A dead gene walking: convergent degeneration of a clade of MADS-box genes in Brassicaceae

ABSTRACT Genes are ‘born’, and eventually they ‘die’. In contrast to gene birth, however, gene death has found only limited scientific interest, even though it is of considerable evolutionary importance. Here we use B sister genes, a subfamily of MIKC-type MADS-box genes, as a model to investigate gene death in unprecedented detail. Typical MIKC-type genes encode conserved transcription factors controlling plant development. We show that ABS -like genes, a clade of B sister genes, are indeed highly conserved in Brassicaceae maintaining the ancestral function of B sister genes in ovule and seed development. In contrast, their closest paralogs, the GOA -like genes, have been undergoing convergent gene death in Brassicaceae. Intriguingly, erosion of GOA -like genes occurred after millions of years of co-existence with ABS -like genes. We thus describe Delayed Convergent Asymmetric Degeneration (DCAD), a so far neglected but possibly frequent pattern of duplicate gene evolution that does not fit classical scenarios. DCAD of GOA -like genes may have been initiated by a reduction in the expression of an ancestral GOA -like gene in the stem group of Brassicaceae and driven by dosage subfunctionalization. Our findings have profound implications for gene annotations in genomics, interpreting patterns of gene evolution and using genes in phylogeny reconstructions of species.