Nuances in Plant Genome Annotation: Those Duplicated and Dead Genes

Repeated rounds of whole genome duplication lead to a higher proportion of genes with apparent paralogs in plants compared to other eukaryotes. Nonetheless, even with this elevated overall duplication rate, the predominant fate of duplicates is pseudogenization, a process that renders a gene non-functional due to accumulating mutations. The abundance of duplicate genes and pseudogenization of duplicates creates two issues in plant gene annotation. The first is that, although many duplicates appear intact, they are likely in various stages of functional decay at the biochemical level. The second issue is that the boundary between a functional gene and a pseudogene is a murky one because putative pseudogenes with apparent stops and frameshifts can still have biochemical activities. Thus, it is not entirely clear if some purported pseudogenes remain functional. In this workshop session, I will present evidence for… and discuss the challenges associated with resolving these two issues.