title: The evolution and function of protein tandem repeats in plants.
abstract: Sequence tandem repeats (TRs) are abundant in proteomes across all domains of life. For plants, little is known about their distribution or contribution to protein function. We exhaustively annotated TRs and studied the evolution of TR unit variations for all Ensembl plants. Using phylogenetic patterns of TR units, we detected conserved TRs with unit number and order preserved during evolution, and those TRs that have diverged via recent TR unit gains/losses. We correlated the mode of evolution of TRs to protein function. TR number was strongly correlated with proteome size, with about one-half of all TRs recognized as common protein domains. The majority of TRs have been highly conserved over long evolutionary distances, some since the separation of red algae and green plants c. 1.6 billion yr ago. Conversely, recurrent recent TR unit mutations were rare. Our results suggest that the first TRs by far predate the first plants, and that TR appearance is an ongoing process with similar rates across the plant kingdom. Interestingly, the few detected highly mutable TRs might provide a source of variation for rapid adaptation. In particular, such TRs are enriched in leucine-rich repeats (LRRs) commonly found in R genes, where TR unit gain/loss may facilitate resistance to emerging pathogens.
authors.affiliation: Department of Computer Science, ETH Zürich, Zürich, 8092, Switzerland.|Institute of Integrative Biology, ETH Zürich, Zürich, 8092, Switzerland.|Vital-IT Competency Center, Swiss Institute for Bioinformatics (SIB), Lausanne, 1015, Switzerland.
authors.forename: Elke
authors.initials: E
authors.lastname: Schaper
authors.affiliation: Institute of Applied Simulation (IAS), School of Life Sciences and Facility Management, Zürich University of Applied Sciences (ZHAW), Wädenswil, 8820, Switzerland.
authors.forename: Maria
authors.initials: M
authors.lastname: Anisimova
mesh_terms: D019143:Evolution, Molecular; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics*; D010944:Plants / Q000235:genetics* / Q000378:metabolism; D020543:Proteome; D020080:Tandem Repeat Sequences / Q000235:genetics*
chemical_list: D010940:Plant Proteins; D020543:Proteome
keywords: R genes; conservation; leucine-rich repeat (LRR); minisatellites; phylogenetic analysis; plant genomics; protein evolution; tandem repeats (TRs)