title: Distinctive expansion of potential virulence genes in the genome of the oomycete fish pathogen Saprolegnia parasitica.
abstract: Oomycetes in the class Saprolegniomycetidae of the Eukaryotic kingdom Stramenopila have evolved as severe pathogens of amphibians, crustaceans, fish and insects, resulting in major losses in aquaculture and damage to aquatic ecosystems. We have sequenced the 63 Mb genome of the fresh water fish pathogen, Saprolegnia parasitica. Approximately 1/3 of the assembled genome exhibits loss of heterozygosity, indicating an efficient mechanism for revealing new variation. Comparison of S. parasitica with plant pathogenic oomycetes suggests that during evolution the host cellular environment has driven distinct patterns of gene expansion and loss in the genomes of plant and animal pathogens. S. parasitica possesses one of the largest repertoires of proteases (270) among eukaryotes that are deployed in waves at different points during infection as determined from RNA-Seq data. In contrast, despite being capable of living saprotrophically, parasitism has led to loss of inorganic nitrogen and sulfur assimilation pathways, strikingly similar to losses in obligate plant pathogenic oomycetes and fungi. The large gene families that are hallmarks of plant pathogenic oomycetes such as Phytophthora appear to be lacking in S. parasitica, including those encoding RXLR effectors, Crinkler's, and Necrosis Inducing-Like Proteins (NLP). S. parasitica also has a very large kinome of 543 kinases, 10% of which is induced upon infection. Moreover, S. parasitica encodes several genes typical of animals or animal-pathogens and lacking from other oomycetes, including disintegrins and galactose-binding lectins, whose expression and evolutionary origins implicate horizontal gene transfer in the evolution of animal pathogenesis in S. parasitica.
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America.
authors.forename: Rays H Y
authors.initials: RH
authors.lastname: Jiang
authors.forename: Irene
authors.initials: I
authors.lastname: de Bruijn
authors.forename: Brian J
authors.initials: BJ
authors.lastname: Haas
authors.forename: Rodrigo
authors.initials: R
authors.lastname: Belmonte
authors.forename: Lars
authors.initials: L
authors.lastname: Löbach
authors.forename: James
authors.initials: J
authors.lastname: Christie
authors.forename: Guido
authors.initials: G
authors.lastname: van den Ackerveken
authors.forename: Arnaud
authors.initials: A
authors.lastname: Bottin
authors.forename: Vincent
authors.initials: V
authors.lastname: Bulone
authors.forename: Sara M
authors.initials: SM
authors.lastname: Díaz-Moreno
authors.forename: Bernard
authors.initials: B
authors.lastname: Dumas
authors.forename: Lin
authors.initials: L
authors.lastname: Fan
authors.forename: Elodie
authors.initials: E
authors.lastname: Gaulin
authors.forename: Francine
authors.initials: F
authors.lastname: Govers
authors.forename: Laura J
authors.initials: LJ
authors.lastname: Grenville-Briggs
authors.forename: Neil R
authors.initials: NR
authors.lastname: Horner
authors.forename: Joshua Z
authors.initials: JZ
authors.lastname: Levin
authors.forename: Marco
authors.initials: M
authors.lastname: Mammella
authors.forename: Harold J G
authors.initials: HJ
authors.lastname: Meijer
authors.forename: Paul
authors.initials: P
authors.lastname: Morris
authors.forename: Chad
authors.initials: C
authors.lastname: Nusbaum
authors.forename: Stan
authors.initials: S
authors.lastname: Oome
authors.forename: Andrew J
authors.initials: AJ
authors.lastname: Phillips
authors.forename: David
authors.initials: D
authors.lastname: van Rooyen
authors.forename: Elzbieta
authors.initials: E
authors.lastname: Rzeszutek
authors.forename: Marcia
authors.initials: M
authors.lastname: Saraiva
authors.forename: Chris J
authors.initials: CJ
authors.lastname: Secombes
authors.forename: Michael F
authors.initials: MF
authors.lastname: Seidl
authors.forename: Berend
authors.initials: B
authors.lastname: Snel
authors.forename: Joost H M
authors.initials: JH
authors.lastname: Stassen
authors.forename: Sean
authors.initials: S
authors.lastname: Sykes
authors.forename: Sucheta
authors.initials: S
authors.lastname: Tripathy
authors.forename: Herbert
authors.initials: H
authors.lastname: van den Berg
authors.forename: Julio C
authors.initials: JC
authors.lastname: Vega-Arreguin
authors.forename: Stephan
authors.initials: S
authors.lastname: Wawra
authors.forename: Sarah K
authors.initials: SK
authors.lastname: Young
authors.forename: Qiandong
authors.initials: Q
authors.lastname: Zeng
authors.forename: Javier
authors.initials: J
authors.lastname: Dieguez-Uribeondo
authors.forename: Carsten
authors.initials: C
authors.lastname: Russ
authors.forename: Brett M
authors.initials: BM
authors.lastname: Tyler
authors.forename: Pieter
authors.initials: P
authors.lastname: van West
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001483:Base Sequence; D019143:Evolution, Molecular; D005399:Fishes / Q000235:genetics / Q000469:parasitology; D022761:Gene Transfer, Horizontal; D016678:Genome; D006790:Host-Parasite Interactions / Q000235:genetics*; D009868:Oomycetes / Q000145:classification / Q000235:genetics* / Q000472:pathogenicity; D010802:Phylogeny; D010944:Plants / Q000469:parasitology; D044762:Saprolegnia / Q000145:classification / Q000235:genetics* / Q000472:pathogenicity; D014774:Virulence / Q000235:genetics*