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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

The early stress responses genes.Expression patterns of early ABA- and stress-responsive gene in P.patens, only genes with high fold change were considered.(a,b) Heatmaps comparison of gene expression among0.5 h stress treatments with high fold change. Columns representindividual treatments, and rows represent transcriptional units. (a)Up regulated genes (b) Down regulated genes. (c), Group ofearly stress-expressed genes, they are in the same manner at low and highexpression value.
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f4: The early stress responses genes.Expression patterns of early ABA- and stress-responsive gene in P.patens, only genes with high fold change were considered.(a,b) Heatmaps comparison of gene expression among0.5 h stress treatments with high fold change. Columns representindividual treatments, and rows represent transcriptional units. (a)Up regulated genes (b) Down regulated genes. (c), Group ofearly stress-expressed genes, they are in the same manner at low and highexpression value.

Mentions: To identify early genes strongly induced by stress treatments, we compared theRPKM-derived read count using a Log2 Ratio calculation to identifygenes representing a high fold change in stress samples as compared to thecontrol one at the 0.5 h time point. There were seven genes highlyup regulated across all stress conditions at 0.5 h with≥50 fold change (Fig. 4a). These highlyregulated early stress genes have distinct functions (Supplementary Table S2). For example,Pp1s370_29V6.1 encodes late embryogenesis abundant protein, LEA-3. The broadsubcellular distribution of LEA proteins highlights the need for each cellularcompartment to be provided with protective mechanisms to cope with desiccationor cold stress, and this gene might be involved in maturation and desiccationtolerance of seeds also25. The Arabidopsis homolog of thistranscript is involved in the salt stress pathway26. Pp1s43_3V6.1and Pp1s55_253V6.1 are members of the AP2/EREBP family of transcription factors;recognize the drought-responsive element (DRE) in target promoters27. All of these genes appear to be over represented in salt anddrought, where both of those treatments are clustered together, and lessrepresented in cold and ABA treatments, where there is another cluster for thosetreatments (Fig. 4a). There were also four genes highlydown regulated across all stress conditions at 0.5 h with a≥10 fold change (Fig. 4b) and they encodedifferent functions (Supplementary TableS3) such as beta-expansin 3 (Pp1s251_59V6.1), which has been shown torespond to water deficiency28, and another expansin transcript(Pp1s11_29V6.1), which is involved in plant-type cell wall organization andperhaps morphological adaptation.


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)

The early stress responses genes.Expression patterns of early ABA- and stress-responsive gene in P.patens, only genes with high fold change were considered.(a,b) Heatmaps comparison of gene expression among0.5 h stress treatments with high fold change. Columns representindividual treatments, and rows represent transcriptional units. (a)Up regulated genes (b) Down regulated genes. (c), Group ofearly stress-expressed genes, they are in the same manner at low and highexpression value.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f4: The early stress responses genes.Expression patterns of early ABA- and stress-responsive gene in P.patens, only genes with high fold change were considered.(a,b) Heatmaps comparison of gene expression among0.5 h stress treatments with high fold change. Columns representindividual treatments, and rows represent transcriptional units. (a)Up regulated genes (b) Down regulated genes. (c), Group ofearly stress-expressed genes, they are in the same manner at low and highexpression value.
Mentions: To identify early genes strongly induced by stress treatments, we compared theRPKM-derived read count using a Log2 Ratio calculation to identifygenes representing a high fold change in stress samples as compared to thecontrol one at the 0.5 h time point. There were seven genes highlyup regulated across all stress conditions at 0.5 h with≥50 fold change (Fig. 4a). These highlyregulated early stress genes have distinct functions (Supplementary Table S2). For example,Pp1s370_29V6.1 encodes late embryogenesis abundant protein, LEA-3. The broadsubcellular distribution of LEA proteins highlights the need for each cellularcompartment to be provided with protective mechanisms to cope with desiccationor cold stress, and this gene might be involved in maturation and desiccationtolerance of seeds also25. The Arabidopsis homolog of thistranscript is involved in the salt stress pathway26. Pp1s43_3V6.1and Pp1s55_253V6.1 are members of the AP2/EREBP family of transcription factors;recognize the drought-responsive element (DRE) in target promoters27. All of these genes appear to be over represented in salt anddrought, where both of those treatments are clustered together, and lessrepresented in cold and ABA treatments, where there is another cluster for thosetreatments (Fig. 4a). There were also four genes highlydown regulated across all stress conditions at 0.5 h with a≥10 fold change (Fig. 4b) and they encodedifferent functions (Supplementary TableS3) such as beta-expansin 3 (Pp1s251_59V6.1), which has been shown torespond to water deficiency28, and another expansin transcript(Pp1s11_29V6.1), which is involved in plant-type cell wall organization andperhaps morphological adaptation.

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