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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

Global analysis of P. patens genes expression in response to abioticstresses.A comparison of commonly and uniquely expressed genes across the treatmentswas done using the obtained RPKM values. The comparison was done for controlversus all stress treatments including the indicated two time points.(a) Venn diagrams showing overlap of expressed genes relative tocontrol among different subgroups of P. patens abiotic stresstreatments. (b) Hierarchical clustering analysis and heatmap of geneexpression based on log2 ratio RPKM data across abiotic stresstreatments and the control sample. Red color represents lower expression,green color represents higher expression (the expression range from−5.644 to 12.889). The heatmap is based on the distance function1, correlation between each test statistic of the expression of each gene,columns represent individual experiments, and rows represent transcriptionalunits. The dendrogram at the top indicates clusters of individualtreatments.
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f1: Global analysis of P. patens genes expression in response to abioticstresses.A comparison of commonly and uniquely expressed genes across the treatmentswas done using the obtained RPKM values. The comparison was done for controlversus all stress treatments including the indicated two time points.(a) Venn diagrams showing overlap of expressed genes relative tocontrol among different subgroups of P. patens abiotic stresstreatments. (b) Hierarchical clustering analysis and heatmap of geneexpression based on log2 ratio RPKM data across abiotic stresstreatments and the control sample. Red color represents lower expression,green color represents higher expression (the expression range from−5.644 to 12.889). The heatmap is based on the distance function1, correlation between each test statistic of the expression of each gene,columns represent individual experiments, and rows represent transcriptionalunits. The dendrogram at the top indicates clusters of individualtreatments.

Mentions: One of the primary goals of RNA sequencing is to compare gene expression levelsbetween samples. RNAseq data were processed to calculate RPKM values, anormalized measure of read density that allows transcript levels to be comparedboth within and between samples. A total of 23,971 genes were detected in thesamples. Their expression in the four abiotic stress treatments with selectedtime points (0.5 and 4.0 h) are summarized in Fig.1a. Venn diagrams show the distribution of expressed genes fromabiotic stress treatments (ABA, cold, drought and salt) with selected timepoints (0.5 and 4.0 h) compared to the control sample (Fig. 1a, SupplementaryDatasets 1–4). Among these genes, the number ofstress-specifically expressed genes was 531 (ABA 0.5 h), 384 (ABA4.0 h), 273 (ABA 0.5/4.0 h), 499 (cold0.5 h), 487 (cold 4.0 h), 468 (cold0.5/4.0 h), 448 (drought 0.5 h), 381 (drought4.0 h), 362 (drought 0.5/4.0 h), 662 (salt0.5 h), 401 (salt 4.0 h), and 435 (salt0.5/4.0 h). Although there were 17,381 genes expressed among allstress treatments and control sample, many of them were quantitatively regulated(Fig. 1b, Supplementary Dataset 5); while some of these genes had littlevariation across abiotic stress treatments, suggesting they fulfill housekeepingfunctions.


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)

Global analysis of P. patens genes expression in response to abioticstresses.A comparison of commonly and uniquely expressed genes across the treatmentswas done using the obtained RPKM values. The comparison was done for controlversus all stress treatments including the indicated two time points.(a) Venn diagrams showing overlap of expressed genes relative tocontrol among different subgroups of P. patens abiotic stresstreatments. (b) Hierarchical clustering analysis and heatmap of geneexpression based on log2 ratio RPKM data across abiotic stresstreatments and the control sample. Red color represents lower expression,green color represents higher expression (the expression range from−5.644 to 12.889). The heatmap is based on the distance function1, correlation between each test statistic of the expression of each gene,columns represent individual experiments, and rows represent transcriptionalunits. The dendrogram at the top indicates clusters of individualtreatments.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f1: Global analysis of P. patens genes expression in response to abioticstresses.A comparison of commonly and uniquely expressed genes across the treatmentswas done using the obtained RPKM values. The comparison was done for controlversus all stress treatments including the indicated two time points.(a) Venn diagrams showing overlap of expressed genes relative tocontrol among different subgroups of P. patens abiotic stresstreatments. (b) Hierarchical clustering analysis and heatmap of geneexpression based on log2 ratio RPKM data across abiotic stresstreatments and the control sample. Red color represents lower expression,green color represents higher expression (the expression range from−5.644 to 12.889). The heatmap is based on the distance function1, correlation between each test statistic of the expression of each gene,columns represent individual experiments, and rows represent transcriptionalunits. The dendrogram at the top indicates clusters of individualtreatments.
Mentions: One of the primary goals of RNA sequencing is to compare gene expression levelsbetween samples. RNAseq data were processed to calculate RPKM values, anormalized measure of read density that allows transcript levels to be comparedboth within and between samples. A total of 23,971 genes were detected in thesamples. Their expression in the four abiotic stress treatments with selectedtime points (0.5 and 4.0 h) are summarized in Fig.1a. Venn diagrams show the distribution of expressed genes fromabiotic stress treatments (ABA, cold, drought and salt) with selected timepoints (0.5 and 4.0 h) compared to the control sample (Fig. 1a, SupplementaryDatasets 1–4). Among these genes, the number ofstress-specifically expressed genes was 531 (ABA 0.5 h), 384 (ABA4.0 h), 273 (ABA 0.5/4.0 h), 499 (cold0.5 h), 487 (cold 4.0 h), 468 (cold0.5/4.0 h), 448 (drought 0.5 h), 381 (drought4.0 h), 362 (drought 0.5/4.0 h), 662 (salt0.5 h), 401 (salt 4.0 h), and 435 (salt0.5/4.0 h). Although there were 17,381 genes expressed among allstress treatments and control sample, many of them were quantitatively regulated(Fig. 1b, Supplementary Dataset 5); while some of these genes had littlevariation across abiotic stress treatments, suggesting they fulfill housekeepingfunctions.

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