A Spirodela BAC library was constructed from high-molecular weight nuclear DNA35 (link). The DNA was partially digested with HindIII, double size-selected and ligated into pIndigoBAC-5 (HindIII-cloning Ready, Epicentre, BACH095H, Madison, WI, USA). A total of 15,360 Spirodela BAC clones with an average insert size of 110 kb representing 10 × genome equivalents were fingerprinted with the SNaPshot HICF fingerprinting method using the LIZ1200 size standard as described somewhere else39 (link). Of the 15,360 fingerprinted clones, 11,770 clones (76.6%) were suitable for contig assembly. There was on average one restriction fragment every 1.19 kb. The final FPC map spanned 200 Mb and contained 269 singletons and 11,501 BAC clones, which were integrated into 320 contigs. In the physical map, 23 contigs had more than 100 clones each, 62 contigs had 50–99 clones each, 160 contigs had 10–49 clones and the residual 75 had <10 clones. Based on the physical map integration, the Newbler scaffolds were ordered by the FPC draft sequence function and pseudomolecules were constructed from joined scaffolds. Scaffolds within one pseudomolecule were interlaced by a stretch of 500 undefined bases (‘N’s).