title: High Gene Family Turnover Rates and Gene Space Adaptation in the Compact Genome of the Carnivorous Plant Utricularia gibba.
abstract: Utricularia gibba is an aquatic carnivorous plant with highly specialized morphology, featuring fibrous floating networks of branches and leaf-like organs, no recognizable roots, and bladder traps that capture and digest prey. We recently described the compressed genome of U. gibba as sufficient to control the development and reproduction of a complex organism. We hypothesized intense deletion pressure as a mechanism whereby most noncoding DNA was deleted, despite evidence for three independent whole-genome duplications (WGDs). Here, we explore the impact of intense genome fractionation in the evolutionary dynamics of U. gibba's functional gene space. We analyze U. gibba gene family turnover by modeling gene gain/death rates under a maximum-likelihood statistical framework. In accord with our deletion pressure hypothesis, we show that the U. gibba gene death rate is significantly higher than those of four other eudicot species. Interestingly, the gene gain rate is also significantly higher, likely reflecting the occurrence of multiple WGDs and possibly also small-scale genome duplications. Gene ontology enrichment analyses of U. gibba-specific two-gene orthogroups, multigene orthogroups, and singletons highlight functions that may represent adaptations in an aquatic carnivorous plant. We further discuss two homeodomain transcription factor gene families (WOX and HDG/HDZIP-IV) showing conspicuous differential expansions and contractions in U. gibba. Our results 1) reconcile the compactness of the U. gibba genome with its accommodation of a typical number of genes for a plant genome, and 2) highlight the role of high gene family turnover in the evolutionary diversification of U. gibba's functional gene space and adaptations to its unique lifestyle and highly specialized body plan.
authors: Department of Biological Sciences, University at Buffalo, Buffalo, NY lcpaulet@gmail.com vaalbert@buffalo.edu.
authors: Lorenzo
authors: L
authors: Carretero-Paulet
authors: Departament de Genètica and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain.
authors: Pablo
authors: P
authors: Librado
authors: Department of Biological Sciences, University at Buffalo, Buffalo, NY.
authors: Tien-Hao
authors: TH
authors: Chang
authors: 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: Enrique
authors: E
authors: Ibarra-Laclette
authors: 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: Luis
authors: L
authors: Herrera-Estrella
authors: Departament de Genètica and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain.
authors: Julio
authors: J
authors: Rozas
authors: Department of Biological Sciences, University at Buffalo, Buffalo, NY lcpaulet@gmail.com vaalbert@buffalo.edu.
authors: Victor A
authors: VA
authors: Albert
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics*; D060435:Carnivory; D019143:Evolution, Molecular; D018745:Genome, Plant; D000068378:Lamiales / Q000235:genetics* / Q000502:physiology; D005810:Multigene Family / Q000235:genetics; D010802:Phylogeny
keywords: carnivorous plants; gene family evolution; genome evolution; transcription factor gene families