The evolution of plants from a common ancestor left collinearities and syntenies in genome structure and function, the fundamental framework to transfer genetic information from model species to less studied relatives. In flowering plants, an important role of model plant species is to serve as a source for transferring genetic knowledge to crop plants via genome sequences and genetic linkage maps (Sato et al. 2007). Among the plant taxa, Brassicaceae, Solanaceae, and Poaceae include botanical models which can be distinguished on the basis of nature and number of rearrangements from their less studied relatives (Bonierbale et al. 1988; Ahn and Tanksley 1993; Prince et al. 1993; Periera et al. 1994; Gale and Devos 1998; Doganlar et al. 2002a), which may lead to reproductive isolation and ultimately speciation (Rieseberg 2001).
The Brassicaceae (or Cruciferae) is a dicot family comprises of 360 genera (Al-Shehbaz 1973) including the agronomically important genus Brassica and the model species A. thaliana. The complete genome sequence information of A. thaliana, detailed information of its physical map position, copy number of genes and intergenic sequences, location of duplicated chromosomal segments (The Arabidopsis Genome Initiative 2000; Blanc et al. 2000; Vision et al. 2000; Bowers et al. 2003b; Ermolaeva et al. 2003; Raes et al. 2003), and its small genome size provides a foundation for comparative mapping studies (Yogeeswaran et al. 2005). Arabidopsis thaliana, the crown botanical model, has now been suggested to actually be a relatively poor model because of its genomic complexity. For example, Arabidopsis which is taxo-nomically closest to papaya among the sequenced genome exhibited two genome duplications since its divergence from Carica (Ming et al. 2008).
Rice is one of the most important plant species of the family Poaceae, and is a genetic model not only for the other members of this family but also for the mono-cotyledonous plants. The map-based sequence of the rice genome (O. sativa ssp. japonica var. Nipponbare) and a draft sequence of the indica subspecies (var. 93-11) (Yu et al. 2002, 2005) have been used in annotating genes and gene prediction and deducing evolutionary consequences in other cereals and grass species (Yuan et al. 2005; Tang et al. 2008a).
In the Solanaceae family, tomato (Solanum lycopersicum) has been investigated both by classical and molecular genetic procedures (Tanksley et al. 1992; Livingstone et al. 1999), facilitated by its diploid (2n = 2x) genome of 12 chromosomes containing long stretches of euchromatin at the distal ends and heterochromatic regions flanking the centromeres (De Jong 1998; Kulikova et al. 2001; Fransz et al. 2003). Tomato served as a model system for studying fruit development and ripening because of its rich genetic resources including both germplasm and mutants; a dense molecular map;
comprehensive EST dataset (http://www.sgn.cornell.edu/); and cDNA microarray (Giovannoni 2004); facilitating comparative genomic studies within and across taxa.
Among the 50 species in the genus Gossypium, the G. raimondii 'D' genome has been prioritized for genome sequencing because of its relatively small genome size and minimal repetitive DNA. The generated information will help in filling the major void in international Gossypium genomics resources, paving the way for dissecting the genetic control of specific Gossypium traits. The first Gossypium genome will also foster tests of hypotheses about features of Gossypium genome organization and/or evolutionary history that may be related to adaptive features that permit different Gossypium taxa to flourish in a wide range of environments, and also to be adapted to agriculture (Chen et al. 2007).
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