Shotgun sequencing failed to determine the whole PaP1 genome. (A) PFGE map of the PaP1 genomic DNA, showing that the PaP1 genome should be approximately 90 kb. (B) Length of the 20 contigs obtained using the shotgun method. Contig20 is the longest contig (approximately 26.1 kb) and all of the contigs could not be assembled in an integral genome sequence. The total length of the 20 contigs is approximately 47.7 kb, almost half of 90 kb.