title: Analysis of Saprolegnia parasitica Transcriptome following Treatment with Copper Sulfate.
abstract: BACKGROUND
  Massive infection caused by oomycete fungus Saprolegnia parasitica is detrimental to freshwater fish. Recently, we showed that copper sulfate demonstrated good efficacy for controlling S. parasitica infection in grass carp. In this study, we investigated the mechanism of inhibition of S. parasitica growth by copper sulfate by analyzing the transcriptome of copper sulfate-treated S. parasitica. To examine the mechanism of copper sulfate inhibiting S. parasitica, we utilized RNA-seq technology to compare differential gene expression in S. parasitica treated with or without copper sulfate.
  
  
  RESULTS
  The total mapped rates of the reads with the reference genome were 90.50% in the control group and 73.50% in the experimental group. In the control group, annotated splice junctions, partial novel splice junctions and complete novel splice junctions were about 83%, 3% and 14%, respectively. In the treatment group, the corresponding values were about 75%, 6% and 19%. Following copper sulfate treatment, a total 310 genes were markedly upregulated and 556 genes were markedly downregulated in S. parasitica. Material metabolism related GO terms including cofactor binding (33 genes), 1,3-beta-D-glucan synthase complex (4 genes), carboxylic acid metabolic process (40 genes) were the most significantly enriched. KEGG pathway analysis also determined that the metabolism-related biological pathways were significantly enriched, including the metabolic pathways (98 genes), biosynthesis of secondary metabolites pathways (42 genes), fatty acid metabolism (13 genes), phenylalanine metabolism (7 genes), starch and sucrose metabolism pathway (12 genes). The qRT-PCR results were largely consistent with the RNA-Seq results.
  
  
  CONCLUSIONS
  Our results indicate that copper sulfate inhibits S. parasitica growth by affecting multiple biological functions, including protein synthesis, energy biogenesis, and metabolism.
authors.affiliation: National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, 999 Hucheng Huan Road, Shanghai 201306, China.
authors.forename: Kun
authors.initials: K
authors.lastname: Hu
authors.affiliation: National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, 999 Hucheng Huan Road, Shanghai 201306, China.|East China Sea Fisheries Research Institute Chinese Academy of Fishery Sciences, Shanghai 201306, PR China.
authors.forename: Rong-Rong
authors.initials: RR
authors.lastname: Ma
authors.affiliation: National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, 999 Hucheng Huan Road, Shanghai 201306, China.
authors.forename: Jun-Ming
authors.initials: JM
authors.lastname: Cheng
authors.affiliation: National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, 999 Hucheng Huan Road, Shanghai 201306, China.
authors.forename: Xin
authors.initials: X
authors.lastname: Ye
authors.affiliation: National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, 999 Hucheng Huan Road, Shanghai 201306, China.
authors.forename: Qi
authors.initials: Q
authors.lastname: Sun
authors.affiliation: National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, 999 Hucheng Huan Road, Shanghai 201306, China.
authors.forename: Hai-Lan
authors.initials: HL
authors.lastname: Yuan
authors.affiliation: National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, 999 Hucheng Huan Road, Shanghai 201306, China.
authors.forename: Nan
authors.initials: N
authors.lastname: Liang
authors.affiliation: East China Sea Fisheries Research Institute Chinese Academy of Fishery Sciences, Shanghai 201306, PR China.
authors.forename: Wen-Hong
authors.initials: WH
authors.lastname: Fang
authors.affiliation: National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, 999 Hucheng Huan Road, Shanghai 201306, China.
authors.forename: Hao-Ran
authors.initials: HR
authors.lastname: Li
authors.affiliation: National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, 999 Hucheng Huan Road, Shanghai 201306, China.
authors.forename: Xian-Le
authors.initials: XL
authors.lastname: Yang
mesh_terms: D000818:Animals; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods; D019327:Copper Sulfate / Q000494:pharmacology*; D005393:Fish Diseases / Q000469:parasitology; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation / Q000187:drug effects*; D016678:Genome; D023281:Genomics; D059014:High-Throughput Nucleotide Sequencing; D058977:Molecular Sequence Annotation; D015203:Reproducibility of Results; D044762:Saprolegnia / Q000235:genetics*; D059467:Transcriptome
chemical_list: D019327:Copper Sulfate