Synteny and Collinearity

The terms synteny and collinearity have been extensively used to denote the presence of two or more genes on corresponding chromosomes and in corresponding order, respectively. The extent of synteny and co-linearity vary among the flowering plant genomes largely due to recurring whole genome duplications followed by massive gene loss, with chromosomal rearrangements superimposed on postduplication gene loss in breaking the ancestral gene ropes (Bowers et al. 2003b). Conventionally, synteny and co-linearity have been estimated by matching one-to-one (pair wise) conservation between the species. Recently, multiple way co-linearity analyses offer improved resolution for inferring ancestral gene order in angio-sperms. For example, in Oryza-Arabidopsis comparison, the longest collinear segment contains 23 orthologous gene pairs. This is improved twofold to 47 genes by incorporating Vitis genome sequence into the comparison (Tang et al. 2008a).

After polyploidization in angiosperms, differential gene loss or retention is a very important factor affecting synteny between corresponding regions on different chromosomes (Paterson et al. 2006). All these properties coupled with variability in DNA substitution rates among plants, make rational of using shared co-linearity as a reliable phylogenetic character. Moreover, accurate synteny/collinearity among different genomes or subgenomes may help in elucidating the ancestral angiosperm genome which will then provide a universal reference point in understanding the nature and genes conferring phenotypic diversity across the angiosperms.

Instances of synteny and or collinearity have been detected in plant taxa that diverged from a common ancestor long ago. For example, cotton and Arabidopsis, diverged from a common ancestor about 83-86 mya (Benton 1993) revealed appreciable conserved gene order (Rong et al. 2005). Our ability to discern conserved gene order is not uniform across a genome - for example, pericentromeric regions that are gene-poor and in which repeat-associated rearrangements may persist a long time, are notoriously difficult in which to discern conserved synteny. Moreover, other genomic regions that went through structural changes may tolerate these changes with different frequencies, provoking tantalizing hypotheses for future study about whether these rapidly-evolving regions have a disproportionate impact on phenotypic divergence or even reproductive isolation between plant taxa.

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