More poplar DR genes were up-regulated in the highly resistant 895/highly active fungus group during infection (especially during the early stage).

<p>(A) The differentially expressed poplar disease-resistant genes between different time points in three groups. (B) The overlapping DE-DR genes among the three groups.</p

A Comprehensive Analysis of the Transcriptomes of <i>Marssonina brunnea</i> and Infected Poplar Leaves to Capture Vital Events in Host-Pathogen Interactions

<div><p>Background</p><p>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.</p><p>Results</p><p>Highly resistant NL895 poplar leaves and weakly resistant NL214 leaves were infected with highly active and weakly active <i>Marssonina brunnea</i>, 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.</p><p>Conclusions</p><p>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.</p></div

The independent network inferred from the top 1000 fungus-poplar relationships.

<p>Individual genes simultaneously connected with many other genes were sequentially marked as 1, 2, 3, 4, 5, and 6. Mark 1 represents a fungal metalloprotease gene that was surrounded by 10 poplar genes, including 2 DR genes; mark 2 is a poplar DR gene that is connected to 16 fungal genes. Marks 3 and 5 are the poplar genes secretory carrier 3 and NAD(P)-binding Rossmann-fold superfamily protein, respectively; marks 4 and 6 are poplar genes with unknown functions. The three arrows denote the position of 3 DR genes. The fungal genes are shown in red, and the poplar genes are shown in blue.</p

Principal component analysis (PCA) of poplar genes during infection.

<p>The graph illustrates the distribution of each sample in the space of the first two principal components (PCs). The samples infected with weakly active fungi are clustered together, whereas the distribution of the highly active group is relatively scattered.</p