Abstract
BackgroundUnderstanding 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.ResultsHighly 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.ConclusionsWe 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.
Highlights
Host-pathogen interactions and co-evolution often involve complicated invasion and defense mechanisms and may exhibit a sophisticated network at the molecular level [1,2]
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
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
Summary
Host-pathogen interactions and co-evolution often involve complicated invasion and defense mechanisms and may exhibit a sophisticated network at the molecular level [1,2]. Understanding these underlying interaction networks helps to elucidate the entire infection process and focus on certain vital events, which is a promising approach for improvement of disease control and selection of treatment strategy [3]. 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. We introduce an efficient method using independence test to infer an independent network that is exclusively concerned with the frequency of gene expression changes
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