The Malvaceae comprises three main species-rich lineages including Gossypieae (n = 10 to 13, Fryxell 1968), Malveae (n = 5 to 21, Bates 1968; Bates and Blanchard 1970) and a group of taxa belonging to the large genus Hibiscus (n = 12 to around 144, while n = 14 or 18 is the most prevalent, Fryxell 1968, 1988; Pfeil et al. 2002, 2004). In comparative genomic investigations, the genus Gossypium belonging to the tribe Gossypieae, received much attention because of its paleopolyploid nature (Rong et al. 2005), and is the leading natural fiber producer. The genus Gossypium includes five allopolyploid and 45 diploid species (Fryxell 1979, 1992) containing eight genomes designated A through G and K (Beasley 1940; Phillips and Strickland 1966; Edwards and Mirza 1979; Endrizzi et al. 1985).

The allotetraploid cotton species originated through uniting the A and D genomes about 1-2 mya (Wendel 1989; Wendel and Albert 1992). Comparative maps developed through surveying RFLP markers on four cotton genomes (A, D, Dt and At) showed conservation of gene order and synteny (Reinisch et al. 1994; Brubaker et al. 1999). Later, detailed STS-based genetic maps reiterated the col-linearity between the A and D genomes (Rong et al. 2004). The A diploid genome can be differentiated from the At genome (representing the diploid A genomes in the tetraploid cotton species) by two reciprocal translocations occurred only in At genome following allotetraploid formation; and one inversion (Brubaker et al. 1999; Rong et al. 2004), complementing earlier findings based on conventional cytogenetic approaches (Brown 1980; Menzel et al. 1982). Similarly, five inversions identified while comparing the maps of the four genomes, can differentiate the D and Dt genomes.

Ancient genome duplication is a very common phenomenon in the evolution of many plants. The Arabidopsis and cotton lineages each have incurred ancient duplication after their divergence, although retaining discernible correspondence in genetic loci (Rong et al. 2005). The second tribe of the family Malvaceae is "Malveae," comprised of the members of the genus Hibiscus (Pfeil et al. 2002) exhibiting a wide range in basic chromosome number (Fryxell 1968, 1988) with a basic haploid set ranging from n = 5 to 21 (Bates 1968; Bates and Blanchard 1970). Like other crop plants, the status of Hibiscus polyploids was studied by exploring a single copy gene rpb2 (Oxelman et al. 2004) which was duplicated before the divergence of the Hibiscus genus (at the subfamily level). Moreover, after duplication, both copies of the gene retain their function and structure in this lineage, a compelling factor motivating selection of this gene in probing relatively old duplication events and in phylogenetic analysis (Pfeil et al. 2004).

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