Figure Legend
Figure 1 CRISPR/Cas systems in K. variicola . (A) The pie
chart shows the proportion of 105 strains with and without CRISPR/Cas
systems. The stacking plot represents the number of each CRISPR/Cas
subtype. (B) Schematic diagram of each CRISPR/Cas subtype. Different
colors are used to represent the CRISPR/Cas system and its gene
neighbor. The K. variicola type I-E system is located between thecysH and iap genes, and the cas genes are shown in
blue. The type I-E* system is located on the downstream of the ABC
transporter system, and the cas genes are shown in green. The
type Ⅳ-A system is adjacent to the umuD and umuC , and thecas genes are shown in orange. The repeats and spacers of CRISPR
are represented by white diamonds and black rectangles, respectively.
All genes are drawn to scale.
Figure 2 (A) Visualization and alignment of nucleotides of
repeat sequences in each CRISPR/Cas subtype. (B) PAM prediction of each
CRISPR/Cas subtype. (C) Secondary structure prediction and MFE value of
each CRISPR/Cas subtype. Nucleotide bases are colored by base-pair
probability. (D) The repeat length of three types of CRISPR/Cas system.
(E) The number of three types of CRISPR/Cas system. The box plot
represents the number of spacers detected in each subtype. *: p< 0.05, **: p < 0.01, ***: p< 0.001, ns: non-significance.
Figure 3 Phylogenetic tree based on MLST. From inside to
outside, the colored rings indicate the type I-E, type I-E*, type Ⅳ-A
CRISPR/Cas systems, respectively. The short band indicates that thecas genes in the system is incomplete, and the long band
indicates that the CRISPR/Cas system is complete.
Figure 4 Hierarchical clustering analysis of spacer
arrangements in type I-E (A), type I-E* (B), type IV-A systems (C). The
various colors correspond to different STs, and the STs are marked on
the left. The blue and gray squares denote the presence and absence of
spacers, respectively.
Figure 5 (A) Comparison of detected spacer-protospacer matches
for type I-E, type I-E*, and type IV-A systems. (B) Spacers target
specific exogenous genes. Nearly one-quarter of K. variicolaspacers have a match to genes with informative annotations, and the
proportion of gene matching is presented.
Figure 6 The network ofK. variicola and MGEs from other species based on
protospacer-spacer matches in type I-E (A), type I-E* (B), type IV-A (C)
systems. Nodes indicate individual spacers and edges represent CRISPR
spacer targeting based on spacer-protospacer matches.
Figure S1 Comparison of cas genes between K.
variicola strain WCHKP19 and 9 K. variicola strains. The genes
(cas3, cse1, cse2, cas7 , and cas5 ) responsible for the
interference are shown in blue. The gene (cas6 ) involve in
expression is highlighted in red. The adaptation genes (cas1 andcas2 ) are depicted in orange. The repeats and spacers are
represented by white diamonds and black rectangles, respectively. All
genes are drawn to scale.