Variations in gene sequences among different plant taxa have been instrumental in constructing the phylogenetic tree of the plant kingdom and also estimating the molecular clock of plant phylogeny (Miller et al. 2004; Caicedo and
Purugganan 2005). Different nuclear introns, exons, ribosomal genes, and plastid gene sequences have increasingly been surveyed for estimating genetic diversity and phylogenies of plant species for which genome sequence information is not available (Cronn et al. 2002; Shaheen et al. 2006; Ahmad et al. 2007). DNA markers including SSRs, RAPD, AFLP and SNPs have also been used for estimating genetic diversity, and understanding the phylogenetic relationship among major plant taxa (Abdalla et al. 2001; Mukhtar et al. 2002; Rahman et al. 2002, 2008).
In distantly related species, if whole genome sequence information is not available, nuclear genes, preferably single copy genes (Qiu et al. 1999; Fulton et al. 2002), and mitochondrial and plastid gene sequences (Qiu et al. 1999; Palmer et al. 2004) were used to construct the tree of life. For example, in Brassicaceae, 338 genera comprising of 3,700 species were classified into 25 tribes (Beilstein et al. 2006) using nuclear (Bailey et al. 2006) and chloroplast based markers (Beilstein et al. 2006).
Sequences of the Arabidopsis, rice, sorghum, papaya, grape and poplar genomes provide reference points to initiate and/or deepen insight into the complex genomes for drawing a comprehensive phylogenetic relationship of flowering plants. In the future, proliferation of genomic data will help in constructing the comprehensive and well adapted phylogenetic tree and also further exploring molecular clocks (Miller et al. 2004).
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