title: Genome-wide expression analysis offers new insights into the origin and evolution of Physcomitrella patens stress response.
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.
authors.affiliation: Laboratory of Algal, Systems, and Synthetic Biology, Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE.|Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE.|Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, KSA.
authors.forename: Basel
authors.initials: B
authors.lastname: Khraiwesh
authors.affiliation: Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE.|Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, KSA.
authors.forename: Enas
authors.initials: E
authors.lastname: Qudeimat
authors.affiliation: Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, KSA.
authors.forename: Manjula
authors.initials: M
authors.lastname: Thimma
authors.affiliation: Laboratory of Algal, Systems, and Synthetic Biology, Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE.
authors.forename: Amphun
authors.initials: A
authors.lastname: Chaiboonchoe
authors.affiliation: Laboratory of Algal, Systems, and Synthetic Biology, Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE.
authors.forename: Kenan
authors.initials: K
authors.lastname: Jijakli
authors.affiliation: Laboratory of Algal, Systems, and Synthetic Biology, Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE.
authors.forename: Amnah
authors.initials: A
authors.lastname: Alzahmi
authors.affiliation: Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE.
authors.forename: Marc
authors.initials: M
authors.lastname: Arnoux
authors.affiliation: Laboratory of Algal, Systems, and Synthetic Biology, Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE.|Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE.
authors.forename: Kourosh
authors.initials: K
authors.lastname: Salehi-Ashtiani
mesh_terms: D000040:Abscisic Acid / Q000494:pharmacology; D005075:Biological Evolution; D019068:Bryopsida / Q000235:genetics*; D002874:Chromosome Mapping; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant / Q000187:drug effects; D063990:Gene Ontology; D018745:Genome, Plant; D055106:Genome-Wide Association Study; D015203:Reproducibility of Results; D013312:Stress, Physiological / Q000235:genetics*; D059467:Transcriptome
chemical_list: D000040:Abscisic Acid