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Background  The proteasome subunit RPT5, which is essential for gametophyte development, is encoded by two genes in  Arabidopsis thaliana ;  RPT5a  and  RPT5b . We showed previously that  RPT5a  and  RPT5b  are fully redundant in the Columbia (Col-0) accession, whereas in the Wassilewskia accession (Ws-4),  RPT5b  does not complement the effect of a strong  rpt5a  mutation in the male gametophyte, and only partially complements  rpt5a  mutation in the sporophyte.  RPT5b Col-0   and  RPT5b Ws-4   differ by only two SNPs, one located in the promoter and the other in the seventh intron of the gene.    Results  By exploiting natural variation at  RPT5b  we determined that the SNP located in  RPT5b  intron seven, rather than the promoter SNP, is the sole basis of this lack of redundancy. In Ws-4 this SNP is predicted to create a new splicing branchpoint sequence that induces a partial mis-splicing of the pre-mRNA, leading to the introduction of a Premature Termination Codon. We characterized 5 accessions carrying this A-to-T substitution in intron seven and observed a complete correlation between this SNP and both a 10 to 20% level of the  RPT5b  pre-mRNA mis-splicing and the lack of ability to complement an  rpt5a  mutant phenotype.    Conclusion  The accession-dependent unequal redundancy between  RPT5a  and  RPT5b  genes illustrates an example of evolutionary drifting between duplicated genes through alternative splicing.

A SNP associated with alternative splicing of RPT5b causes unequal redundancy between RPT5a and RPT5b among Arabidopsis thaliananatural variation