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Genome-wide expression analysis offers new insights into the origin and evolution of Physcomitrella patens stress response.

Khraiwesh B, Qudeimat E, Thimma M, Chaiboonchoe A, Jijakli K, Alzahmi A, Arnoux M, Salehi-Ashtiani K - Sci Rep (2015)

Bottom Line: Changes in the environment, such as those caused by climate change, can exert stress on plant growth, diversity and ultimately global food security.Thus, focused efforts to fully understand plant response to stress are urgently needed in order to develop strategies to cope with the effects of climate change.We identified more than 20,000 genes expressed under each aforementioned stress treatments, of which 9,668 display differential expression in response to stress.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Algal, Systems, and Synthetic Biology, Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE.

ABSTRACT
Changes in the environment, such as those caused by climate change, can exert stress on plant growth, diversity and ultimately global food security. Thus, focused efforts to fully understand plant response to stress are urgently needed in order to develop strategies to cope with the effects of climate change. Because Physcomitrella patens holds a key evolutionary position bridging the gap between green algae and higher plants, and because it exhibits a well-developed stress tolerance, it is an excellent model for such exploration. Here, we have used Physcomitrella patens to study genome-wide responses to abiotic stress through transcriptomic analysis by a high-throughput sequencing platform. We report a comprehensive analysis of transcriptome dynamics, defining profiles of elicited gene regulation responses to abiotic stress-associated hormone Abscisic Acid (ABA), cold, drought, and salt treatments. We identified more than 20,000 genes expressed under each aforementioned stress treatments, of which 9,668 display differential expression in response to stress. The comparison of Physcomitrella patens stress regulated genes with unicellular algae, vascular and flowering plants revealed genomic delineation concomitant with the evolutionary movement to land, including a general gene family complexity and loss of genes associated with different functional groups.

No MeSH data available.


Related in: MedlinePlus

A network of GO categories combined with representative heatmaps for P.patens orphan stressed-DEGs.BiNGO, a cytoscape plugin was used to visualize the GO terms that werestatistically (hypergeometric test) over-represented from the P.patens orphan DEGs. Representative heatmaps clustering analysis ofgene expression based on RPKM log2 ratio. The color scale (fromwhite, yellow to dark orange) is based on (corrected) p-value (5%FDR, p = 0.05). Dark orange categories are mostsignificantly overrepresented, white nodes are not significantlyoverrepresented (NA); they are included to show other nodes in the contextof the GO hierarchy. The area of a node is proportional to the number ofgenes in the test set annotated to the corresponding GO category. Theheatmaps were generated using the R gplots package. The RPKMs were used asinput for the hierarchical clustering using Euclidean measure to obtaindistance matrix, complete agglomeration and dendograms. The color scale(from white, red to green) is based on log2 fold change. Greenrepresents the up-regulated genes; red represent the down-regulated onesamong the different stress treatments. White color indicated no geneexpression in certain stress treatment (NA), A: ABA, C: cold: D: drought, S:salt.
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f7: A network of GO categories combined with representative heatmaps for P.patens orphan stressed-DEGs.BiNGO, a cytoscape plugin was used to visualize the GO terms that werestatistically (hypergeometric test) over-represented from the P.patens orphan DEGs. Representative heatmaps clustering analysis ofgene expression based on RPKM log2 ratio. The color scale (fromwhite, yellow to dark orange) is based on (corrected) p-value (5%FDR, p = 0.05). Dark orange categories are mostsignificantly overrepresented, white nodes are not significantlyoverrepresented (NA); they are included to show other nodes in the contextof the GO hierarchy. The area of a node is proportional to the number ofgenes in the test set annotated to the corresponding GO category. Theheatmaps were generated using the R gplots package. The RPKMs were used asinput for the hierarchical clustering using Euclidean measure to obtaindistance matrix, complete agglomeration and dendograms. The color scale(from white, red to green) is based on log2 fold change. Greenrepresents the up-regulated genes; red represent the down-regulated onesamong the different stress treatments. White color indicated no geneexpression in certain stress treatment (NA), A: ABA, C: cold: D: drought, S:salt.

Mentions: Over-representation of GO terms combined with differentially regulated orphangenes across all the stress treatments were determined by using the BiologicalNetworks Gene Ontology tool (BiNGO). These were categorized into 82 functionalgroups (Supplementary Dataset 22).Most of these groups showed statistically significant GO representation (Fig. 7 and Supplementary Fig. S5). Among these groups, the terms of response tocold (GO:0009409), response to abiotic stimulus (GO:0009628), response totemperature stimulus (GO:0009266) and response to stimulus (GO:0050896) showedsignificant over-representation based on the obtained P-values (Supplementary Fig. S5). Notably,over-representation of GO terms in P. patens orphan stressed-DEGs wasobserved for different functional groups involved in different morphological,physiological and metabolic pathways. This suggests that there are considerabledifferences between the physiological processes among these genes.


Genome-wide expression analysis offers new insights into the origin and evolution of Physcomitrella patens stress response.

Khraiwesh B, Qudeimat E, Thimma M, Chaiboonchoe A, Jijakli K, Alzahmi A, Arnoux M, Salehi-Ashtiani K - Sci Rep (2015)

A network of GO categories combined with representative heatmaps for P.patens orphan stressed-DEGs.BiNGO, a cytoscape plugin was used to visualize the GO terms that werestatistically (hypergeometric test) over-represented from the P.patens orphan DEGs. Representative heatmaps clustering analysis ofgene expression based on RPKM log2 ratio. The color scale (fromwhite, yellow to dark orange) is based on (corrected) p-value (5%FDR, p = 0.05). Dark orange categories are mostsignificantly overrepresented, white nodes are not significantlyoverrepresented (NA); they are included to show other nodes in the contextof the GO hierarchy. The area of a node is proportional to the number ofgenes in the test set annotated to the corresponding GO category. Theheatmaps were generated using the R gplots package. The RPKMs were used asinput for the hierarchical clustering using Euclidean measure to obtaindistance matrix, complete agglomeration and dendograms. The color scale(from white, red to green) is based on log2 fold change. Greenrepresents the up-regulated genes; red represent the down-regulated onesamong the different stress treatments. White color indicated no geneexpression in certain stress treatment (NA), A: ABA, C: cold: D: drought, S:salt.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4663497&req=5

f7: A network of GO categories combined with representative heatmaps for P.patens orphan stressed-DEGs.BiNGO, a cytoscape plugin was used to visualize the GO terms that werestatistically (hypergeometric test) over-represented from the P.patens orphan DEGs. Representative heatmaps clustering analysis ofgene expression based on RPKM log2 ratio. The color scale (fromwhite, yellow to dark orange) is based on (corrected) p-value (5%FDR, p = 0.05). Dark orange categories are mostsignificantly overrepresented, white nodes are not significantlyoverrepresented (NA); they are included to show other nodes in the contextof the GO hierarchy. The area of a node is proportional to the number ofgenes in the test set annotated to the corresponding GO category. Theheatmaps were generated using the R gplots package. The RPKMs were used asinput for the hierarchical clustering using Euclidean measure to obtaindistance matrix, complete agglomeration and dendograms. The color scale(from white, red to green) is based on log2 fold change. Greenrepresents the up-regulated genes; red represent the down-regulated onesamong the different stress treatments. White color indicated no geneexpression in certain stress treatment (NA), A: ABA, C: cold: D: drought, S:salt.
Mentions: Over-representation of GO terms combined with differentially regulated orphangenes across all the stress treatments were determined by using the BiologicalNetworks Gene Ontology tool (BiNGO). These were categorized into 82 functionalgroups (Supplementary Dataset 22).Most of these groups showed statistically significant GO representation (Fig. 7 and Supplementary Fig. S5). Among these groups, the terms of response tocold (GO:0009409), response to abiotic stimulus (GO:0009628), response totemperature stimulus (GO:0009266) and response to stimulus (GO:0050896) showedsignificant over-representation based on the obtained P-values (Supplementary Fig. S5). Notably,over-representation of GO terms in P. patens orphan stressed-DEGs wasobserved for different functional groups involved in different morphological,physiological and metabolic pathways. This suggests that there are considerabledifferences between the physiological processes among these genes.

Bottom Line: Changes in the environment, such as those caused by climate change, can exert stress on plant growth, diversity and ultimately global food security.Thus, focused efforts to fully understand plant response to stress are urgently needed in order to develop strategies to cope with the effects of climate change.We identified more than 20,000 genes expressed under each aforementioned stress treatments, of which 9,668 display differential expression in response to stress.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Algal, Systems, and Synthetic Biology, Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE.

ABSTRACT
Changes in the environment, such as those caused by climate change, can exert stress on plant growth, diversity and ultimately global food security. Thus, focused efforts to fully understand plant response to stress are urgently needed in order to develop strategies to cope with the effects of climate change. Because Physcomitrella patens holds a key evolutionary position bridging the gap between green algae and higher plants, and because it exhibits a well-developed stress tolerance, it is an excellent model for such exploration. Here, we have used Physcomitrella patens to study genome-wide responses to abiotic stress through transcriptomic analysis by a high-throughput sequencing platform. We report a comprehensive analysis of transcriptome dynamics, defining profiles of elicited gene regulation responses to abiotic stress-associated hormone Abscisic Acid (ABA), cold, drought, and salt treatments. We identified more than 20,000 genes expressed under each aforementioned stress treatments, of which 9,668 display differential expression in response to stress. The comparison of Physcomitrella patens stress regulated genes with unicellular algae, vascular and flowering plants revealed genomic delineation concomitant with the evolutionary movement to land, including a general gene family complexity and loss of genes associated with different functional groups.

No MeSH data available.


Related in: MedlinePlus