title: Living apart together: crosstalk between the core and supernumerary genomes in a fungal plant pathogen.
abstract: Eukaryotes display remarkable genome plasticity, which can include supernumerary chromosomes that differ markedly from the core chromosomes. Despite the widespread occurrence of supernumerary chromosomes in fungi, their origin, relation to the core genome and the reason for their divergent characteristics are still largely unknown. The complexity of genome assembly due to the presence of repetitive DNA partially accounts for this.
  
  
  
  Here we use single-molecule real-time (SMRT) sequencing to assemble the genome of a prominent fungal wheat pathogen, Fusarium poae, including at least one supernumerary chromosome. The core genome contains limited transposable elements (TEs) and no gene duplications, while the supernumerary genome holds up to 25 % TEs and multiple gene duplications. The core genome shows all hallmarks of repeat-induced point mutation (RIP), a defense mechanism against TEs, specific for fungi. The absence of RIP on the supernumerary genome accounts for the differences between the two (sub)genomes, and results in a functional crosstalk between them. The supernumerary genome is a reservoir for TEs that migrate to the core genome, and even large blocks of supernumerary sequence (>200 kb) have recently translocated to the core. Vice versa, the supernumerary genome acts as a refuge for genes that are duplicated from the core genome.
  
  
  
  For the first time, a mechanism was determined that explains the differences that exist between the core and supernumerary genome in fungi. Different biology rather than origin was shown to be responsible. A "living apart together" crosstalk exists between the core and supernumerary genome, accelerating chromosomal and organismal evolution.
authors.affiliation: Department of Applied Biosciences, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium.|Wageningen UR, Wageningen, The Netherlands.
authors.forename: Adriaan
authors.identifier: 0000-0002-2664-8169
authors.initials: A
authors.lastname: Vanheule
authors.affiliation: Department of Applied Biosciences, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium.
authors.forename: Kris
authors.initials: K
authors.lastname: Audenaert
authors.affiliation: Wageningen UR, Wageningen, The Netherlands.
authors.forename: Sven
authors.initials: S
authors.lastname: Warris
authors.affiliation: Wageningen UR, Wageningen, The Netherlands.
authors.forename: Henri
authors.initials: H
authors.lastname: van de Geest
authors.affiliation: Wageningen UR, Wageningen, The Netherlands.
authors.forename: Elio
authors.initials: E
authors.lastname: Schijlen
authors.affiliation: Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium.
authors.forename: Monica
authors.initials: M
authors.lastname: Höfte
authors.affiliation: Department of Bioanalysis, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium.
authors.forename: Sarah
authors.initials: S
authors.lastname: De Saeger
authors.affiliation: Department of Applied Biosciences, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium.
authors.forename: Geert
authors.initials: G
authors.lastname: Haesaert
authors.affiliation: Wageningen UR, Wageningen, The Netherlands.
authors.forename: Cees
authors.initials: C
authors.lastname: Waalwijk
authors.affiliation: Wageningen UR, Wageningen, The Netherlands. theo.vanderlee@wur.nl.
authors.forename: Theo
authors.initials: T
authors.lastname: van der Lee
mesh_terms: D001482:Base Composition; D015825:Chromosomes, Fungal / Q000235:genetics*; D004251:DNA Transposable Elements; D019143:Evolution, Molecular; D005658:Fungi / Q000235:genetics*; D020440:Gene Duplication; D059646:Genome Size; D017354:Point Mutation; D060888:Real-Time Polymerase Chain Reaction; D017422:Sequence Analysis, DNA / Q000379:methods*; D014908:Triticum / Q000382:microbiology*
chemical_list: D004251:DNA Transposable Elements
keywords: Fusarium; Gene duplications; Repeat-induced point mutation; Single-molecule real-time sequencing; Supernumerary chromosomes; Translocation; Transposable elements