title: Evolutionary Dynamics of the Leucine-Rich Repeat Receptor-Like Kinase (LRR-RLK) Subfamily in Angiosperms.
abstract: Gene duplications are an important factor in plant evolution, and lineage-specific expanded (LSE) genes are of particular interest. Receptor-like kinases expanded massively in land plants, and leucine-rich repeat receptor-like kinases (LRR-RLK) constitute the largest receptor-like kinases family. Based on the phylogeny of 7,554 LRR-RLK genes from 31 fully sequenced flowering plant genomes, the complex evolutionary dynamics of this family was characterized in depth. We studied the involvement of selection during the expansion of this family among angiosperms. LRR-RLK subgroups harbor extremely contrasting rates of duplication, retention, or loss, and LSE copies are predominantly found in subgroups involved in environmental interactions. Expansion rates also differ significantly depending on the time when rounds of expansion or loss occurred on the angiosperm phylogenetic tree. Finally, using a dN/dS-based test in a phylogenetic framework, we searched for selection footprints on LSE and single-copy LRR-RLK genes. Selective constraint appeared to be globally relaxed at LSE genes, and codons under positive selection were detected in 50% of them. Moreover, the leucine-rich repeat domains, and specifically four amino acids in them, were found to be the main targets of positive selection. Here, we provide an extensive overview of the expansion and evolution of this very large gene family.
authors.affiliation: Institut National de la Recherche Agronomique, Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales, F-34060 Montpellier, France (I.F., N.C.); andCentre de Coopération Internationale en Recherche Agronomique Pour le Développement, Unité Mixte de Recherche AGAP, F-34398 Montpellier, France (A.D., G.D., J.-F.D.) irisfischer402@gmail.com chantret@supagro.inra.fr.
authors.forename: Iris
authors.identifier: http://orcid.org/0000-0002-5080-1223
authors.initials: I
authors.lastname: Fischer
authors.affiliation: Institut National de la Recherche Agronomique, Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales, F-34060 Montpellier, France (I.F., N.C.); andCentre de Coopération Internationale en Recherche Agronomique Pour le Développement, Unité Mixte de Recherche AGAP, F-34398 Montpellier, France (A.D., G.D., J.-F.D.).
authors.forename: Anne
authors.identifier: http://orcid.org/0000-0001-9460-4638
authors.initials: A
authors.lastname: Diévart
authors.affiliation: Institut National de la Recherche Agronomique, Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales, F-34060 Montpellier, France (I.F., N.C.); andCentre de Coopération Internationale en Recherche Agronomique Pour le Développement, Unité Mixte de Recherche AGAP, F-34398 Montpellier, France (A.D., G.D., J.-F.D.).
authors.forename: Gaetan
authors.identifier: http://orcid.org/0000-0003-1849-1269
authors.initials: G
authors.lastname: Droc
authors.affiliation: Institut National de la Recherche Agronomique, Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales, F-34060 Montpellier, France (I.F., N.C.); andCentre de Coopération Internationale en Recherche Agronomique Pour le Développement, Unité Mixte de Recherche AGAP, F-34398 Montpellier, France (A.D., G.D., J.-F.D.).
authors.forename: Jean-François
authors.initials: JF
authors.lastname: Dufayard
authors.affiliation: Institut National de la Recherche Agronomique, Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales, F-34060 Montpellier, France (I.F., N.C.); andCentre de Coopération Internationale en Recherche Agronomique Pour le Développement, Unité Mixte de Recherche AGAP, F-34398 Montpellier, France (A.D., G.D., J.-F.D.) irisfischer402@gmail.com chantret@supagro.inra.fr.
authors.forename: Nathalie
authors.initials: N
authors.lastname: Chantret
mesh_terms: D020816:Amino Acid Motifs; D019143:Evolution, Molecular; D020440:Gene Duplication; D014644:Genetic Variation; D019684:Magnoliopsida / Q000145:classification / Q000235:genetics*; D008957:Models, Genetic; D005810:Multigene Family; D010802:Phylogeny; D010940:Plant Proteins / Q000145:classification / Q000235:genetics*; D020794:Receptor Protein-Tyrosine Kinases / Q000145:classification / Q000235:genetics*; D020449:Repetitive Sequences, Amino Acid; D012641:Selection, Genetic; D013045:Species Specificity; D013997:Time Factors
chemical_list: D010940:Plant Proteins; D020794:Receptor Protein-Tyrosine Kinases