Recent degeneration of an old duplicated flowering time gene in Brassica nigra

Abstract

Gene and genome duplications play a major role in the evolution of plant species. The Brassica nigra genome is highly replicated as a result of ancient polyploidization events. Two copies of the flowering time gene CONSTANS (COa and COb) have been identified in B. nigra, and previous studies showed that COa is functional. In the present study, the polymorphism of 92 COb alleles sampled in seven populations was analyzed. Both polymorphism and recombination levels were elevated and varied strongly among populations and 8% of COb alleles exhibit apparently disabling mutations. Sequence data, however, do not provide unambiguous support for the presence of relaxed selective constraint on COb as compared to known functional CO genes. On the one hand, some of the disabling mutations reached high-frequency arguing for a loss of function but, on the other hand, the ratio of nonsynonymous to synonymous nucleotide polymorphism and diversity is low and similar to that observed in other B. nigra CO and CO-like genes, supporting the conservation of some function. We also showed that COb is still transcribed. Finally, the flowering time of Arabidopsis thaliana co mutant plants transformed with COb alleles with and without apparent disabling mutations was similar. We propose that COb was retained for a long period after duplication, but a recent fixation of a detrimental mutation, possibly as an effect of a bottleneck, resulted in its nonfunctionalization. We also speculate as to the presence of subsequent selection for rapid degeneration of the gene.

Birth-and-Death Evolution of the Fatty Acyl-CoA Reductase (FAR) Gene Family and Diversification of Cuticular Hydrocarbon Synthesis in Drosophila

“…1972). In contrast, the birth-and-death model proposes that the members of a gene family evolve independently, meaning that while some members of a gene family are phylogenetically stable, others are unstable and are gained or lost over time by DNA duplications, deletions, and other pseudogenization events (Hughes and Nei 1989; Lynch and Conery 2000; Sjodin et al. 2007; Plata and Vitkup 2014).…”

Birth-and-death evolution of the fatty acyl-CoA reductase (FAR) gene family and diversification of cuticular hydrocarbon synthesis in Drosophila

“…This model is capable of explaining aspects of the evolution of clustered ribosomal RNAs (Brown, et al 1972). In contrast, the birth-and-death model proposes that the members of a gene family evolve independently, meaning that while some members of a gene family are phylogenetically stable, others are unstable and are gained or lost over time by DNA duplications, deletions, and other pseudogenization events (Hughes and Nei 1989;Lynch and Conery 2000;Sjodin, et al 2007;Plata and Vitkup 2014). Gene repertoire expansion and contraction has been found in diverse gene families such as innate immune genes (Zhang, et al 2015;Sackton, et al 2017), plant secondary metabolic genes (Lespinet, et al 2002;Jiang, et al 2015;Wang, et al 2018), developmental transcription factors (Amores, et al 2004;Tanabe, et al 2005;Finet, et al 2012), and snake toxin genes (Dowell, et al 2016).…”