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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

Differential expression of P. patens genes in response to abioticstresses.Differentially Expressed Genes (DEGs) were identified relative to the controlsample grown under standard conditions. The differences in gene expressionamong the abiotic stress treatments and the control sample were obtainedbased on the RPKM-derived read count using a Log2 Ratiocalculation. (a) Number of up regulated (green bars) and downregulated (orange bars) genes are shown for each stress treatment at thetime point in hours. (b) Venn diagram showing overlap of DEGs amongthe two time points (0.5 and 4.0 h). (c) Venn diagramsshowing overlap of DEGs in response to the four assayed abiotic stresses attwo time points (0.5 and 4.0 h). Upper diagrams indicate upregulated genes and lower ones indicate down regulated genes. The numbers ofgenes in each region of the diagrams are indicated. The Venn diagrams depictthe overlaps between each pairwise comparison.
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f2: Differential expression of P. patens genes in response to abioticstresses.Differentially Expressed Genes (DEGs) were identified relative to the controlsample grown under standard conditions. The differences in gene expressionamong the abiotic stress treatments and the control sample were obtainedbased on the RPKM-derived read count using a Log2 Ratiocalculation. (a) Number of up regulated (green bars) and downregulated (orange bars) genes are shown for each stress treatment at thetime point in hours. (b) Venn diagram showing overlap of DEGs amongthe two time points (0.5 and 4.0 h). (c) Venn diagramsshowing overlap of DEGs in response to the four assayed abiotic stresses attwo time points (0.5 and 4.0 h). Upper diagrams indicate upregulated genes and lower ones indicate down regulated genes. The numbers ofgenes in each region of the diagrams are indicated. The Venn diagrams depictthe overlaps between each pairwise comparison.

Mentions: Differentially Expressed Genes (DEGs) were identified relative to the controlsample grown under standard conditions (see Methods). To obtain significantdifferences in gene expression among the abiotic stress treatments and thecontrol sample, we compared the RPKM-derived read count using a Log2Ratio calculation (a log ratio of 1 represents a 2-fold change). There wereabout 17,381 genes that were expressed across all stress conditions with RPKMvalues above zero. To minimize false positives, we set a relatively conservativethreshold of an RPKM value ≥10. The results indicated that a set of7,921 (ABA 0.5 h), 9,426 (ABA 4.0 h), 8,524 (cold0.5 h), 8,084 (cold 4.0 h), 7,285 (drought0.5 h), 7,791 (drought 4.0 h), 7,605 (salt0.5 h), 8,407 (salt 4.0 h) and 9,668 genes across allstress treatments without any redundancy were DEGs above RPKM 10 (Fig. 2a, Supplementary Dataset6).


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)

Differential expression of P. patens genes in response to abioticstresses.Differentially Expressed Genes (DEGs) were identified relative to the controlsample grown under standard conditions. The differences in gene expressionamong the abiotic stress treatments and the control sample were obtainedbased on the RPKM-derived read count using a Log2 Ratiocalculation. (a) Number of up regulated (green bars) and downregulated (orange bars) genes are shown for each stress treatment at thetime point in hours. (b) Venn diagram showing overlap of DEGs amongthe two time points (0.5 and 4.0 h). (c) Venn diagramsshowing overlap of DEGs in response to the four assayed abiotic stresses attwo time points (0.5 and 4.0 h). Upper diagrams indicate upregulated genes and lower ones indicate down regulated genes. The numbers ofgenes in each region of the diagrams are indicated. The Venn diagrams depictthe overlaps between each pairwise comparison.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f2: Differential expression of P. patens genes in response to abioticstresses.Differentially Expressed Genes (DEGs) were identified relative to the controlsample grown under standard conditions. The differences in gene expressionamong the abiotic stress treatments and the control sample were obtainedbased on the RPKM-derived read count using a Log2 Ratiocalculation. (a) Number of up regulated (green bars) and downregulated (orange bars) genes are shown for each stress treatment at thetime point in hours. (b) Venn diagram showing overlap of DEGs amongthe two time points (0.5 and 4.0 h). (c) Venn diagramsshowing overlap of DEGs in response to the four assayed abiotic stresses attwo time points (0.5 and 4.0 h). Upper diagrams indicate upregulated genes and lower ones indicate down regulated genes. The numbers ofgenes in each region of the diagrams are indicated. The Venn diagrams depictthe overlaps between each pairwise comparison.
Mentions: Differentially Expressed Genes (DEGs) were identified relative to the controlsample grown under standard conditions (see Methods). To obtain significantdifferences in gene expression among the abiotic stress treatments and thecontrol sample, we compared the RPKM-derived read count using a Log2Ratio calculation (a log ratio of 1 represents a 2-fold change). There wereabout 17,381 genes that were expressed across all stress conditions with RPKMvalues above zero. To minimize false positives, we set a relatively conservativethreshold of an RPKM value ≥10. The results indicated that a set of7,921 (ABA 0.5 h), 9,426 (ABA 4.0 h), 8,524 (cold0.5 h), 8,084 (cold 4.0 h), 7,285 (drought0.5 h), 7,791 (drought 4.0 h), 7,605 (salt0.5 h), 8,407 (salt 4.0 h) and 9,668 genes across allstress treatments without any redundancy were DEGs above RPKM 10 (Fig. 2a, Supplementary Dataset6).

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