title: Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderma.
abstract: BACKGROUND
  Mycoparasitism, a lifestyle where one fungus is parasitic on another fungus, has special relevance when the prey is a plant pathogen, providing a strategy for biological control of pests for plant protection. Probably, the most studied biocontrol agents are species of the genus Hypocrea/Trichoderma.
  
  
  RESULTS
  Here we report an analysis of the genome sequences of the two biocontrol species Trichoderma atroviride (teleomorph Hypocrea atroviridis) and Trichoderma virens (formerly Gliocladium virens, teleomorph Hypocrea virens), and a comparison with Trichoderma reesei (teleomorph Hypocrea jecorina). These three Trichoderma species display a remarkable conservation of gene order (78 to 96%), and a lack of active mobile elements probably due to repeat-induced point mutation. Several gene families are expanded in the two mycoparasitic species relative to T. reesei or other ascomycetes, and are overrepresented in non-syntenic genome regions. A phylogenetic analysis shows that T. reesei and T. virens are derived relative to T. atroviride. The mycoparasitism-specific genes thus arose in a common Trichoderma ancestor but were subsequently lost in T. reesei.
  
  
  CONCLUSIONS
  The data offer a better understanding of mycoparasitism, and thus enforce the development of improved biocontrol strains for efficient and environmentally friendly protection of plants.
authors.affiliation: Area Gene Technology and Applied Biochemistry, Institute of Chemical Engineering Vienna University of Technology, Getreidemarkt 9, 1060 Vienna, Austria. ckubicek@mail.zserv.tuwien.ac.at
authors.forename: Christian P
authors.initials: CP
authors.lastname: Kubicek
authors.forename: Alfredo
authors.initials: A
authors.lastname: Herrera-Estrella
authors.forename: Verena
authors.initials: V
authors.lastname: Seidl-Seiboth
authors.forename: Diego A
authors.initials: DA
authors.lastname: Martinez
authors.forename: Irina S
authors.initials: IS
authors.lastname: Druzhinina
authors.forename: Michael
authors.initials: M
authors.lastname: Thon
authors.forename: Susanne
authors.initials: S
authors.lastname: Zeilinger
authors.forename: Sergio
authors.initials: S
authors.lastname: Casas-Flores
authors.forename: Benjamin A
authors.initials: BA
authors.lastname: Horwitz
authors.forename: Prasun K
authors.initials: PK
authors.lastname: Mukherjee
authors.forename: Mala
authors.initials: M
authors.lastname: Mukherjee
authors.forename: László
authors.initials: L
authors.lastname: Kredics
authors.forename: Luis D
authors.initials: LD
authors.lastname: Alcaraz
authors.forename: Andrea
authors.initials: A
authors.lastname: Aerts
authors.forename: Zsuzsanna
authors.initials: Z
authors.lastname: Antal
authors.forename: Lea
authors.initials: L
authors.lastname: Atanasova
authors.forename: Mayte G
authors.initials: MG
authors.lastname: Cervantes-Badillo
authors.forename: Jean
authors.initials: J
authors.lastname: Challacombe
authors.forename: Olga
authors.initials: O
authors.lastname: Chertkov
authors.forename: Kevin
authors.initials: K
authors.lastname: McCluskey
authors.forename: Fanny
authors.initials: F
authors.lastname: Coulpier
authors.forename: Nandan
authors.initials: N
authors.lastname: Deshpande
authors.forename: Hans
authors.initials: H
authors.lastname: von Döhren
authors.forename: Daniel J
authors.initials: DJ
authors.lastname: Ebbole
authors.forename: Edgardo U
authors.initials: EU
authors.lastname: Esquivel-Naranjo
authors.forename: Erzsébet
authors.initials: E
authors.lastname: Fekete
authors.forename: Michel
authors.initials: M
authors.lastname: Flipphi
authors.forename: Fabian
authors.initials: F
authors.lastname: Glaser
authors.forename: Elida Y
authors.initials: EY
authors.lastname: Gómez-Rodríguez
authors.forename: Sabine
authors.initials: S
authors.lastname: Gruber
authors.forename: Cliff
authors.initials: C
authors.lastname: Han
authors.forename: Bernard
authors.initials: B
authors.lastname: Henrissat
authors.forename: Rosa
authors.initials: R
authors.lastname: Hermosa
authors.forename: Miguel
authors.initials: M
authors.lastname: Hernández-Oñate
authors.forename: Levente
authors.initials: L
authors.lastname: Karaffa
authors.forename: Idit
authors.initials: I
authors.lastname: Kosti
authors.forename: Stéphane
authors.initials: S
authors.lastname: Le Crom
authors.forename: Erika
authors.initials: E
authors.lastname: Lindquist
authors.forename: Susan
authors.initials: S
authors.lastname: Lucas
authors.forename: Mette
authors.initials: M
authors.lastname: Lübeck
authors.forename: Peter S
authors.initials: PS
authors.lastname: Lübeck
authors.forename: Antoine
authors.initials: A
authors.lastname: Margeot
authors.forename: Benjamin
authors.initials: B
authors.lastname: Metz
authors.forename: Monica
authors.initials: M
authors.lastname: Misra
authors.forename: Helena
authors.initials: H
authors.lastname: Nevalainen
authors.forename: Markus
authors.initials: M
authors.lastname: Omann
authors.forename: Nicolle
authors.initials: N
authors.lastname: Packer
authors.forename: Giancarlo
authors.initials: G
authors.lastname: Perrone
authors.forename: Edith E
authors.initials: EE
authors.lastname: Uresti-Rivera
authors.forename: Asaf
authors.initials: A
authors.lastname: Salamov
authors.forename: Monika
authors.initials: M
authors.lastname: Schmoll
authors.forename: Bernhard
authors.initials: B
authors.lastname: Seiboth
authors.forename: Harris
authors.initials: H
authors.lastname: Shapiro
authors.forename: Serenella
authors.initials: S
authors.lastname: Sukno
authors.forename: Juan Antonio
authors.initials: JA
authors.lastname: Tamayo-Ramos
authors.forename: Doris
authors.initials: D
authors.lastname: Tisch
authors.forename: Aric
authors.initials: A
authors.lastname: Wiest
authors.forename: Heather H
authors.initials: HH
authors.lastname: Wilkinson
authors.forename: Michael
authors.initials: M
authors.lastname: Zhang
authors.forename: Pedro M
authors.initials: PM
authors.lastname: Coutinho
authors.forename: Charles M
authors.initials: CM
authors.lastname: Kenerley
authors.forename: Enrique
authors.initials: E
authors.lastname: Monte
authors.forename: Scott E
authors.initials: SE
authors.lastname: Baker
authors.forename: Igor V
authors.initials: IV
authors.lastname: Grigoriev
mesh_terms: D002874:Chromosome Mapping; D004251:DNA Transposable Elements / Q000235:genetics; D016681:Genome, Fungal / Q000235:genetics*; D035901:Hypocrea / Q000145:classification / Q000235:genetics; D010572:Pest Control, Biological; D010802:Phylogeny; D010944:Plants / Q000469:parasitology; D017422:Sequence Analysis, DNA / Q000379:methods*; D013045:Species Specificity; D014242:Trichoderma / Q000145:classification / Q000235:genetics*
chemical_list: D004251:DNA Transposable Elements