nly at early stage, and thus they belong to the group of early stage specific genes. In this early stage specific group, the genes encoding components involved in cell wall metabolism and transcription are of particular interest. First, there are six Probesets that could poten tially represent the genes involved in cell wall biogenesis or property. Second, five Probe sets represent the transcription factors homologous to Arabidopsis ERF5, ATAF1 and ARR9. In addition, Cit. 16537. 1. S1 at represents a GCN5 related N acetyltransferase family protein, which might be involved in global transcriptional control through chromatin remodeling. This result implies that transcriptional control and cell wall property regulation are among the early events in citrus in response to the HLB bacterial attack.
In addition, 103 up regulated and 74 down regulated Probesets are specific to the late stage of Las infection. Interestingly, these Probesets repre sent some genes that belong to the categories of metabol ism of carbohydrate, nitrogen and lipids, hormone IAA metabolism, response to chemical stimulus, endomem brane systems and extracellular regions. In addition, while several genes involved in cell wall property regulation are up regulated, some genes encoding transcription factors and protein kinases are down regulated. The most striking feature is that only seven Probesets rep resent the very late stage specific genes. These include the genes that are most closely related to Arabidopsis C domain containing protein 71, a copper binding family protein, a trypsin and protease inhibitor family pro tein Kunitz family protein, a myosin heavy chain related protein, two basic chitinase and one unknown protein encoded by At1g42430.
The small number of genes belonging to this very late stage specific category is likely due to the various experi mental Brefeldin_A conditions because only 26 Probesets are commonly up or down regulated even in the four studies within the same very late stage of Las infec tion. Nevertheless, as this group of genes were identified from four studies specifically at the very late stage compared to only one study for early and late stages respectively, they could be more reliable than groups of early and late stage specific genes.
Construction and characterization of gene coexpression network for citrus response to HLB To provide a systems view of citrus host response to the HLB bacterial infection, the Pearson correlation coeffi cient method was used to infer the gene coexpression network using the four datasets reported in the four transcriptomic studies. A total of 10,668 Probesets, which are present in at least two chips of the transcriptomic stud ies with strong expression and or belong to the group of the HLB responsive genes, were used for network analysis. This number represents 35% of 30,173 Probesets in the citrus Gene Chip. Pcc was computed between each pair of these Probesets. A Pcc threshold of 0. 93 was selected, based on the overall consi