title: Insights into Adaptations to a Near-Obligate Nematode Endoparasitic Lifestyle from the Finished Genome of Drechmeria coniospora.
abstract: Nematophagous fungi employ three distinct predatory strategies: nematode trapping, parasitism of females and eggs, and endoparasitism. While endoparasites play key roles in controlling nematode populations in nature, their application for integrated pest management is hindered by the limited understanding of their biology. We present a comparative analysis of a high quality finished genome assembly of Drechmeria coniospora, a model endoparasitic nematophagous fungus, integrated with a transcriptomic study. Adaptation of D. coniospora to its almost completely obligate endoparasitic lifestyle led to the simplification of many orthologous gene families involved in the saprophytic trophic mode, while maintaining orthologs of most known fungal pathogen-host interaction proteins, stress response circuits and putative effectors of the small secreted protein type. The need to adhere to and penetrate the host cuticle led to a selective radiation of surface proteins and hydrolytic enzymes. Although the endoparasite has a simplified secondary metabolome, it produces a novel peptaibiotic family that shows antibacterial, antifungal and nematicidal activities. Our analyses emphasize the basic malleability of the D. coniospora genome: loss of genes advantageous for the saprophytic lifestyle; modulation of elements that its cohort species utilize for entomopathogenesis; and expansion of protein families necessary for the nematode endoparasitic lifestyle.
authors.affiliation: Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China.
authors.forename: Liwen
authors.initials: L
authors.lastname: Zhang
authors.affiliation: Key Laboratory of Agricultural Genomics (Beijing), Ministry of Agriculture, China.
authors.forename: Zhengfu
authors.initials: Z
authors.lastname: Zhou
authors.affiliation: Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China.
authors.forename: Qiannan
authors.initials: Q
authors.lastname: Guo
authors.affiliation: Molecular Plant Pathology, University of Amsterdam, Amsterdam, the Netherlands.
authors.forename: Like
authors.initials: L
authors.lastname: Fokkens
authors.affiliation: Department of Biotechnology and Microbiology, Faculty of Science and Technology, University of Debrecen, Hungary.|Department of Biochemistry and Molecular Biology, University of Debrecen, Debrecen, Hungary.
authors.forename: Márton
authors.initials: M
authors.lastname: Miskei
authors.affiliation: Department of Biotechnology and Microbiology, Faculty of Science and Technology, University of Debrecen, Hungary.
authors.forename: István
authors.initials: I
authors.lastname: Pócsi
authors.affiliation: Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China.
authors.forename: Wei
authors.initials: W
authors.lastname: Zhang
authors.affiliation: Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China.
authors.forename: Ming
authors.initials: M
authors.lastname: Chen
authors.affiliation: Tianjin Key Laboratory of Microbial Functional Genomics, TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin, China.
authors.forename: Lei
authors.initials: L
authors.lastname: Wang
authors.affiliation: Tianjin Key Laboratory of Microbial Functional Genomics, TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin, China.
authors.forename: Yamin
authors.initials: Y
authors.lastname: Sun
authors.affiliation: Plant Pathology &Plant-Microbe Biology, Cornell University, Ithaca, New York, USA.
authors.forename: Bruno G G
authors.initials: BG
authors.lastname: Donzelli
authors.affiliation: USDA-ARS, Robert W. Holley Center for Agriculture and Health, Ithaca, New York, USA.
authors.forename: Donna M
authors.initials: DM
authors.lastname: Gibson
authors.affiliation: Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee, USA.
authors.forename: David R
authors.initials: DR
authors.lastname: Nelson
authors.affiliation: State Key Laboratory of Natural Medicines, Department of Natural Medicinal Chemistry, China Pharmaceutical University, Nanjing, China.
authors.forename: Jian-Guang
authors.initials: JG
authors.lastname: Luo
authors.affiliation: Molecular Plant Pathology, University of Amsterdam, Amsterdam, the Netherlands.
authors.forename: Martijn
authors.initials: M
authors.lastname: Rep
authors.affiliation: Key Laboratory of Agricultural Genomics (Beijing), Ministry of Agriculture, China.
authors.forename: Hang
authors.initials: H
authors.lastname: Liu
authors.affiliation: Key Laboratory of Agricultural Genomics (Beijing), Ministry of Agriculture, China.
authors.forename: Shengnan
authors.initials: S
authors.lastname: Yang
authors.affiliation: Key Laboratory of Agricultural Genomics (Beijing), Ministry of Agriculture, China.
authors.forename: Jing
authors.initials: J
authors.lastname: Wang
authors.affiliation: USDA-ARS, Robert W. Holley Center for Agriculture and Health, Ithaca, New York, USA.
authors.forename: Stuart B
authors.initials: SB
authors.lastname: Krasnoff
authors.affiliation: Key Laboratory of Agricultural Genomics (Beijing), Ministry of Agriculture, China.
authors.forename: Yuquan
authors.initials: Y
authors.lastname: Xu
authors.affiliation: Natural Products Center, School of Natural Resources and the Environment, University of Arizona, Tucson, Arizona, USA.
authors.forename: István
authors.initials: I
authors.lastname: Molnár
authors.affiliation: Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China.
authors.forename: Min
authors.initials: M
authors.lastname: Lin
mesh_terms: D000222:Adaptation, Physiological; D000818:Animals; D005656:Fungal Proteins / Q000235:genetics; D016681:Genome, Fungal; D054884:Host-Pathogen Interactions; D006999:Hypocreales / Q000235:genetics* / Q000502:physiology; D009348:Nematoda / Q000382:microbiology*; D059467:Transcriptome
chemical_list: D005656:Fungal Proteins