Buffering of crucial functions by paleologous duplicated genes may contribute cyclicality to angiosperm genome duplication

Chapman et al. 10.1073/pnas.0507782103.

Supporting Information

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Supporting Table 2
Supporting Results

Table 2. Mean KS and KA values for singleton and duplicate genes

Duplicate genes substitution values are calculated based on the best alignment between the duplicate pairs. Singleton values are calculated based on alignments against best-detectable homologs of pre- and postduplication species. Rates of synonymous and nonsynonymous substitution for duplicates and singletons aligned to homologs were calculated by using maximum likelihood as implemented in PAML.

Supporting Results

     To quantify the expected divergence of duplicates and singletons compared with pre- and postduplication species, we estimated the probability of a mutation in any codon based on median synonymous and nonsynonymous substitution rates between pairs of duplicated genes and between singletons and their pre- and postduplication homologs (Table 2).

     To use duplicate and singleton gene substitution values to estimate the probability of nonidentity in a codon, the ages of divergence of outgroups surrounding a duplication were considered. Ages were chosen allowing for the largest estimated time period between divergence of the two organisms flanking a duplication event: Arabidopsis and Brassica, 14.5 million years ago (MYA) (1); Arabidopsis and Malvaceae, 86 MYA (1); rice and sorghum, 41 MYA; and rice and banana, 142 MYA (2). With these substitution values and ranges for the age of duplication events, the following approximation was used to calculate the probability of change in a codon:

 

Number of codon positions (3) ´ [(KS + KA)/10⁹years] ´ divergence time.

 

For the Arabidopsis a duplicates, each codon had an average probability of between 0.045 and 0.264 of being mutated over the 14.5-86 MYA age range of the dated duplication. These results fall between the preduplication singleton probability of 0.553 and postduplication probability of 0.024. Thus, even for the most conservative estimate of the age of the a duplication (14.5 MYA; the 0.045 result), the probability of sustaining a mutation in a codon are twice as large in the duplicated genes as in the postduplication singletons. Similarly, the rice duplicates had a codon mutation probability of 0.170 to 0.588, which falls between the preduplication (0.873) and postduplication (0.101) probabilities. Based on these calculations, we would expect stretches of identical codons in duplicates to fall between pre- and postduplication homologs. Deviation from these expectations would indicate different patterns of change then could be predicted from synonymous and nonsynonymous rates alone.

1. Bowers, J. E., Chapman, B. A., Rong, J. K. & Paterson, A. H. (2003) Nature 422, 433–438.

2. Paterson, A. H., Bowers, J. E. & Chapman, B. A. (2004) Proc. Natl. Acad. Sci. USA 101, 9903–9908.

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