Fig. 2. Schematic of genome mapping, genetic and physical, and integration of whole-genome shotgun sequences (WGSS). A typical chromosome (ideogram) is shown at left of figure, immediately to the right is a linkage map with units of centimorgans. Genetic markers on the linkage map with sequence information can be used to anchor bacterial artificial chromosomes (BACs) or BAC contigs to the genetic map (integrated map). Individual BACs (third layer from right) are assembled into contigs based on fingerprint information (FPC map). Traditionally, overlapping BACs are used to make a BAC tiling path for sequencing (i.e., yellow BAC clones). End sequences from BACs (BES, orange balls on end of BACs) are used to provide large spanning clones for assembling WGSS and, in the interim, to provide genetic markers to further anchor BAC contigs. A WGSS is made in the form of end-sequenced randomly sheared clones of various sizes (colored bars at right of figure). Paired sequences are computationally assembled into contigs (completely overlapping sequence information) and then scaffolds (ordered contigs where clones span sequence gaps). The BES and sequence-based markers are used to anchor sequence contigs and scaffolds to the BAC-based physical and genetic maps.