Direct Implications in Gene Loss Gain for Attaining New Functions

The recurring whole genome duplications in angiosperms over the last 200 million years followed by gene loss and mobile element activities yielded many novel plant taxa (Bowers et al. 2003b; Tang et al. 2008a). However, the number and size of gene families are similar in the well studied genomes such as sorghum, Arabidopsis, rice and poplar (Paterson et al. 2009). Around 58% of gene families were shared among all four species; 24% were monocot specific and 7% were unique to sorghum, a fraction which is similar to Arabidopsis (6.7%, The Arabidopsis Genome Initiative 2000). However, fewer gene families are specific to rice (3.7%, Matsumoto et al. 2005) while many are unique to poplar (15.7%, Tuskan et al. 2006). A high number of genes being orthologous between the rice and sorghum suggests that most gene loss occurred in a common rice ancestor (Paterson et al. 2009). Lineage specific genes may have been derived from non-functional DNA sequences (Itoh et al. 2007); genes with high divergence rates and independent gene deletions among plant taxa are the major evolutionary forces for making genes unique to a particular species (Salzberg et al. 2001; Stanhope et al. 2001). In addition to the genomic changes, the impact of natural selection on favoring certain genes significantly contributed in shaping the genomes of plant species including papaya (Itoh et al. 2007; Ming et al. 2008).

Every plant species evolved new functions to sustain their survival, for example, papaya and poplar have more genes than Arabidopsis which are involved in cell expansion, larger plant size and lignin biosynthesis for evolving treelike habits. An abundance of genes associated with volatile features in papaya is the outcome of strong natural selection for enhanced attractants which may facilitate fruit dispersal by animals (Ming et al. 2008). Similarly, cytochrome P450 domain-containing genes that scavenge toxic compounds accumulated in response to stresses, are more abundant in sorghum (326, Paterson et al. 2009) than rice (228). There are many other gene families including expansin domain, kafirin (Song et al. 2004), NBS-LRR, and carbonic anhydrase (cah) gene families that fluctuate in their numbers among different crop species (Paterson et al. 2009).

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