SignificanceEthylene is a gaseous hormone that controls plant life throughout development. Being a simple hydrophobic molecule, it can freely enter cells; therefore, the cell type specificity of its action is challenging. By means of tissue-specific expression of two negative regulators of the signaling cascade, we selectively disrupted the ethylene signal in different cell types without affecting its biosynthesis. We demonstrate that ethylene restricts plant growth by dampening the effect of auxins in the outermost cell layer. We further show that this epidermis-specific signaling has an impact on the growth of neighboring cells, suggesting that the master controller of cell expansion resides in the epidermis, where it senses the environment and, subsequently drives growth, of the inner tissues.

Regulatory networks of salt stress and abscisic acid (ABA) responses have previously been analyzed in seed plants. Here, we report microarray expression profiles of 439 genes encoding transcription-associated proteins (TAPs) in response to salt stress and ABA in the salt-tolerant moss Physcomitrella patens. Fourteen and 56 TAP genes were differentially expressed within 60 min of NaCl and ABA treatment, respectively, indicating that these responses are regulated at the transcriptional level. Overlapping expression profiles, as well as the up-regulation of ABA biosynthesis genes, suggest that ABA mediates the salt stress responses in P. patens. Comparison to public gene expression data of Arabidopsis thaliana and phylogenetic analyses suggest that the role of DREB-like, Dof, and bHLH TAPs in salt stress responses have been conserved during embryophyte evolution, and that the function of ABI3-like, bZIP, HAP3, and CO-like TAPs in seed development and flowering emerged from pre-existing ABA and light signalling pathways.

SummaryThe cloning of abiotic stress-inducible genes from the moss Physcomitrella patens led to the identification of the gene PpTSPO1, encoding a protein homologous to the mammalian mitochondrial peripheral-type benzodiazepine receptor and the bacterial tryptophane-rich sensory protein. This class of proteins is involved in the transport of intermediates of the tetrapyrrole biosynthesis pathway. Like the mammalian homologue, the PpTSPO1 protein is localized to mitochondria. The generation of PpTSPO1-targeted moss knock-out lines revealed an essential function of the gene in abiotic stress adaptation. Under stress conditions, the PpTSPO1 null mutants show elevated H 2 O 2 levels, enhanced lipid peroxidation and cell death, indicating an important role of PpTSPO1 in redox homeostasis. We hypothesize that PpTSPO1 acts to direct porphyrin precursors to the mitochondria for heme formation, and is involved in the removal of photoreactive tetrapyrrole intermediates.

Transient cytosolic Ca 2+ ([Ca 2+ ] cyt ) elevations are early events in plant signaling pathways including those related to abiotic stress. The restoration of [Ca 2+ ] cyt to prestimulus levels involves ATP-driven Ca 2+ pumps, but direct evidence for an essential role of a plant Ca 2+ -ATPase in abiotic stress adaptation is missing. Here, we report on a stress-responsive Ca 2+ -ATPase gene ( PCA1 ) from the moss Physcomitrella patens. Functional analysis of PCA1 in a Ca 2+ transport-deficient yeast mutant suggests that PCA1 encodes a P IIB -type Ca 2+ -ATPase harboring an N-terminal autoinhibitory domain. In vivo localizations identified membranes of small vacuoles as the integration site for a PCA1:GFP fusion protein. PCA1 mRNA levels are up-regulated by dehydration, NaCl, and abscisic acid, and PCA1 loss-of-function mutants (Δ PCA1 ) exhibit an enhanced susceptibility to salt stress. The Δ PCA1 lines show sustained elevated [Ca 2+ ] cyt in response to salt treatment in contrast to WT that shows transient Ca 2+ elevations, indicating a direct role for PCA1 in the restoration of prestimulus [Ca 2+ ] cyt . The altered Ca 2+ response of the Δ PCA1 mutant lines correlates with altered expression levels of stress-induced genes, suggesting disturbance of a stress-associated signaling pathway. We propose that PCA1 is an essential component for abiotic stress adaptation in Physcomitrella involved in the generation of a specific salt-induced Ca 2+ signature.

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.

The gray mangrove [Avicennia marina (Forsk.) Vierh.] is the most widely distributed mangrove species, ranging throughout the Indo-West Pacific. It presents remarkable levels of geographic variation both in phenotypic traits and habitat, often occupying extreme environments at the edges of its distribution. However, subspecific evolutionary relationships and adaptive mechanisms remain understudied, especially across populations of the West Indian Ocean. High-quality genomic resources accounting for such variability are also sparse. Here we report the first chromosome-level assembly of the genome of A. marina. We used a previously release draft assembly and proximity ligation libraries Chicago and Dovetail HiC for scaffolding, producing a 456,526,188-bp long genome. The largest 32 scaffolds (22.4–10.5 Mb) accounted for 98% of the genome assembly, with the remaining 2% distributed among much shorter 3,759 scaffolds (62.4–1 kb). We annotated 45,032 protein-coding genes using tissue-specific RNA-seq data in combination with de novo gene prediction, from which 34,442 were associated to GO terms. Genome assembly and annotated set of genes yield a 96.7% and 95.1% completeness score, respectively, when compared with the eudicots BUSCO dataset. Furthermore, an FST survey based on resequencing data successfully identified a set of candidate genes potentially involved in local adaptation and revealed patterns of adaptive variability correlating with a temperature gradient in Arabian mangrove populations. Our A. marina genomic assembly provides a highly valuable resource for genome evolution analysis, as well as for identifying functional genes involved in adaptive processes and speciation.

30The gray mangrove [Avicennia marina (Forsk.) Vierh.] is the most widely distributed mangrove 31 species, ranging throughout the Indo-West Pacific. It presents remarkable levels of geographic 32 variation both in phenotypic traits and habitat, often occupying extreme environments at the 33 edges of its distribution. However, subspecific evolutionary relationships and adaptive 34 mechanisms remain understudied, especially across populations of the West Indian Ocean. High-35 quality genomic resources accounting for such variability are sparse. We sequenced and 36 assembled the genome of A. marina from the Arabian Gulf, which is the harshest region that the 37 species occupies and at the northern-most limit of its distribution. We used proximity ligation 38 libraries Chicago and Dovetail HiC, and the HiRise assembly pipeline, producing a 456,556,596 39 bp long genome. The largest 32 scaffolds (22.4 Mb to 10.5 Mb) accounted for 98 % of the 40 genome assembly, with the remaining 2% distributed among much shorter 3,777 scaffolds (62.4 41 Kb to 1 Kb). We annotated 23,331 protein-coding genes using tissue-specific RNA-seq data, 42 from which 13,312 were associated to GO terms. Genome assembly and annotated set of genes 43 yield a 96.7% and 92.3% completeness score, respectively, when compared with the eudicots 44 BUSCO dataset. Furthermore, an FST survey based on resequencing data successfully identified a 45 set of candidate genes potentially involved in local adaptation, and revealed patterns of adaptive 46 variability correlating with a temperature gradient in Arabian mangrove populations. Our A. 47 marina genomic assembly provides a highly valuable resource for genome evolution analysis, as 48 well as for identifying functional genes involved in adaptive processes and speciation. 49 50

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