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.

Metatranscriptomic and metabolite profiling reveals vertical heterogeneity within a Zygnema green algal mat from Svalbard (High Arctic)

“…mat clearly showed that the top layer had a higher metabolic turnover compared with the cells from the bottom layer and exhibited acclimation to light and UVR, and in general stress protection. The induction of stress-related transcript changes observed here are very similar to observations in the charophytes Coleochaete and Spirogyra (Timme and Delwiche, 2010), the moss Physcomitrella (Khraiwesh et al, 2015), pointing out the evolutionary significance of our findings.…”

Foster thy young: Enhanced prediction of orphan genes in assembled genomes

“…Using RNA-Seq data with high representation of orphan gene expression dramatically improves the efficacy of gene prediction by MAKER, by the Direct Inference pipeline, and by the BIND and MIND combination pipelines. Thus, the accuracy of an initial genome annotation will be maximized by selecting RNA-Seq data from diverse samples, including samples that typically express high levels of young genes, e.g., reproductive tissues and stressed tissues 10,14,54,[72][73][74][75][76][77][78]83 . Additionally, reannotation 70,84,85 outcomes can be optimized by utilizing evidence from diverse samples in the expanded body of public RNA-Seq datasets.…”

“…The "orphan-rich" dataset is designed to maximize orphan gene representation. We reasoned that selecting samples which contain a breadth of orphan gene transcripts could be important because many, though by no means all 10 , orphans are highly expressed under only a very limited set of conditions 10,14,54,[72][73][74][75][76][77][78] . The "orphan-rich" RNA-Seq samples were chosen from over a thousand samples in SRA; over 60% of all Araport11-annotated orphans are transcribed in each sample.…”

Mechanisms of Coix Seed Compositions in the Treatment of Spleen Deficiency and Wet Dampness Zheng

“…It has already been applied in the study of clinical diseases (Khraiwesh et al, 2015). It detects the whole genome of the objects, which may provide possible therapeutic effect and clarify the mechanism.…”