Thellungiella parvula1 is related to Arabidopsis thaliana and is endemic to saline, resource-poor habitats2, making it a model for the evolution of plant adaptation to extreme environments. Here we present the draft genome for this extremophile species. Exclusively by next generation sequencing, we obtained the de novo assembled genome in 1,496 gap-free contigs, closely approximating the estimated genome size of 140 Mb. We anchored these contigs to seven pseudo chromosomes without the use of maps. We show that short reads can be assembled to a near-complete chromosome level for a eukaryotic species lacking prior genetic information. The sequence identifies a number of tandem duplications that, by the nature of the duplicated genes, suggest a possible basis for T. parvula’s extremophile lifestyle. Our results provide essential background for developing genomically influenced testable hypotheses for the evolution of environmental stress tolerance.

The mechanisms of salt stress response and tolerance have eluded definition despite reasonable success in defining their physiological manifestations. In this review, we consider the integrated salt metabolism of plants, essentially as a problem in meganutrient physiology. Two critical aspects of cellular and organismal metabolism are given particular attention-those involved in the control and integration of Na+ acquisition and allocation in plants and those involved in readjustment of other aspects of metabolism, especially those involving carbon as a resource.The responses of plants to salt and other environmental stresses have been important to students of agronomy, ecology, and physiology since the disciplines were first defined. It is, therefore, all the more frustrating that, in spite of years of research attention, the mechanisms which impart salt tolerance to some plants and sensitivity to others are still unresolved.In this review, we will discuss these mechanisms using references selected as representative of recent work and as suitable entrance points to the relevant literature. We will restrict our consideration to Na+ and to plants lacking salt glands or other excretory appendages (were we to emphasize Cl-instead, the conclusions would be similar, but based on fewer data). Then, to avoid some of the problems associated with semantic differences, we will issue three simplifying proclamations. First, the mechanisms of salt tolerance cannot be known, because salt tolerance itself is a qualitative descriptor, largely reflecting correlations between size or mortality and external salinity. Second, the term salt stress is uninterpretable at the mechanistic level, because it is based on manipulations of an external environmental state which is only indirectly linked to readjustment of cellular and integrated organismal metabolism. Third, the usual classification of plants according to 'strategy' as 'includers' and 'excluders' imposes terminology sufficiently imprecise to obstruct the definition of mechanistic research problems. Even the most salt-sensitive plants accumulate salt when it is available, and the fact that degree of accumulation varies is not inherently important to the fundamental questions.Therefore, it is more reasonable to be concerned with the metabolism of salt itself, essentially as a specialized problem in meganutrient physiology. For this review, we will designate the mechanisms of interest as (a) those involved in transport and in the control and integration of Na+ acquisition and allocation in plants and (b) those involved in readjustment of other aspects of metabolism, especially carbon.Transmembrane Sodium Movements. The majority of the research on Na+ metabolism in plants has been concerned with the initial uptake across the 'root cell plasmalemma.' Beyond that, variations in the sophistication of the integrated transport network are responsible for the designations of salt includer and salt excluder, but it is unclear how many different types of transporters must actuall...

Thellungiella salsuginea, a close relative of Arabidopsis , represents an extremophile model for abiotic stress tolerance studies. We present the draft sequence of the T. salsuginea genome, assembled based on ∼134-fold coverage to seven chromosomes with a coding capacity of at least 28,457 genes. This genome provides resources and evidence about the nature of defense mechanisms constituting the genetic basis underlying plant abiotic stress tolerance. Comparative genomics and experimental analyses identified genes related to cation transport, abscisic acid signaling, and wax production prominent in T. salsuginea as possible contributors to its success in stressful environments.

While H2O2 has been implicated in numerous plant environmental responses, normal levels and variabilities are poorly established, and estimates of leaf tissue concentrations span more than three orders of magnitude, even in a single species under similar conditions. Here, leaf tissue H2O2 contents under natural conditions are reported after determining (i) that H2O2 in extracts was stable with time, (ii) that H2O2 added to the extract was recovered quantitatively, and (iii) that the H2O2 calibration curve was unaffected (or quantifiably affected) by the extract. The broad applicability of the protocol and variability in leaf concentrations were demonstrated using tissue collected from several habitats in association with three, more extensive, experiments. The first involved nychthemeral studies of the mangrove, Rhizophora mangle L. Lowest H2O2 levels occurred in the early morning and near sunset, with higher levels both at midday and at night. Second, using five temperate species in Spring, concentrations were compared on a warm, sunny day and a cool, cloudy day. Higher concentrations were found on the warm day for Aesculus glabra Willd., Glechoma hederacea L., Plantago major L., and Viola soraria Willd., while there were no differences in Quercus macrocarpa Michx. Finally, the effects of elevated CO2 and ozone were examined in soybean, Glycine max L. Pioneer 93B15 under Free Air gas Concentration Enrichment (FACE) conditions. Both supplements led to elevated H2O2. Overall, mean leaf, midday, and mid-summer H2O2 concentrations ranged from 0.67 micromol (gFW)(-1) in mangrove to 3.6 micromol (gFW)(-1) in A. glabra Willd. Greatest within-species differences were only 2.5-fold in any of the studies.

Summary• The tropical intertidal ecosystem is defined by trees -mangroves -which are adapted to an extreme and extremely variable environment. The genetic basis underlying these adaptations is, however, virtually unknown. Based on advances in pyrosequencing, we present here the first transcriptome analysis for plants for which no prior genomic information was available. We selected the mangroves Rhizophora mangle (Rhizophoraceae) and Heritiera littoralis (Malvaceae) as ecologically important extremophiles employing markedly different physiological and life-history strategies for survival and dominance in this extreme environment.• For maximal representation of conditional transcripts, mRNA was obtained from a variety of developmental stages, tissues types, and habitats. For each species, a normalized cDNA library of pooled mRNAs was analysed using GSFLX pyrosequencing.• A total of 537 635 sequences were assembled de novo and annotated as > 13 000 distinct gene models for each species. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) orthology annotations highlighted remarkable similarities in the mangrove transcriptome profiles, which differed substantially from the model plants Arabidopsis and Populus.• Similarities in the two species suggest a unique mangrove lifestyle overarching the effects of transcriptome size, habitat, tissue type, developmental stage, and biogeographic and phylogenetic differences between them.