title: A Comprehensive Analysis of the Transcriptomes of Marssonina brunnea and Infected Poplar Leaves to Capture Vital Events in Host-Pathogen Interactions.
abstract: BACKGROUND
  Understanding host-pathogen interaction mechanisms helps to elucidate the entire infection process and focus on important events, and it is a promising approach for improvement of disease control and selection of treatment strategy. Time-course host-pathogen transcriptome analyses and network inference have been applied to unravel the direct or indirect relationships of gene expression alterations. However, time series analyses can suffer from absent time points due to technical problems such as RNA degradation, which limits the application of algorithms that require strict sequential sampling. Here, we introduce an efficient method using independence test to infer an independent network that is exclusively concerned with the frequency of gene expression changes.
  
  
  RESULTS
  Highly resistant NL895 poplar leaves and weakly resistant NL214 leaves were infected with highly active and weakly active Marssonina brunnea, respectively, and were harvested at different time points. The independent network inference illustrated the top 1,000 vital fungus-poplar relationships, which contained 768 fungal genes and 54 poplar genes. These genes could be classified into three categories: a fungal gene surrounded by many poplar genes; a poplar gene connected to many fungal genes; and other genes (possessing low degrees of connectivity). Notably, the fungal gene M6_08342 (a metalloprotease) was connected to 10 poplar genes, particularly including two disease-resistance genes. These core genes, which are surrounded by other genes, may be of particular importance in complicated infection processes and worthy of further investigation.
  
  
  CONCLUSIONS
  We provide a clear framework of the interaction network and identify a number of candidate key effectors in this process, which might assist in functional tests, resistant clone selection, and disease control in the future.
authors.affiliation: State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, People's Republic of China; Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, People's Republic of China; Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China.
authors.forename: Chengwen
authors.initials: C
authors.lastname: Chen
authors.affiliation: State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, People's Republic of China; Center for Computational Systems Biology and School of Mathematical Sciences, Fudan University, Shanghai, People's Republic of China.
authors.forename: Ye
authors.initials: Y
authors.lastname: Yao
authors.affiliation: Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, People's Republic of China.
authors.forename: Liang
authors.initials: L
authors.lastname: Zhang
authors.affiliation: State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, People's Republic of China; Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, People's Republic of China.
authors.forename: Minjie
authors.initials: M
authors.lastname: Xu
authors.affiliation: State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, People's Republic of China; Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, People's Republic of China.
authors.forename: Jianping
authors.initials: J
authors.lastname: Jiang
authors.affiliation: State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, People's Republic of China.
authors.forename: Tonghai
authors.initials: T
authors.lastname: Dou
authors.affiliation: State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, People's Republic of China; Center for Computational Systems Biology and School of Mathematical Sciences, Fudan University, Shanghai, People's Republic of China.
authors.forename: Wei
authors.initials: W
authors.lastname: Lin
authors.affiliation: Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, People's Republic of China.
authors.forename: Guoping
authors.initials: G
authors.lastname: Zhao
authors.affiliation: Jiangsu Key Laboratory for Poplar Germplasm Enhancement and Variety Improvement, Nanjing Forestry University, Nanjing, People's Republic of China.
authors.forename: Minren
authors.initials: M
authors.lastname: Huang
authors.affiliation: State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, People's Republic of China; Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, People's Republic of China.
authors.forename: Yan
authors.initials: Y
authors.lastname: Zhou
mesh_terms: D001203:Ascomycota / Q000235:genetics* / Q000472:pathogenicity*; D020869:Gene Expression Profiling; D015966:Gene Expression Regulation, Fungal; D018506:Gene Expression Regulation, Plant; D053263:Gene Regulatory Networks; D005800:Genes, Fungal; D017343:Genes, Plant; D054884:Host-Pathogen Interactions / Q000235:genetics; D010935:Plant Diseases / Q000382:microbiology; D018515:Plant Leaves / Q000382:microbiology; D032107:Populus / Q000235:genetics / Q000382:microbiology*; D059467:Transcriptome