Examples of gap filing, gap calling and sequence assembly discordances detected by alignments between in silico (pseudomolecule sequence) and optical maps. Panels A-D show types of discordances revealed through alignment of optical maps with in silico restriction maps from IRGSPBuild4 and TIGRBuild4 pseudomolecules; red arrows show their basepair locations, and green bars highlight the size of reported gaps in pseudomolecules. Aligned in silico (blue) and optical maps (gold) are shown as tracks comprising individual restriction fragments drawn as numbered bars whose length scales with size (kb). Identified discordances are annotated by color-keyed bars describing restriction map features presented by optical maps, but not found within corresponding in silico restriction maps: magenta = consecutive restriction fragments; red = restriction cut site(s); turquoise = missing restriction site(s). A: The top panel (IRGSPBuild4 Ch01, 10,043,782 – 10,107,330 bp) shows an overestimated sequence gap (green bar; 50.0 kb vs. optical map = 13.10 kb + 12.22 kb); bottom panel (IRGSPBuild4 Ch10, 3,968,375 – 4,068,843 bp), an underestimated gap (green bar; 100.468 kb vs. 26 optical restriction fragments = 507.18 kb, arrow). B: Discovered gaps in pseudomolecules: IRGSPBuild4 Ch08 (3,241,575 bp; 0.41 kb + 30.07 kb) and TIGRBuild4 Ch11 (27,515,267 bp; 2.65 kb + 47.26 kb). C: Extra sequence: IRGSPBuild4 Ch10 (14,828,584 – 14,978,980 bp, 150.396 kb vs. 48.36 kb, turquoise bar); TIGRBuild4 Ch11 (19,298,056 – 19,328,366 bp, 30.310 kb vs. 11.65 kb, turquoise bar). D: Misassembly: IRGSPBuild4 Ch04 (12,428,850 – 12,585,538 bp) vs. a stretch of 11 unaligned optical restriction fragments; TIGRBuild4 Ch04 (15,179,265 – 15,246,346 bp) vs. 5 unaligned restriction fragments. Panels E and F show examples of large-scale misassembly of sequence. In silico and optical maps are horizontal tracks comprising restriction fragments demarcated by vertical lines with aligned portions color-keyed and indicated by connecting lines; unaligned restriction fragments are white. E: IRGSPBulid4 Ch11 (29,945,713 – 30,823,503 bp; 877.790 kb) shows an 89.796 kb inversion (blue) and two significant portions (18.121 kb, 202.752 kb; white) unaligned to the optical map. F: IRGSPBuild4 & TIGRBuild4 Ch11 (18,181,576 – 18,600,983 bp; 419.407 kb & 15,853,410 – 16,272,766 bp; 419.356 kb, blue lettering for TIGRBuild4) show a 39.334 kb inversion (blue), a small insertion and portion (18,356,214 – 18,365,879 bp) missing a possible repetitive region characterized by the optical map.
Zhou et al. BMC Genomics 2007 8:278 doi:10.1186/1471-2164-8-278