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Transcriptome comparison and gene coexpression network analysis provide a systems view of citrus response to 'Candidatus Liberibacter asiaticus' infection - PubMed

  • ️Tue Jan 01 2013

Transcriptome comparison and gene coexpression network analysis provide a systems view of citrus response to 'Candidatus Liberibacter asiaticus' infection

Zhi-Liang Zheng et al. BMC Genomics. 2013.

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.

Conclusion: 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.

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Figures

Figure 1
Figure 1

HLB response network. The citrus HLB response network is displayed using Cytoscape. A white circle represents a node (Probeset), and a black edge connecting the two nodes indicates an interaction (coexpression) with a Pcc value of > =0.93. Six categories of major biological processes are color-coded.

Figure 2
Figure 2

Summary of the network characteristics. The distribution of number of nodes (Probesets) in different ranges of edge numbers (1; 2; 3–10; 11–50, 51–100; 101–150; 151–200; 201–250; 251–300; and 300–369) in the HLB response network is presented.

Figure 3
Figure 3

HLB disease response subnetwork. (A) The HLB defense subnetwork is displayed with three categories of major biological processes highlighted by different colors. (B) The close-up of the box in the subnetwork shown in Figure 3A.

Figure 4
Figure 4

HLB hormore subnetwork. The HLB hormone response subnetwork is displayed, with six hormone response groups coded with distinct colors.

Figure 5
Figure 5

SA response subnetwor. The SA hormone response subnetwork is displayed. Nine large hubs are labeled with Probeset ID.

Figure 6
Figure 6

A subset of SA response subnetwork. A subset of the SA hormone response subnetwork with four large hubs is displayed.

Figure 7
Figure 7

Early stage HLB response subnetwork. The HLB early response subnetwork is displayed. Nodes belonging to five categories of major biological processes are coded with distinct colors. The arrows indicate the two nodes (Probesets) that are discussed in the text.

Figure 8
Figure 8

Early stage HLB response subnetworks based on two representative genes. Two gene-specific subnetworks are displayed with all Probesets labeled. (A) A subset of early stage HLB response subnetwork centered on the hub Cit.29252.1.S1_s_at. Because many second degree interactions exist for most of the first degree nodes connecting to Cit.29252.1.S1_s_at, only the first degree interaction-based subnetwork is presented. (B) The NAC096 transcription factor subnetwork is displayed.

Figure 9
Figure 9

HLB response core subnetwork. The HLB response core subnetwork is constructed using the 21 commonly up-regulated Probesets (see Table 2) as the seed nodes (highlighted in red). First degree interactions are shown. Green nodes indicate “transport”, yellow nodes represent “hormone response”, and blue nodes indicate “carbohydrate metabolic process”. Nodes overlapped in the categories of “transport” and “hormone response” exhibit a mixed color of green and yellow.

Figure 10
Figure 10

Phloem protein (PP2) subnetwork. The subnetworks for the PP2, based on first (A) and second (B) degree neighbors of Cit.35955.1.S1_at. Six of the Probesets belonging to the second degree interactions (B) are labeled with yellow.

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