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

We performed an RNA sequencing-based inference of the grain filling gene network in bread wheat and identified a 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 to 70 million years) exhibit more than 80% gene loss and expression divergence while recent duplicates (dating back 1.5 to 3 million years) show only 54% gene loss and 36 to 49% expression divergence.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 structurally and functionally altered within 10 million years of evolution, and the diploidization process is completed after 45 to 50 million years following polyploidization.More than 40 years ago, based on a few protein sequences from vertebrates, Susumu Ohno proposed polyploidization as a major source of new biological pathways created from duplicated gene copies [1]. The vertebrate genomes can be considered as paleopolyploids that had become modern diploids by means of ancestral chromosome fusions as well as sequence divergence between duplicated chromosomes. Recent paleogenomic analyses in plants have confirmed and refined Ohno's conclusions and led to the identification of polyploid common ancestors, showing that present-day species have been shaped through several rounds of whole genome duplications (WGDs), small scale duplications (SSDs) as well as copy number variations (CNVs) of tandem duplicat