title: Sequencing and functional analysis of the genome of a nematode egg-parasitic fungus, Pochonia chlamydosporia.
abstract: Pochonia chlamydosporia is a worldwide-distributed soil fungus with a great capacity to infect and destroy the eggs and kill females of plant-parasitic nematodes. Additionally, it has the ability to colonize endophytically roots of economically-important crop plants, thereby promoting their growth and eliciting plant defenses. This multitrophic behavior makes P. chlamydosporia a potentially useful tool for sustainable agriculture approaches. We sequenced and assembled ∼41 Mb of P. chlamydosporia genomic DNA and predicted 12,122 gene models, of which many were homologous to genes of fungal pathogens of invertebrates and fungal plant pathogens. Predicted genes (65%) were functionally annotated according to Gene Ontology, and 16% of them found to share homology with genes in the Pathogen Host Interactions (PHI) database. The genome of this fungus is highly enriched in genes encoding hydrolytic enzymes, such as proteases, glycoside hydrolases and carbohydrate esterases. We used RNA-Seq technology in order to identify the genes expressed during endophytic behavior of P. chlamydosporia when colonizing barley roots. Functional annotation of these genes showed that hydrolytic enzymes and transporters are expressed during endophytism. This structural and functional analysis of the P. chlamydosporia genome provides a starting point for understanding the molecular mechanisms involved in the multitrophic lifestyle of this fungus. The genomic information provided here should also prove useful for enhancing the capabilities of this fungus as a biocontrol agent of plant-parasitic nematodes and as a plant growth-promoting organism.
authors: Department of Marine Sciences and Applied Biology, University of Alicante, P.O. Box. 99, E-03080 Alicante, Spain; Multidisciplinary Institute for Environmental Studies (MIES) "Ramón Margalef", University of Alicante, Alicante, Spain. Electronic address: eduardo.larriba@ua.es.
authors: Eduardo
authors: E
authors: Larriba
authors: Department of Cell and Systems Biology, University of Toronto, M5S 3G5 Mississauga, Ontario, Canada. Electronic address: maria.jaime@gmail.com.
authors: María D L A
authors: MD
authors: Jaime
authors: Institute for Computational Genomics, Príncipe Felipe Research Center, Avda. Eduardo Primo Yúfera 3, E-46012 Valencia, Spain. Electronic address: jcarbonell@cipf.es.
authors: José
authors: J
authors: Carbonell-Caballero
authors: Institute for Computational Genomics, Príncipe Felipe Research Center, Avda. Eduardo Primo Yúfera 3, E-46012 Valencia, Spain. Electronic address: aconesa@cipf.es.
authors: Ana
authors: A
authors: Conesa
authors: Institute for Computational Genomics, Príncipe Felipe Research Center, Avda. Eduardo Primo Yúfera 3, E-46012 Valencia, Spain. Electronic address: jdopazo@cipf.es.
authors: Joaquín
authors: J
authors: Dopazo
authors: Department of Molecular Genetics, University of Toronto, M5S 1A8 Toronto, Ontario, Canada; Banting and Best Department of Medical Research, University of Toronto, M5S 3E1 Toronto, Ontario, Canada; Terrence Donnelly Centre for Cellular and Biomedical Research, University of Toronto, M5S 3E1 Toronto, Ontario, Canada. Electronic address: corey.nislow@gmail.com.
authors: Corey
authors: C
authors: Nislow
authors: Multidisciplinary Institute for Environmental Studies (MIES) "Ramón Margalef", University of Alicante, Alicante, Spain; Department of Physiology, Genetics and Microbiology, University of Alicante, E-03080 Alicante, Spain. Electronic address: jmnieto@ua.es.
authors: José
authors: J
authors: Martín-Nieto
authors: Department of Marine Sciences and Applied Biology, University of Alicante, P.O. Box. 99, E-03080 Alicante, Spain; Multidisciplinary Institute for Environmental Studies (MIES) "Ramón Margalef", University of Alicante, Alicante, Spain. Electronic address: lv.lopez@ua.es.
authors: Luis Vicente
authors: LV
authors: Lopez-Llorca
mesh_terms: D000818:Animals; D001203:Ascomycota / Q000235:genetics / Q000472:pathogenicity / Q000502:physiology*; D005260:Female; D015966:Gene Expression Regulation, Fungal; D063990:Gene Ontology; D016681:Genome, Fungal; D001467:Hordeum / Q000382:microbiology; D054884:Host-Pathogen Interactions; D009348:Nematoda / Q000382:microbiology*; D010063:Ovum / Q000382:microbiology; D010802:Phylogeny; D018517:Plant Roots / Q000382:microbiology; D017422:Sequence Analysis, DNA; D015398:Signal Transduction; D059467:Transcriptome
keywords: Endophyte; Gene Ontology; Genome sequencing; Hydrolytic enzymes; Nematophagous fungus; Pochonia chlamydosporia