title: Pinpointing genes underlying annual/perennial transitions with comparative genomics.
abstract: Transitions between perennial and an annual life history occur often in plant lineages, but the genes that control whether a plant is an annual or perennial are largely unknown. To identify genes that confer differences between annuals and perennials we compared the gene content of four pairs of sister lineages (Arabidopsis thaliana/Arabidopsis lyrata, Arabis montbretiana/Arabis alpina, Arabis verna/Aubrieta parviflora and Draba nemorosa/Draba hispanica) in the Brassicaceae in which each pair contains one annual and one perennial, plus one extra annual species (Capsella rubella).
  
  
  
  After sorting all genes in all nine species into gene families, we identified five families in which well-annotated genes are present in the perennials A. lyrata and A. alpina, but are not present in any of the annual species. For the eleven genes in perennials in these families, an orthologous pseudogene or otherwise highly diverged gene was found in the syntenic region of the annual species in six cases. The five candidate families identified encode: a kinase, an oxidoreductase, a lactoylglutathione lyase, a F-box protein and a zinc finger protein. By comparing the active gene in the perennial to the pseudogene or heavily altered gene in the annual, dN and dS were calculated. The low dN/dS values in one kinase suggest that it became pseudogenized more recently, while the other kinase, F-box, oxidoreductase and zinc-finger became pseudogenized closer to the divergence between the annual-perennial pair.
  
  
  
  We identified five gene families that may be involved in the life history switch from perennial to annual. Considering the dN and dS data and whether syntenic pseudogenes were found and the potential functions of the genes, the F-box family is considered the most promising candidate for future functional studies to determine if it affects life history.
authors.affiliation: Institute of Population Genetics, Heinrich-Heine-Universität, Universitätsstraße 1, Düsseldorf, D-40225, Germany.|Faculty of Biology & Pharmacy, Department of Bioinformatics, University of Jena, Ernst Abbe Pl 2, Jena, D-07743, Germany.|Cluster of Excellence on Plant Science, Düsseldorf, 40225, Germany.
authors.forename: Andrew J
authors.initials: AJ
authors.lastname: Heidel
authors.affiliation: Cluster of Excellence on Plant Science, Düsseldorf, 40225, Germany.|Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, Cologne, D-50829, Germany.
authors.forename: Christiane
authors.initials: C
authors.lastname: Kiefer
authors.affiliation: Cluster of Excellence on Plant Science, Düsseldorf, 40225, Germany.|Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, Cologne, D-50829, Germany.
authors.forename: George
authors.initials: G
authors.lastname: Coupland
authors.affiliation: Institute of Population Genetics, Heinrich-Heine-Universität, Universitätsstraße 1, Düsseldorf, D-40225, Germany. Laura.Rose@hhu.de.|Cluster of Excellence on Plant Science, Düsseldorf, 40225, Germany. Laura.Rose@hhu.de.
authors.forename: Laura E
authors.initials: LE
authors.lastname: Rose
mesh_terms: D017360:Arabidopsis / Q000145:classification / Q000235:genetics*; D019295:Computational Biology / Q000379:methods; D019143:Evolution, Molecular; D017343:Genes, Plant; D056726:Genetic Association Studies; D018745:Genome, Plant; D023281:Genomics; D005810:Multigene Family; D010802:Phylogeny; D011544:Pseudogenes; D019655:Quantitative Trait, Heritable
keywords: Evolution; Gene loss; Life history; Plants