prefix ‘CYA_’ (for Syn OS-A), ‘CYB_’ (for Syn OS-B′), RoseRS_ (for Roseiflexus RS-1) or STH (for Symbiobacterium thermophilum). Additional figure conventions are as described in Figure 2. Details about the genes can be found in Table S3.
Table 2.
CRISPR viritopes with similarity to virome sequences.
Figure 5.
Example of a putative gene encoding a lysozyme derived from the virome.
The location of the CRISPR viritopes is highlighted. The yellow highlighted region matches CRISPR_II_YMBCR81TF-SP-2 and the bold highlighted region is CRISPR_II_YMIA938TF-SP-4/5.
Table 3.
Virome sequences showing silent or conservative changes relative to the viritope Cluster_2_YMBCR81TF-SP-2 sequence.