Figure 1. Components of a genome project. On the left, a schematic representation of a molecular marker map (A) for a chromosome is shown. Molecular markers are depicted as horizontal lines. Yeast artificial chromosome (YAC) clones, shown as long vertical black lines, are anchored by molecular markers on to the genetic map. The marker content of all clones in a particular region of the chromosome is assessed to build large contigs (B). High-density bacterial artificial chromosome (BAC) contigs (C), displayed as short vertical black lines, are established by fingerprinting techniques. Molecular markers anchor the contigs on the genetic map. For a completely sequenced BAC (D), predicted genes are shown as open boxes in the right part of the figure for the Watson and Crick strands. A gene corresponding to one of the genes of the sequenced BAC has been used to anchor YAC clones and for genetic mapping experiments, thus it provides a direct link between the genetic map, the physical map and the genomic sequence indicated by the dashed line.

Figure 2. Insertion mutagenesis. (a) Gene inactivation upon insertion of a mobile element. The gene is displayed as an open box with a black rectangle corresponding to the mobile element. Upon insertion of the element, transcription of the gene indicated by an arrow can no longer proceed. If the nature of the element is known, the inactivated gene can be isolated. (b) The rationale of a reverse genetic approach. Only if a known element is inserted in the gene of interest, shown as an open box, can a DNA fragment be generated if primers specific for the gene of interest and the transposon, indicated by a black rectangle, are used for amplification of DNA sequences by polymerase chain reaction (PCR). Arrows correspond to primer sequences. The resulting PCR product is shown as a hatched bar.

Figure 3. Patterns of genome colinearity. (a) Comparative genetic mapping. Using the same set of molecular markers for genetic mapping experiments in different species (A and B) allows the alignment of chromosome maps. Molecular markers are depicted as horizontal bars and markers, which have been mapped in both species to the chromosomes shown, are connected by lines. The chromosome of species A shares colinear segments with two chromosomes of species B, indicating translocation events. An example for an inversion event of a chromosomal segment is highlighted as a box. (b) Micro-colinearity. A comparison of homologous genomic regions derived from two different species (A and B) at the sequence level is shown. Gene sequences, black and white boxes, are highly conserved as indicated by grey bars. In contrast, intergenic sequences do not show significant sequence similarity. The gene marked by an asterisk is duplicated in species A, whereas the gene indicated by an arrow is not found in species A. (c) Differential gene loss in duplicated regions. A past duplication event generated duplicated segments in species A that diverged by differential gene loss (A1, A2). The duplicated segments differ in gene content when compared to each other and to the corresponding segment in species B that was not subjected to duplication. Arrows mark those genes that are only found in one of the copies of the duplicated segments in species A.