ArticleGenome biology2011
RNA-seq in grain unveils fate of neo- and paleopolyploidization events in bread wheat (Triticum aestivum L.).
Article in Genome biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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36 citing papers in PubMed, 74 citations in OpenAlex.
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- The defence-associated transcriptome of hexaploid wheat displays homoeolog expression and induction bias.Plant biotechnology journal · 2017Article
- Combined Genomic and Genetic Data Integration of Major Agronomical Traits in Bread Wheat (Frontiers in plant science · 2017Article
- Mapping and Identifying a Candidate Gene (Frontiers in plant science · 2017Article
- Transcriptomic Profiles Reveal the Interactions of Cd/Zn in Dwarf Polish Wheat (Frontiers in physiology · 2017Article
- Creating Order from Chaos: Epigenome Dynamics in Plants with Complex Genomes.The Plant cell · 2016Review
- De Novo Assembled Wheat Transcriptomes Delineate Differentially Expressed Host Genes in Response to Leaf Rust Infection.PloS one · 2016Article
- Transcriptome Analysis Provides Insights into the Mechanisms Underlying Wheat Plant Resistance to Stripe Rust at the Adult Plant Stage.PloS one · 2016Article
- RNA-Seq and iTRAQ Reveal the Dwarfing Mechanism of Dwarf Polish Wheat (Triticum polonicum L.).International journal of biological sciences · 2016Article
- Single-molecule real-time transcript sequencing facilitates common wheat genome annotation and grain transcriptome research.BMC genomics · 2015Article
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Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundWhole 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.
resultsWe 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.
conclusionsWe 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.
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