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

Chen C, Yao Y, Zhang L, Xu M, Jiang J, Dou T, Lin W, Zhao G, Huang M, Zhou Y - PLoS ONE (2015)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, People's Republic of China; Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, People's Republic of China; Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China.

ABSTRACT

Background: 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.

Results: Highly 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.

Conclusions: 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.

No MeSH data available.


Related in: MedlinePlus

More poplar DR genes were up-regulated in the highly resistant 895/highly active fungus group during infection (especially during the early stage).(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.
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pone.0134246.g004: More poplar DR genes were up-regulated in the highly resistant 895/highly active fungus group during infection (especially during the early stage).(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.

Mentions: We concentrated on the expression changes in disease-resistance (DR) genes, which include a variety of intracellular receptors that could induce effector-triggered immunity (ETI)[24]. Of the 41,335 predicted genes in Populus, 761 were defined as DR genes. Fig 4 demonstrates the alterations in DR gene expression of all three groups. The number of significantly differentially expressed disease-resistance genes (DE-DR genes) was greater in the 895/weakly active group than that in the 895/highly active and 214/highly active groups, but most of these DR genes (95%) were down-regulated in the 895/weakly active group. Conversely, in the 895/highly active group, the gene expression levels of half of the DE-DR genes increased from the early to late stage. In particular, from 12 to 48 h, the up-regulated DE-DR genes far exceeded the down-regulated genes (Fig 4A). When suffering from infection caused by highly active fungi, more DR genes might be activated (up-regulated) to induce the immune response in highly resistant 895 clones. However, weakly active fungi might be unable to trigger many immune responses due to their different influence on the host. The 214/highly active group only had 15 DE-DR genes (48 vs. 96 h), and most overlapped with other two groups. Otherwise, the 895/weakly active group only shared 34% of DE-DR genes with the 895/highly active group (Fig 4B). Of the 761 DR genes, only 214 showed significant expression changes during the entire infection. We found that, of the DR genes, the DE-DR genes mainly originated from NB-ARC domain-containing disease-resistance proteins and TIR-NBS-LRR class family disease-resistance proteins (S2 Table).


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

Chen C, Yao Y, Zhang L, Xu M, Jiang J, Dou T, Lin W, Zhao G, Huang M, Zhou Y - PLoS ONE (2015)

More poplar DR genes were up-regulated in the highly resistant 895/highly active fungus group during infection (especially during the early stage).(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.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4519268&req=5

pone.0134246.g004: More poplar DR genes were up-regulated in the highly resistant 895/highly active fungus group during infection (especially during the early stage).(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.
Mentions: We concentrated on the expression changes in disease-resistance (DR) genes, which include a variety of intracellular receptors that could induce effector-triggered immunity (ETI)[24]. Of the 41,335 predicted genes in Populus, 761 were defined as DR genes. Fig 4 demonstrates the alterations in DR gene expression of all three groups. The number of significantly differentially expressed disease-resistance genes (DE-DR genes) was greater in the 895/weakly active group than that in the 895/highly active and 214/highly active groups, but most of these DR genes (95%) were down-regulated in the 895/weakly active group. Conversely, in the 895/highly active group, the gene expression levels of half of the DE-DR genes increased from the early to late stage. In particular, from 12 to 48 h, the up-regulated DE-DR genes far exceeded the down-regulated genes (Fig 4A). When suffering from infection caused by highly active fungi, more DR genes might be activated (up-regulated) to induce the immune response in highly resistant 895 clones. However, weakly active fungi might be unable to trigger many immune responses due to their different influence on the host. The 214/highly active group only had 15 DE-DR genes (48 vs. 96 h), and most overlapped with other two groups. Otherwise, the 895/weakly active group only shared 34% of DE-DR genes with the 895/highly active group (Fig 4B). Of the 761 DR genes, only 214 showed significant expression changes during the entire infection. We found that, of the DR genes, the DE-DR genes mainly originated from NB-ARC domain-containing disease-resistance proteins and TIR-NBS-LRR class family disease-resistance proteins (S2 Table).

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, People's Republic of China; Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, People's Republic of China; Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China.

ABSTRACT

Background: 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.

Results: Highly 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.

Conclusions: 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.

No MeSH data available.


Related in: MedlinePlus