The family Brassicaceae, also called the "mustard family" contains the most important model species A thaliana and also many important agricultural species including three diploids (B. rapa, B. nigra, and B. oleracea) and three tetraploids (B. juncea,

B. napus and B. carinata) (Schranz et al. 2006). Comparative mapping in Brassicaceae has been active since the development of genetic linkage maps using DNA markers in the early 1990s (Karp 1998) for major crop species of the genus Brassica (Slocum et al. 1990; Landry et al. 1991; Song et al. 1991; Chyi et al. 1992; Kianian and Quiros 1992; Figdore et al. 1993; Ferreira et al. 1994; Kowalski et al. 1994; Teutenico and Osborn 1994; Uzunova et al. 1995; Lagercrantz and Lydiate 1996; Truco et al. 1996; Lan et al. 2000). These maps showed substantial collinear-ity interrupted by small inversions (Kianian and Quiros 1992; Lan et al. 2000). Extensive genome changes in synthetic polyploids fueled the debate on rapid genome changes following polyploidization (Song et al. 1995) which set the stage to explore this mechanism (Osborn 2004; Soltis et al. 2004).

The role of A. thaliana (n = 5) in building a Brassicaceae genomics circle is marginal because of its derived nature. A total of 38% of the species contain chromosome number n = 8 (Warwick and Al-Shehbaz 2006) and several chromosomal rearrangements are unique to A. thaliana (Lysak et al. 2007). The two species

C. rubella and A. lyrata (Kuittinen et al. 2004; Yogeeswaran et al. 2005) containing n = 8 may be better reference points in comparative genomic studies based on sharing genomic collinearity, the conservativeness of genomic blocks (Boivin et al. 2004; Kuittinen et al. 2004; Yogeeswaran et al. 2005) and similar genome structure (Koch and Kiefer 2005) with A. thaliana. Through comparative chromosome painting, the pattern of chromosome specific BAC contig probes derived from A. thaliana suggested a common mechanism (pericentric inversion followed by reciprocal translocation/fusion event) of chromosome number reduction in all the species of Brassicaceae (Boivin et al. 2004; Kuittinen et al. 2004; Yogeeswaran et al. 2005) and position of centromeres in the ancestral karyotype (Lysak et al. 2006), confirmed by genetic mapping in A. lyrata (Hansson et al. 2006; Kawabe et al. 2006).

Despite the aforementioned difficulties in comparing the genome of Arabidopsis with Brassica species (Koch et al. 2007), 21 conserved syntenic blocks making 90% of the genome of B. napus (n = 19) were found collinear, having been maintained since the divergence of the Arabidopsis and Brassica lineages around 20 mya (Kowalski et al. 1994; Yang et al. 1999; Koch et al. 2003; Lysak et al. 2005). In another study, sequences of a set of five genes (located on a 15 kbp segment of A. thaliana chromosome 3) in B. rapa, B. oleracea and B. nigra were physically closely linked (Sadowski et al. 1996). A 30 kbp segment of A. thaliana chromosome 4 harboring six genes were found in comparable organization in the corresponding regions in B. nigra, however, this region of the genome was considerably larger in B. nigra than in A. thaliana (Sadowski and Quiros 1998). The S locus region from B. campestris and A. thaliana revealed extensive collinearity in the homeologous region (Conner et al. 1998).

Later, an ancestral karyotype containing 24 conserved blocks (n = 8) was drawn based on comparative maps between Arabidopsis and two Camelineae species n = 8 (Arabidopsis lyrata and Capsella rubella, Lysak et al. 2006) which was aligned with the 21 conserved blocks in Brassica to infer the ancestral karyotype (Schranz et al. 2006). These regions share a common mechanism of genome evolution. Moreover, macrosynteny between Boechera stricta (n = 7) and Brassicaceae species helps in clarifying the chromosome number reduction in the genus Boechera (Schranz et al. 2007).

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