Limits...
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 genes were up-regulated in the highly resistant 895/highly active fungus group at the early stage.(A) The differentially expressed poplar genes between different time points in three groups. (B) The overlapping DEGs among the three groups.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4519268&req=5

pone.0134246.g003: More poplar genes were up-regulated in the highly resistant 895/highly active fungus group at the early stage.(A) The differentially expressed poplar genes between different time points in three groups. (B) The overlapping DEGs among the three groups.

Mentions: We adopted the same comparison patterns for the poplar transcriptome analysis as we did for the fungal analysis. In the 895/highly active group, 2,946 poplar genes displayed different levels of expression from 12 to 48 h (P<0.001 and ratio >2 or <0.5), and 4,712 genes did so from 12 to 96 h (Fig 3A). Unexpectedly, more genes were significantly differentially expressed in the 895/weakly active group (4,371 DEGs from 6 to 24 h; 8,064 DEGs from 6 to 72 h), and most were down-regulated. However, compared with the 895/weakly active group, more poplar genes were up-regulated in the 895/highly active group at the early stage (from 12 to 48 h), which reflects the host’s powerful response to pathogenic invasion. The overlapping genes (3,846) only constituted a small portion of these two groups, which might also suggest that different interaction mechanisms were triggered when a highly active or weakly active pathogen infected the plant (Fig 3B). The 214/highly active group only had two samples and 1,654 DEGs (48 vs. 96 h), most of which overlapped with the two other groups.


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 genes were up-regulated in the highly resistant 895/highly active fungus group at the early stage.(A) The differentially expressed poplar genes between different time points in three groups. (B) The overlapping DEGs among the three groups.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0134246.g003: More poplar genes were up-regulated in the highly resistant 895/highly active fungus group at the early stage.(A) The differentially expressed poplar genes between different time points in three groups. (B) The overlapping DEGs among the three groups.
Mentions: We adopted the same comparison patterns for the poplar transcriptome analysis as we did for the fungal analysis. In the 895/highly active group, 2,946 poplar genes displayed different levels of expression from 12 to 48 h (P<0.001 and ratio >2 or <0.5), and 4,712 genes did so from 12 to 96 h (Fig 3A). Unexpectedly, more genes were significantly differentially expressed in the 895/weakly active group (4,371 DEGs from 6 to 24 h; 8,064 DEGs from 6 to 72 h), and most were down-regulated. However, compared with the 895/weakly active group, more poplar genes were up-regulated in the 895/highly active group at the early stage (from 12 to 48 h), which reflects the host’s powerful response to pathogenic invasion. The overlapping genes (3,846) only constituted a small portion of these two groups, which might also suggest that different interaction mechanisms were triggered when a highly active or weakly active pathogen infected the plant (Fig 3B). The 214/highly active group only had two samples and 1,654 DEGs (48 vs. 96 h), most of which overlapped with the two other groups.

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