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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

Validation of P. patens gene expression patterns in response toabiotic stresses.Selected expression gene profiles were validated with quantitative real-timePCR (qPCR). (a) qPCR validation and expression analysis ofPp1s13_134V6.1 and Pp1s56_240V6.1, which they were used as reference genes.(b) qPCR validation and expression analysis of10 DEGs (up and down) under different stress conditions and theywere encode different functions. Blue bars indicate the expression level andLog2 (fold changes) obtained from qPCR for the threereplicates. Red lines indicate the expression level and Log2(fold change) from RNAseq data analyses. Error bars represent the standarderror of the mean.
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f5: Validation of P. patens gene expression patterns in response toabiotic stresses.Selected expression gene profiles were validated with quantitative real-timePCR (qPCR). (a) qPCR validation and expression analysis ofPp1s13_134V6.1 and Pp1s56_240V6.1, which they were used as reference genes.(b) qPCR validation and expression analysis of10 DEGs (up and down) under different stress conditions and theywere encode different functions. Blue bars indicate the expression level andLog2 (fold changes) obtained from qPCR for the threereplicates. Red lines indicate the expression level and Log2(fold change) from RNAseq data analyses. Error bars represent the standarderror of the mean.

Mentions: We further validated the accuracy and reproducibility of gene expression resultsthrough using quantitative real-time PCR (qPCR) as an orthogonal method of geneexpression analysis. The transcriptional levels of two reference genes and 10DEGs were independently analyzed by qPCR (Fig. 5). Basedon the RPKM results, the two genes (Pp1s13_134V6.1 and Pp1s56_240V6.1) areconstitutively expressed with no significant difference among all stresstreatments and control samples (Fig. 5a), and they encode3-hydroxyisobutyryl-coenzyme A and riboflavin kinase, respectively. The qPCRresults also showed the same expression patterns with no difference inexpression among the samples tested (Fig. 5a and Supplementary Fig. 4). Thus, thesetwo genes were considered endogenous controls (reference genes) for qPCR datanormalization. Additionally, we designed primer pairs to specifically detect thetranscript level of 10 DEGs (up- and down-regulated) that were encodingdifferent functions (Supplementary TableS5). The transcript levels of the 10 DEGs were obtained by the qPCRassays, normalized with the above reference genes and compared with RPKM-derivedread count using a Log2 Ratio calculation. Indeed, the transcriptlevels for the 10 selected genes were differentially regulated under stressconditions, and the expression patterns showed high degrees of concordancebetween qPCR assays and RNAseq analyzed data (Fig. 5b).Taken together, this independent qPCR evaluation confirms the reproducibilityand validity of our method for identifying RNAseq-derived expressionpatterns.


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)

Validation of P. patens gene expression patterns in response toabiotic stresses.Selected expression gene profiles were validated with quantitative real-timePCR (qPCR). (a) qPCR validation and expression analysis ofPp1s13_134V6.1 and Pp1s56_240V6.1, which they were used as reference genes.(b) qPCR validation and expression analysis of10 DEGs (up and down) under different stress conditions and theywere encode different functions. Blue bars indicate the expression level andLog2 (fold changes) obtained from qPCR for the threereplicates. Red lines indicate the expression level and Log2(fold change) from RNAseq data analyses. Error bars represent the standarderror of the mean.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f5: Validation of P. patens gene expression patterns in response toabiotic stresses.Selected expression gene profiles were validated with quantitative real-timePCR (qPCR). (a) qPCR validation and expression analysis ofPp1s13_134V6.1 and Pp1s56_240V6.1, which they were used as reference genes.(b) qPCR validation and expression analysis of10 DEGs (up and down) under different stress conditions and theywere encode different functions. Blue bars indicate the expression level andLog2 (fold changes) obtained from qPCR for the threereplicates. Red lines indicate the expression level and Log2(fold change) from RNAseq data analyses. Error bars represent the standarderror of the mean.
Mentions: We further validated the accuracy and reproducibility of gene expression resultsthrough using quantitative real-time PCR (qPCR) as an orthogonal method of geneexpression analysis. The transcriptional levels of two reference genes and 10DEGs were independently analyzed by qPCR (Fig. 5). Basedon the RPKM results, the two genes (Pp1s13_134V6.1 and Pp1s56_240V6.1) areconstitutively expressed with no significant difference among all stresstreatments and control samples (Fig. 5a), and they encode3-hydroxyisobutyryl-coenzyme A and riboflavin kinase, respectively. The qPCRresults also showed the same expression patterns with no difference inexpression among the samples tested (Fig. 5a and Supplementary Fig. 4). Thus, thesetwo genes were considered endogenous controls (reference genes) for qPCR datanormalization. Additionally, we designed primer pairs to specifically detect thetranscript level of 10 DEGs (up- and down-regulated) that were encodingdifferent functions (Supplementary TableS5). The transcript levels of the 10 DEGs were obtained by the qPCRassays, normalized with the above reference genes and compared with RPKM-derivedread count using a Log2 Ratio calculation. Indeed, the transcriptlevels for the 10 selected genes were differentially regulated under stressconditions, and the expression patterns showed high degrees of concordancebetween qPCR assays and RNAseq analyzed data (Fig. 5b).Taken together, this independent qPCR evaluation confirms the reproducibilityand validity of our method for identifying RNAseq-derived expressionpatterns.

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