RNA-seq in grain unveils fate of neo- and paleopolyploidization events in bread wheat (Triticum aestivum L.).

摘要

Background: Whole genome duplication is a common evolutionary event in plants. Bread wheat (Triticum aestivum L.) is a good model to investigate the impact of paleo- and neoduplications on the organization and function of modern plant genomes. Results: We performed an RNA sequencing-based inference of the grain filling gene network in bread wheat and identified a unigene set of 37,695 non-redundant sequence clusters, which is an unprecedented resolution corresponding to an estimated half of the wheat genome unigene repertoire. Using the Brachypodium distachyon genome as a reference for the Triticeae, we classified gene clusters into orthologous, paralogous, and homoeologous relationships. Based on this wheat gene evolutionary classification, older duplicated copies (dating back 50-70 million years) exhibit more than 80% gene loss and expression divergence while recent duplicates (dating back 1.5-3 million years) show only 54% gene loss and 36-49% expression divergence. Conclusions: We suggest that structural shuffling due to duplicated gene loss is a rapid process, whereas functional shuffling due to neo- and/or subfunctionalization of duplicates is a longer process, and that both shuffling mechanisms drive functional redundancy erosion. We conclude that, as a result of these mechanisms, half the gene duplicates in plants are functionally eroded within 10 million years of evolution, and the diploidization process is completed within 45-50 million years following polyploidization.