Fig. 1

A group of type II CRISPR arrays captured in long reads containing shared CRISPR spacers. a Representative CRISPR-Cas system characterized from a single long read (SRR2822456.206102, reverse complement). Green arrows represent cas genes, open hexagon represents a CRISPR array containing 19 repeats, and the red arrow denotes a putative anti-repeat that may be part of the tracrRNA [62]. b Representative organization of spacer-sharing CRISPR arrays. Spacers are each represented as a square with a unique spacer ID, whereas diamonds represent the repeats. The number of reads found to contain a CRISPR array with the same organization of spacers are denoted in red, right of the representative sequence. Complete CRISPR arrays, where ends of arrays are not fragmented or truncated as a result of sequencing, are denoted by a red diamond at the end of CRISPR arrays; fragmented ends of arrays remain as a gray diamond. c Compressed spacer graph constructed from CRISPRs sharing spacers. Uninterrupted blocks of repeat-spacer units are represented as a single node. Directed edges between nodes indicate the ordering of spacers found in a CRISPR array, where the path consisting of red edges represent the most frequent spacer-repeat organization observed in the group of CRISPRs. In the compressed spacer graph, source nodes (without incoming edges) are highlighted in blue, and they are likely to contain newly gained spacers; the sink node (without outgoing edges), which contains the trailer end spacer, is highlighted in yellow