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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

The characteristics of 584 DEGs in dynamic transcriptome analysis suggested intense rivalry in the highly resistant 895/highly active fungus group.(A) The differentially expressed fungal genes between different time points in three groups. (B) The overlapping and specific DEGs among the three groups. The numbers in the brackets represent the number of DEGs belonging to the annotation.
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pone.0134246.g002: The characteristics of 584 DEGs in dynamic transcriptome analysis suggested intense rivalry in the highly resistant 895/highly active fungus group.(A) The differentially expressed fungal genes between different time points in three groups. (B) The overlapping and specific DEGs among the three groups. The numbers in the brackets represent the number of DEGs belonging to the annotation.

Mentions: In the 895/highly active group, 238 M. brunnea genes displayed different levels of expression from 12 to 48 h (P<0.01, ratio >2 or <0.5), and 326 genes did so from 12 to 96 h (Fig 2A). However, the number of DEGs in the 895/weakly active group decreased to 23 (from 6 to 24 h) and 32 (from 6 to 72 h). Furthermore, the 214/highly active group had only two samples and 28 DEGs (48 vs. 96 h), which was far less than the comparison between 48 and 96 h for the 895/highly active group. Lastly, in the dynamic transcriptome analysis, we obtained 584 fungal DEGs, most of which originated from the 895/highly active group, which might suggest an intense rivalry between highly resistant poplar leaves and highly active fungi.


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)

The characteristics of 584 DEGs in dynamic transcriptome analysis suggested intense rivalry in the highly resistant 895/highly active fungus group.(A) The differentially expressed fungal genes between different time points in three groups. (B) The overlapping and specific DEGs among the three groups. The numbers in the brackets represent the number of DEGs belonging to the annotation.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0134246.g002: The characteristics of 584 DEGs in dynamic transcriptome analysis suggested intense rivalry in the highly resistant 895/highly active fungus group.(A) The differentially expressed fungal genes between different time points in three groups. (B) The overlapping and specific DEGs among the three groups. The numbers in the brackets represent the number of DEGs belonging to the annotation.
Mentions: In the 895/highly active group, 238 M. brunnea genes displayed different levels of expression from 12 to 48 h (P<0.01, ratio >2 or <0.5), and 326 genes did so from 12 to 96 h (Fig 2A). However, the number of DEGs in the 895/weakly active group decreased to 23 (from 6 to 24 h) and 32 (from 6 to 72 h). Furthermore, the 214/highly active group had only two samples and 28 DEGs (48 vs. 96 h), which was far less than the comparison between 48 and 96 h for the 895/highly active group. Lastly, in the dynamic transcriptome analysis, we obtained 584 fungal DEGs, most of which originated from the 895/highly active group, which might suggest an intense rivalry between highly resistant poplar leaves and highly active fungi.

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