title: Transcriptome comparison and gene coexpression network analysis provide a systems view of citrus response to 'Candidatus Liberibacter asiaticus' infection.
abstract: BACKGROUND
  Huanglongbing (HLB) is arguably the most destructive disease for the citrus industry. HLB is caused by infection of the bacterium, Candidatus Liberibacter spp. Several citrus GeneChip studies have revealed thousands of genes that are up- or down-regulated by infection with Ca. Liberibacter asiaticus. However, whether and how these host genes act to protect against HLB remains poorly understood.
  
  
  RESULTS
  As a first step towards a mechanistic view of citrus in response to the HLB bacterial infection, we performed a comparative transcriptome analysis and found that a total of 21 Probesets are commonly up-regulated by the HLB bacterial infection. In addition, a number of genes are likely regulated specifically at early, late or very late stages of the infection. Furthermore, using Pearson correlation coefficient-based gene coexpression analysis, we constructed a citrus HLB response network consisting of 3,507 Probesets and 56,287 interactions. Genes involved in carbohydrate and nitrogen metabolic processes, transport, defense, signaling and hormone response were overrepresented in the HLB response network and the subnetworks for these processes were constructed. Analysis of the defense and hormone response subnetworks indicates that hormone response is interconnected with defense response. In addition, mapping the commonly up-regulated HLB responsive genes into the HLB response network resulted in a core subnetwork where transport plays a key role in the citrus response to the HLB bacterial infection. Moreover, analysis of a phloem protein subnetwork indicates a role for this protein and zinc transporters or zinc-binding proteins in the citrus HLB defense response.
  
  
  CONCLUSIONS
  Through integrating transcriptome comparison and gene coexpression network analysis, we have provided for the first time a systems view of citrus in response to the Ca. Liberibacter spp. infection causing HLB.
authors: Plant Nutrient Signaling and Fruit Quality Improvement Laboratory, Citrus Research Institute & College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing 400712, China. zlzheng48@gmail.com
authors: Zhi-Liang
authors: ZL
authors: Zheng
authors: Yihong
authors: Y
authors: Zhao
mesh_terms: D001692:Biological Transport / Q000235:genetics; D032084:Citrus sinensis / Q000166:cytology / Q000235:genetics* / Q000378:metabolism / Q000382:microbiology*; D020869:Gene Expression Profiling; D053263:Gene Regulatory Networks; D017343:Genes, Plant / Q000235:genetics; D010935:Plant Diseases / Q000276:immunology / Q000382:microbiology*; D010937:Plant Growth Regulators / Q000378:metabolism; D012230:Rhizobiaceae / Q000502:physiology*; D015398:Signal Transduction / Q000235:genetics; D013997:Time Factors; D015854:Up-Regulation; D015032:Zinc / Q000378:metabolism
chemical_list: D010937:Plant Growth Regulators; D015032:Zinc