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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

Evolutionary dynamics and orphan transcripts of DEGs.(a) Venn diagram showing overlap of P. patens DEGs betweenC. reinhardtii, S. moellendorffii and A. thalianabased on BLAST-P analysis as well as the P. patens orphan DEGs.(b) Differentiating the GO enriched functional categories ofP. patens orphan DEGs with P. patens/C.reinhardtii, P. patens/S. moellendorffii, and P.patens/A. thaliana genes (green represents the orphans andblue represents the genes conserved with other model organisms). (c)Comparative analysis between GO enriched functional categories of P.patens/S. moellendorffii and P. patens/A.thaliana groups (green represents the P. patens/A.thaliana enriched functional groups and blue represents the P.patens/S. moellendorffii enriched functional groups, arrowsindicate the shared and connected GO enriched functional categories betweenthe two groups). (d) Comparative analysis between GO enrichedfunctional categories of P. patens/C. reinhardtii, and P.patens/S. moellendorffii groups (green represents the P.patens/S. moellendorffii enriched functional groups and bluerepresents the P. patens/C. reinhardtii enriched functionalgroups). (e) Comparative analysis between GO enriched functionalcategories of P. patens/C. reinhardtii, and P.patens/A. thaliana groups (green represents the P.patens/A. thaliana enriched functional groups and bluerepresents the P. patens/C. reinhardtii enriched functionalgroups). Cytoscape and Enrichment Map was used for visualization of the GSEAresults from BiNGO plug-in. Node size represent the number of genes in P.patens. The color varies based on the BiNGO p-valuesignificance. Edge size reflects the number of overlapping genes between thetwo connected gene-sets.
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f6: Evolutionary dynamics and orphan transcripts of DEGs.(a) Venn diagram showing overlap of P. patens DEGs betweenC. reinhardtii, S. moellendorffii and A. thalianabased on BLAST-P analysis as well as the P. patens orphan DEGs.(b) Differentiating the GO enriched functional categories ofP. patens orphan DEGs with P. patens/C.reinhardtii, P. patens/S. moellendorffii, and P.patens/A. thaliana genes (green represents the orphans andblue represents the genes conserved with other model organisms). (c)Comparative analysis between GO enriched functional categories of P.patens/S. moellendorffii and P. patens/A.thaliana groups (green represents the P. patens/A.thaliana enriched functional groups and blue represents the P.patens/S. moellendorffii enriched functional groups, arrowsindicate the shared and connected GO enriched functional categories betweenthe two groups). (d) Comparative analysis between GO enrichedfunctional categories of P. patens/C. reinhardtii, and P.patens/S. moellendorffii groups (green represents the P.patens/S. moellendorffii enriched functional groups and bluerepresents the P. patens/C. reinhardtii enriched functionalgroups). (e) Comparative analysis between GO enriched functionalcategories of P. patens/C. reinhardtii, and P.patens/A. thaliana groups (green represents the P.patens/A. thaliana enriched functional groups and bluerepresents the P. patens/C. reinhardtii enriched functionalgroups). Cytoscape and Enrichment Map was used for visualization of the GSEAresults from BiNGO plug-in. Node size represent the number of genes in P.patens. The color varies based on the BiNGO p-valuesignificance. Edge size reflects the number of overlapping genes between thetwo connected gene-sets.

Mentions: Given the phylogenetic position of P. patens, the specific adaptations tothe new environmental conditions required for the transition from aquatic toterrestrial life can be studied within this model plant1. Toinvestigate the evolutionary conservation of stress responses in land plants, weconducted a comparative analysis of stressed-DEGs between unicellular algae(C. reinhardtii), bryophytes (P. patens), lycophytes (S.moellendorffii) and angiosperms (A. thaliana) to uncover the corenetworks of processes that led to the diversity of responses observed amongextant plants. The resulting non-redundant 9,668 P. patens stressed-DEGs(Supplementary Dataset 6) weresubjected to BLAST-P analysis (Supplementary Dataset 17), and 512, 3,708 and 106 genes were sharedwith A. thaliana, S. moellendorffii, and C. reinhardtii,respectively. Additionally, 565 genes were predicted to be orphan genes (Fig. 6a, SupplementaryDatasets 18–20). Gene set enrichment analysis, inconjunction with ortholog analysis was used to identify enrichment,conservation, and rewiring of functional categories of the ortholog genesbetween P. patens and A. thaliana, S. moellendorffii andC. reinhardtii. The entire ortholog sets found between theaforementioned species were used to examine the functional categories. Weidentified the multiple GO enriched functional categories that were conserved orvaried between these model organisms (Fig.6b–e and Supplementary Datasets 22–25). We also compared the GOenriched categories of P. patens orphan genes with P. patens/C.reinhardtii, P. patens/S. moellendorffii, and P.patens/A. thaliana genes. Remarkably, we found that there is noshared GO enriched term in any functional group between the conserved and theorphan genes (Fig. 6b). A comparative analysis between GOenriched functional categories of P. patens/C. reinhardtii, P.patens/S. moellendorffii, and P. patens/A. thalianagenes indicated that the GO enriched genes for GMP (guanosine monophosphate)biosynthetic and GMP metabolic process among the P. patens/C.reinhardtii group are not connected with those from P.patens/S. moellendorffii, and P. patens/A. thaliana(Fig. 6d,e). On the other hand, the GO terms enrichedwith gene expression, translation and protein metabolic process are shared andconnected between P. patens/S. moellendorffii, and P.patens/A. thalina groups (Fig. 6b). Thecomparison of P. patens stress regulated genes with unicellular algae,vascular and flowering plants revealed genomic changes concomitant with theevolutionary movement to land, including a general gene family complexity andloss of genes associated with different functional groups.


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)

Evolutionary dynamics and orphan transcripts of DEGs.(a) Venn diagram showing overlap of P. patens DEGs betweenC. reinhardtii, S. moellendorffii and A. thalianabased on BLAST-P analysis as well as the P. patens orphan DEGs.(b) Differentiating the GO enriched functional categories ofP. patens orphan DEGs with P. patens/C.reinhardtii, P. patens/S. moellendorffii, and P.patens/A. thaliana genes (green represents the orphans andblue represents the genes conserved with other model organisms). (c)Comparative analysis between GO enriched functional categories of P.patens/S. moellendorffii and P. patens/A.thaliana groups (green represents the P. patens/A.thaliana enriched functional groups and blue represents the P.patens/S. moellendorffii enriched functional groups, arrowsindicate the shared and connected GO enriched functional categories betweenthe two groups). (d) Comparative analysis between GO enrichedfunctional categories of P. patens/C. reinhardtii, and P.patens/S. moellendorffii groups (green represents the P.patens/S. moellendorffii enriched functional groups and bluerepresents the P. patens/C. reinhardtii enriched functionalgroups). (e) Comparative analysis between GO enriched functionalcategories of P. patens/C. reinhardtii, and P.patens/A. thaliana groups (green represents the P.patens/A. thaliana enriched functional groups and bluerepresents the P. patens/C. reinhardtii enriched functionalgroups). Cytoscape and Enrichment Map was used for visualization of the GSEAresults from BiNGO plug-in. Node size represent the number of genes in P.patens. The color varies based on the BiNGO p-valuesignificance. Edge size reflects the number of overlapping genes between thetwo connected gene-sets.
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f6: Evolutionary dynamics and orphan transcripts of DEGs.(a) Venn diagram showing overlap of P. patens DEGs betweenC. reinhardtii, S. moellendorffii and A. thalianabased on BLAST-P analysis as well as the P. patens orphan DEGs.(b) Differentiating the GO enriched functional categories ofP. patens orphan DEGs with P. patens/C.reinhardtii, P. patens/S. moellendorffii, and P.patens/A. thaliana genes (green represents the orphans andblue represents the genes conserved with other model organisms). (c)Comparative analysis between GO enriched functional categories of P.patens/S. moellendorffii and P. patens/A.thaliana groups (green represents the P. patens/A.thaliana enriched functional groups and blue represents the P.patens/S. moellendorffii enriched functional groups, arrowsindicate the shared and connected GO enriched functional categories betweenthe two groups). (d) Comparative analysis between GO enrichedfunctional categories of P. patens/C. reinhardtii, and P.patens/S. moellendorffii groups (green represents the P.patens/S. moellendorffii enriched functional groups and bluerepresents the P. patens/C. reinhardtii enriched functionalgroups). (e) Comparative analysis between GO enriched functionalcategories of P. patens/C. reinhardtii, and P.patens/A. thaliana groups (green represents the P.patens/A. thaliana enriched functional groups and bluerepresents the P. patens/C. reinhardtii enriched functionalgroups). Cytoscape and Enrichment Map was used for visualization of the GSEAresults from BiNGO plug-in. Node size represent the number of genes in P.patens. The color varies based on the BiNGO p-valuesignificance. Edge size reflects the number of overlapping genes between thetwo connected gene-sets.
Mentions: Given the phylogenetic position of P. patens, the specific adaptations tothe new environmental conditions required for the transition from aquatic toterrestrial life can be studied within this model plant1. Toinvestigate the evolutionary conservation of stress responses in land plants, weconducted a comparative analysis of stressed-DEGs between unicellular algae(C. reinhardtii), bryophytes (P. patens), lycophytes (S.moellendorffii) and angiosperms (A. thaliana) to uncover the corenetworks of processes that led to the diversity of responses observed amongextant plants. The resulting non-redundant 9,668 P. patens stressed-DEGs(Supplementary Dataset 6) weresubjected to BLAST-P analysis (Supplementary Dataset 17), and 512, 3,708 and 106 genes were sharedwith A. thaliana, S. moellendorffii, and C. reinhardtii,respectively. Additionally, 565 genes were predicted to be orphan genes (Fig. 6a, SupplementaryDatasets 18–20). Gene set enrichment analysis, inconjunction with ortholog analysis was used to identify enrichment,conservation, and rewiring of functional categories of the ortholog genesbetween P. patens and A. thaliana, S. moellendorffii andC. reinhardtii. The entire ortholog sets found between theaforementioned species were used to examine the functional categories. Weidentified the multiple GO enriched functional categories that were conserved orvaried between these model organisms (Fig.6b–e and Supplementary Datasets 22–25). We also compared the GOenriched categories of P. patens orphan genes with P. patens/C.reinhardtii, P. patens/S. moellendorffii, and P.patens/A. thaliana genes. Remarkably, we found that there is noshared GO enriched term in any functional group between the conserved and theorphan genes (Fig. 6b). A comparative analysis between GOenriched functional categories of P. patens/C. reinhardtii, P.patens/S. moellendorffii, and P. patens/A. thalianagenes indicated that the GO enriched genes for GMP (guanosine monophosphate)biosynthetic and GMP metabolic process among the P. patens/C.reinhardtii group are not connected with those from P.patens/S. moellendorffii, and P. patens/A. thaliana(Fig. 6d,e). On the other hand, the GO terms enrichedwith gene expression, translation and protein metabolic process are shared andconnected between P. patens/S. moellendorffii, and P.patens/A. thalina groups (Fig. 6b). Thecomparison of P. patens stress regulated genes with unicellular algae,vascular and flowering plants revealed genomic changes concomitant with theevolutionary movement to land, including a general gene family complexity andloss of genes associated with different functional groups.

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