title: Genome-wide analysis of adaptive molecular evolution in the carnivorous plant Utricularia gibba.
abstract: The genome of the bladderwort Utricularia gibba provides an unparalleled opportunity to uncover the adaptive landscape of an aquatic carnivorous plant with unique phenotypic features such as absence of roots, development of water-filled suction bladders, and a highly ramified branching pattern. Despite its tiny size, the U. gibba genome accommodates approximately as many genes as other plant genomes. To examine the relationship between the compactness of its genome and gene turnover, we compared the U. gibba genome with that of four other eudicot species, defining a total of 17,324 gene families (orthogroups). These families were further classified as either 1) lineage-specific expanded/contracted or 2) stable in size. The U. gibba-expanded families are generically related to three main phenotypic features: 1) trap physiology, 2) key plant morphogenetic/developmental pathways, and 3) response to environmental stimuli, including adaptations to life in aquatic environments. Further scans for signatures of protein functional specialization permitted identification of seven candidate genes with amino acid changes putatively fixed by positive Darwinian selection in the U. gibba lineage. The Arabidopsis orthologs of these genes (AXR, UMAMIT41, IGS, TAR2, SOL1, DEG9, and DEG10) are involved in diverse plant biological functions potentially relevant for U. gibba phenotypic diversification, including 1) auxin metabolism and signal transduction, 2) flowering induction and floral meristem transition, 3) root development, and 4) peptidases. Taken together, our results suggest numerous candidate genes and gene families as interesting targets for further experimental confirmation of their functional and adaptive roles in the U. gibba's unique lifestyle and highly specialized body plan.
authors.affiliation: Department of Biological Sciences, University at Buffalo Department of Biological Sciences, University at Buffalo lcpaulet@gmail.com vaalbert@buffalo.edu.
authors.forename: Lorenzo
authors.initials: L
authors.lastname: Carretero-Paulet
authors.affiliation: Department of Biological Sciences, University at Buffalo lcpaulet@gmail.com vaalbert@buffalo.edu.
authors.forename: Tien-Hao
authors.initials: TH
authors.lastname: Chang
authors.affiliation: Departament de Genètica and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Spain.
authors.forename: Pablo
authors.initials: P
authors.lastname: Librado
authors.affiliation: Laboratorio Nacional de Genómica para la Biodiversidad-Langebio/Unidad de Genómica Avanzada UGA, Centro de Investigación y Estudios Avanzados del IPN, Irapuato, Guanajuato, México Present address: Red de Estudios Moleculares Avanzados, Instituto de Ecología A.C., Xalapa, Veracruz, México.
authors.forename: Enrique
authors.initials: E
authors.lastname: Ibarra-Laclette
authors.affiliation: Laboratorio Nacional de Genómica para la Biodiversidad-Langebio/Unidad de Genómica Avanzada UGA, Centro de Investigación y Estudios Avanzados del IPN, Irapuato, Guanajuato, México.
authors.forename: Luis
authors.initials: L
authors.lastname: Herrera-Estrella
authors.affiliation: Departament de Genètica and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Spain.
authors.forename: Julio
authors.initials: J
authors.lastname: Rozas
authors.affiliation: Department of Biological Sciences, University at Buffalo lcpaulet@gmail.com vaalbert@buffalo.edu.
authors.forename: Victor A
authors.initials: VA
authors.lastname: Albert
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics*; D059001:Aquatic Organisms / Q000502:physiology; D044822:Biodiversity; D019143:Evolution, Molecular; D063990:Gene Ontology; D017343:Genes, Plant; D056726:Genetic Association Studies; D018745:Genome, Plant; D019684:Magnoliopsida / Q000235:genetics* / Q000502:physiology*; D008958:Models, Molecular; D058977:Molecular Sequence Annotation; D005810:Multigene Family; D010641:Phenotype; D010802:Phylogeny; D010940:Plant Proteins / Q000737:chemistry / Q000235:genetics; D017434:Protein Structure, Tertiary; D013045:Species Specificity
chemical_list: D010940:Plant Proteins
keywords: carnivorous plants; gene family expansions and contractions; genome evolution; phenotypic diversification; positive selection