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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

Heatmaps of gene set enrichment analysis (GSEA) of DEGs based on RNAseq datain response to abiotic stresses.GO annotation from P. patens genome annotation (v1.6) was analyzedwith Blast2GO using the default parameters. The g:Profiler tool was used toclassify the GSEA of P. patens stressed-DEGs for each condition basedon up- and down-regulation status of the genes. (a) Selectedfunctional groups for up regulated genes. (b) Selected functionalgroups for down regulated genes. The color intensities indicate the level ofenrichment score of each GO term. Enrichments score is log10(gene number). See SupplementaryDatasets 15 and16 forthe complete lists.
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f3: Heatmaps of gene set enrichment analysis (GSEA) of DEGs based on RNAseq datain response to abiotic stresses.GO annotation from P. patens genome annotation (v1.6) was analyzedwith Blast2GO using the default parameters. The g:Profiler tool was used toclassify the GSEA of P. patens stressed-DEGs for each condition basedon up- and down-regulation status of the genes. (a) Selectedfunctional groups for up regulated genes. (b) Selected functionalgroups for down regulated genes. The color intensities indicate the level ofenrichment score of each GO term. Enrichments score is log10(gene number). See SupplementaryDatasets 15 and16 forthe complete lists.

Mentions: The g:Profiler tool24 was used to classify the gene set enrichmentanalyses (GSEA) of P. patens stressed-DEGs for each condition (ABA, cold,drought and salt) based on up and down regulated genes, and they werecategorized into 710 and 579 functional groups, respectively (Supplementary Datasets 15 and 16). Among these groups, the terms related tobiological process (GO:0008150), metabolic process (GO:0008152), cellularprocess (GO:0009987), biosynthetic process (GO:0009058), gene expression(GO:0010467), translation (GO:0006412) and response to stimulus (GO:0050896)were dominant in all stress treatments. Most of these groups showedstatistically significant differences in GSEA based on GO terms (biologicalprocess) for up and down regulated genes (Fig. 3a,b). Wedetected a high percentage of down regulated genes from functional groups ofsingle organism process (GO:0044699) in treatments of drought 0.5 hand cold 4.0 h, and high percentage of up regulated genes fromfunctional groups of cellular metabolic process (GO:0044237) in ABA4.0 h and cold 4.0 h treatments. Additionally, the upregulated genes from functional groups of signaling (GO:0023052) were present inABA, cold and drought but not in salt treatments; and RNA metabolic process(GO:0016070) functional group for down regulated genes was present only in4.0 h stress treatments. Interestingly, the functional group relatedto response to salt stress (GO:0009651) in down regulated genes was absent insalt 0.5 and 4 h (Fig. 3b). Furthermore, itwas observed that some functional groups are present for certain stresstreatments in up regulated genes yet were absent in the same treatments for downregulated ones and conversely. Notably, GSEA of DEGs was observed for differentfunctional groups involved in different pathways, which suggests that there areconsiderable differences between the physiological processes among P.patens stressed-DEGs.


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)

Heatmaps of gene set enrichment analysis (GSEA) of DEGs based on RNAseq datain response to abiotic stresses.GO annotation from P. patens genome annotation (v1.6) was analyzedwith Blast2GO using the default parameters. The g:Profiler tool was used toclassify the GSEA of P. patens stressed-DEGs for each condition basedon up- and down-regulation status of the genes. (a) Selectedfunctional groups for up regulated genes. (b) Selected functionalgroups for down regulated genes. The color intensities indicate the level ofenrichment score of each GO term. Enrichments score is log10(gene number). See SupplementaryDatasets 15 and16 forthe complete lists.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f3: Heatmaps of gene set enrichment analysis (GSEA) of DEGs based on RNAseq datain response to abiotic stresses.GO annotation from P. patens genome annotation (v1.6) was analyzedwith Blast2GO using the default parameters. The g:Profiler tool was used toclassify the GSEA of P. patens stressed-DEGs for each condition basedon up- and down-regulation status of the genes. (a) Selectedfunctional groups for up regulated genes. (b) Selected functionalgroups for down regulated genes. The color intensities indicate the level ofenrichment score of each GO term. Enrichments score is log10(gene number). See SupplementaryDatasets 15 and16 forthe complete lists.
Mentions: The g:Profiler tool24 was used to classify the gene set enrichmentanalyses (GSEA) of P. patens stressed-DEGs for each condition (ABA, cold,drought and salt) based on up and down regulated genes, and they werecategorized into 710 and 579 functional groups, respectively (Supplementary Datasets 15 and 16). Among these groups, the terms related tobiological process (GO:0008150), metabolic process (GO:0008152), cellularprocess (GO:0009987), biosynthetic process (GO:0009058), gene expression(GO:0010467), translation (GO:0006412) and response to stimulus (GO:0050896)were dominant in all stress treatments. Most of these groups showedstatistically significant differences in GSEA based on GO terms (biologicalprocess) for up and down regulated genes (Fig. 3a,b). Wedetected a high percentage of down regulated genes from functional groups ofsingle organism process (GO:0044699) in treatments of drought 0.5 hand cold 4.0 h, and high percentage of up regulated genes fromfunctional groups of cellular metabolic process (GO:0044237) in ABA4.0 h and cold 4.0 h treatments. Additionally, the upregulated genes from functional groups of signaling (GO:0023052) were present inABA, cold and drought but not in salt treatments; and RNA metabolic process(GO:0016070) functional group for down regulated genes was present only in4.0 h stress treatments. Interestingly, the functional group relatedto response to salt stress (GO:0009651) in down regulated genes was absent insalt 0.5 and 4 h (Fig. 3b). Furthermore, itwas observed that some functional groups are present for certain stresstreatments in up regulated genes yet were absent in the same treatments for downregulated ones and conversely. Notably, GSEA of DEGs was observed for differentfunctional groups involved in different pathways, which suggests that there areconsiderable differences between the physiological processes among P.patens stressed-DEGs.

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