Dna level characteristics and phenotypic features revealed by knockout, overexpression and addition mutants for duplication-resistant genes
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Gene duplication provides raw material for evolution in the genomes of higher eukaryotes. The propensity for genes to return to single copy dosage after duplication varies, and is partly reflected by their copy numbers in other species. Arabidopsis single copy genes can be divided into subsets with different characteristics, including different likelihoods of showing knockout (KO) phenotypes. We are particularly interested in the subset that was consistently restored to single copy dosage after independent whole-genome duplications in multiple lineages, known as duplication-resistant (DR) genes. The recurring removal of duplicated gene copies is associated with gene function, as implied by GO terms enriched in DR genes, making functional study of DR genes an approach to decipher the basis of duplication resistance. In this study, we assessed Arabidopsis DR gene functions via their KO phenotypes. Compared to non-DR singletons, T-DNA insertion mutants of DR genes were not prone to exhibit phenotypes under stress conditions, showing a low occurrence of ABA and cold sensitive phenotypes and an overrepresentation of salt-related phenotypes. On the other hand, severe phenotypes, including visible seedling alternations and phenotypes indicative of homozygous lethality, occurred more frequently in DR genes than other singletons. In addition, Arabidopsis genotypes with artificial duplication (Addition, AD) (OE, by coupling to 35S promoters) of DR genes were made, to examine the consequences of having multiple copies of these genes. Visible duplication effects, as reflected by AD phenotypes, were more likely to occur in DR genes than in other singletons. Seedling phenotypes, absent in AD lines, were found in OE lines at a higher percentage than KO mutants. As for other genes, duplication and overexpression of DR genes can also result in stress tolerance. Genes with both OE and KO phenotypes constitute approximately one third of DR genes with OE lines, indicating that dosage sensitivity may be responsible for duplication resistance of some DR genes.