Natural variation in abiotic stress responsive gene expression and local adaptation to climate in Arabidopsis thaliana.

Gene expression varies widely in natural populations, yet the proximate and ultimate causes of this variation are poorly known. Understanding how variation in gene expression affects abiotic stress tolerance, fitness, and adaptation is central to the field of evolutionary genetics. We tested the hypothesis that genes with natural genetic variation in their expression responses to abiotic stress are likely to be involved in local adaptation to climate in Arabidopsis thaliana. Specifically, we compared genes with consistent expression responses to environmental stress (expression stress responsive, "eSR") to genes with genetically variable responses to abiotic stress (expression genotype-by-environment interaction, "eGEI"). We found that on average genes that exhibited eGEI in response to drought or cold had greater polymorphism in promoter regions and stronger associations with climate than those of eSR genes or genomic controls. We also found that transcription factor binding sites known to respond to environmental stressors, especially abscisic acid responsive elements, showed significantly higher polymorphism in drought eGEI genes in comparison to eSR genes. By contrast, eSR genes tended to exhibit relatively greater pairwise haplotype sharing, lower promoter diversity, and fewer nonsynonymous polymorphisms, suggesting purifying selection or selective sweeps. Our results indicate that cis-regulatory evolution and genetic variation in stress responsive gene expression may be important mechanisms of local adaptation to climatic selective gradients

Patterns of pan-genome occupancy and gene coexpression under water-deficit in Brachypodium distachyon

Natural populations are characterized by abundant genetic diversity driven by a range of different types of mutation. The tractability of sequencing complete genomes has allowed new insights into the variable composition of genomes, summarized as a species pan-genome. These analyses demonstrate that many genes are absent from the first reference genomes, whose analysis dominated the initial years of the genomic era. Our field now turns towards understanding the functional consequence of these highly variable genomes. Here, we analysed weighted gene coexpression networks from leaf transcriptome data for drought response in the purple false brome Brachypodium distachyon and the differential expression of genes putatively involved in adaptation to this stressor. We specifically asked whether genes with variable “occupancy” in the pan-genome – genes which are either present in all studied genotypes or missing in some genotypes – show different distributions among coexpression modules. Coexpression analysis united genes expressed in drought-stressed plants into nine modules covering 72 hub genes (87 hub isoforms), and genes expressed under controlled water conditions into 13 modules, covering 190 hub genes (251 hub isoforms). We find that low occupancy pan-genes are under-represented among several modules, while other modules are over-enriched for low-occupancy pan-genes. We also provide new insight into the regulation of drought response in B. distachyon, specifically identifying one module with an apparent role in primary metabolism that is strongly responsive to drought. Our work shows the power of integrating pan-genomic analysis with transcriptomic data using factorial experiments to understand the functional genomics of environmental respons

Clay minerals in delta deposits and organic preservation potential on Mars

Clay-rich sedimentary deposits are often sites of organic matter preservation and have therefore been sought in Mars exploration. However, regional deposits of hydrous minerals, including phyllosilicates and sulphates are not typically associated with valley networks and layered sediments that provide geomorphic evidence of surface water transport on early Mars. The Compact Reconnaissance Imaging Spectrometer for Mars (CRISM) has recently identified phyllosilicates within three lake basins with fans or deltas that indicate sustained sediment deposition: Eberswalde crater Holden crater and Jezero crater. Here we use high-resolution data from the Mars Reconnaissance Orbiter (MRO) to identify clay-rich fluvial–lacustrine sediments within Jezero crater, which has a diameter of 45 km. The crater is an open lake basin on Mars with sedimentary deposits of hydrous minerals sourced from a smectite-rich catchment in the Nili Fossae region. We find that the two deltas and the lowest observed stratigraphic layer within the crater host iron–magnesium smectite clay. Jezero crater holds sediments that record multiple episodes of aqueous activity on early Mars. We suggest that this depositional setting and the smectite mineralogy make these deltaic deposits well suited for the sequestration and preservation of organic material

Signature Lipids and Stable Carbon Isotope Analyses of Octopus Spring Hyperthermophilic Communities Compared with those of Aquificales Representatives

The molecular and isotopic compositions of lipid biomarkers of cultured Aquificales genera have been used to study the community and trophic structure of the hyperthermophilic pink streamers and vent biofilm from Octopus Spring. Thermocrinis ruber, Thermocrinis sp. strain HI 11/12, Hydrogenobacter thermophilus TK-6, Aquifex pyrophilus, and Aquifex aeolicus all contained glycerol-ether phospholipids as well as acyl glycerides. The n-C20:1 and cy-C21 fatty acids dominated all of the Aquificales, while the alkyl glycerol ethers were mainly C18:0. These Aquificales biomarkers were major constituents of the lipid extracts of two Octopus Spring samples, a biofilm associated with the siliceous vent walls, and the well-known pink streamer community (PSC). Both the biofilm and the PSC contained mono- and dialkyl glycerol ethers in which C18 and C20 alkyl groups were prevalent. Phospholipid fatty acids included both the Aquificales n-C20:1 and cy-C21, plus a series of isobranched fatty acids (i-C15:0 to i-C21:0), indicating an additional bacterial component. Biomass and lipids from the PSC were depleted in 13C relative to source water CO2 by 10.9 and 17.2%, respectively. The C20?21 fatty acids of the PSC were less depleted than the iso-branched fatty acids, 18.4 and 22.6%, respectively. The biomass of T. ruber grown on CO2 was depleted in 13C by only 3.3% relative to C source. In contrast, biomass was depleted by 19.7% when formate was the C source. Independent of carbon source, T. ruber lipids were heavier than biomass (1.3%). The depletion in the C20?21 fatty acids from the PSC indicates that Thermocrinis biomass must be similarly depleted and too light to be explained by growth on CO2. Accordingly, Thermocrinis in the PSC is likely to have utilized formate, presumably generated in the spring source region

Identification of hydrated silicate minerals on Mars using MRO-CRISM: Geologic context near Nili Fossae and implications for aqueous alteration

The Noachian terrain west of the Isidis basin hosts a diverse collection of alteration minerals in rocks comprising varied geomorphic units within a 100,000 km2 region in and near the Nili Fossae. Prior investigations in this region by the Observatoire pour l'Minéralogie, l'Eau, les Glaces, et l'Activité (OMEGA) instrument on Mars Express revealed large exposures of both mafic minerals and iron magnesium phyllosilicates in stratigraphic context. Expanding on the discoveries of OMEGA, the Compact Reconnaissance Imaging Spectrometer for Mars (CRISM) aboard the Mars Reconnaissance Orbiter (MRO) has found more spatially widespread and mineralogically diverse alteration minerals than previously realized, which represent multiple aqueous environments. Using CRISM near-infrared spectral data, we detail the basis for identification of iron and magnesium smectites (including both nontronite and more Mg-rich varieties), chlorite, prehnite, serpentine, kaolinite, potassium mica (illite or muscovite), hydrated (opaline) silica, the sodium zeolite analcime, and magnesium carbonate. The detection of serpentine and analcime on Mars is reported here for the first time. We detail the geomorphic context of these minerals using data from high-resolution imagers onboard MRO in conjunction with CRISM. We find that the distribution of alteration minerals is not homogeneous; rather, they occur in provinces with distinctive assemblages of alteration minerals. Key findings are (1) a distinctive stratigraphy, in and around the Nili Fossae, of kaolinite and magnesium carbonate in bedrock units always overlying Fe/Mg smectites and (2) evidence for mineral phases and assemblages indicative of low-grade metamorphic or hydrothermal aqueous alteration in cratered terrains. The alteration minerals around the Nili Fossae are more typical of those resulting from neutral to alkaline conditions rather than acidic conditions, which appear to have dominated much of Mars. Moreover, the mineralogic diversity and geologic context of alteration minerals found in the region around the Nili Fossae indicates several episodes of aqueous activity in multiple distinct environments

A synthesis of Martian aqueous mineralogy after 1 Mars year of observations from the Mars Reconnaissance Orbiter

Martian aqueous mineral deposits have been examined and characterized using data acquired during Mars Reconnaissance Orbiter's (MRO) primary science phase, including Compact Reconnaissance Imaging Spectrometer for Mars hyperspectral images covering the 0.4–3.9 μm wavelength range, coordinated with higher–spatial resolution HiRISE and Context Imager images. MRO's new high-resolution measurements, combined with earlier data from Thermal Emission Spectrometer; Thermal Emission Imaging System; and Observatoire pour la Minéralogie, L'Eau, les Glaces et l'Activitié on Mars Express, indicate that aqueous minerals are both diverse and widespread on the Martian surface. The aqueous minerals occur in 9–10 classes of deposits characterized by distinct mineral assemblages, morphologies, and geologic settings. Phyllosilicates occur in several settings: in compositionally layered blankets hundreds of meters thick, superposed on eroded Noachian terrains; in lower layers of intracrater depositional fans; in layers with potential chlorides in sediments on intercrater plains; and as thousands of deep exposures in craters and escarpments. Carbonate-bearing rocks form a thin unit surrounding the Isidis basin. Hydrated silica occurs with hydrated sulfates in thin stratified deposits surrounding Valles Marineris. Hydrated sulfates also occur together with crystalline ferric minerals in thick, layered deposits in Terra Meridiani and in Valles Marineris and together with kaolinite in deposits that partially infill some highland craters. In this paper we describe each of the classes of deposits, review hypotheses for their origins, identify new questions posed by existing measurements, and consider their implications for ancient habitable environments. On the basis of current data, two to five classes of Noachian-aged deposits containing phyllosilicates and carbonates may have formed in aqueous environments with pH and water activities suitable for life

Low Hesperian P_(CO2) constrained from in situ mineralogical analysis at Gale Crater, Mars

Carbon dioxide is an essential atmospheric component in martian climate models that attempt to reconcile a faint young sun with planetwide evidence of liquid water in the Noachian and Early Hesperian. In this study, we use mineral and contextual sedimentary environmental data measured by the Mars Science Laboratory (MSL) Rover Curiosity to estimate the atmospheric partial pressure of CO_2 (P_(CO2)) coinciding with a long-lived lake system in Gale Crater at ∼3.5 Ga. A reaction–transport model that simulates mineralogy observed within the Sheepbed member at Yellowknife Bay (YKB), by coupling mineral equilibria with carbonate precipitation kinetics and rates of sedimentation, indicates atmospheric P_(CO2) levels in the 10s mbar range. At such low P_(CO2) levels, existing climate models are unable to warm Hesperian Mars anywhere near the freezing point of water, and other gases are required to raise atmospheric pressure to prevent lake waters from being lost to the atmosphere. Thus, either lacustrine features of Gale formed in a cold environment by a mechanism yet to be determined, or the climate models still lack an essential component that would serve to elevate surface temperatures, at least locally, on Hesperian Mars. Our results also impose restrictions on the potential role of atmospheric CO_2 in inferred warmer conditions and valley network formation of the late Noachian

Extensive gene content variation in the <i>Brachypodium distachyon</i> pan-genome correlates with population structure

13 Pags.- 6 Figs. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holderWhile prokaryotic pan-genomes have been shown to contain many more genes than any individual organism, the prevalence and functional significance of differentially present genes in eukaryotes remains poorly understood. Whole-genome de novo assembly and annotation of 54 lines of the grass Brachypodium distachyon yield a pan-genome containing nearly twice the number of genes found in any individual genome. Genes present in all lines are enriched for essential biological functions, while genes present in only some lines are enriched for conditionally beneficial functions (e.g., defense and development), display faster evolutionary rates, lie closer to transposable elements and are less likely to be syntenic with orthologous genes in other grasses. Our data suggest that differentially present genes contribute substantially to phenotypic variation within a eukaryote species, these genes have a major influence in population genetics, and transposable elements play a key role in pan-genome evolution.The work conducted by the US DOE Joint Genome Institute is supported by the Office of Science of the US Department of Energy under Contract no. DE-AC02-05CH11231. D.P. W. and R.A. were funded in part by the National Science Foundation (grant no. IOS–1258126), and the Great Lakes Bioenergy Research Center (Department of Energy Biological and Environmental Research Office of Science grant no. DE– FCO2–07ER64494). TEJ and DLDM were supported by NSF PGRP grant IOS-0922457. P.C. and B.C.M. were funded by Spanish MINECO (CGL2012-39953-C02-01 and CGL2016-79790-P). B.C.M. was partially funded by DGA—Obra Social La Caixa (grant number GA-LC-059-2011) and Spanish MINECO (AGL2013-48756-R, CSIC13-4E-2490). PC was partially funded by Spanish Aragon Government-European Social Fund (Bioflora).Peer reviewe

Orbital Identification of Carbonate-Bearing Rocks on Mars

Geochemical models for Mars predict carbonate formation during aqueous alteration. Carbonate-bearing rocks had not previously been detected on Mars' surface, but Mars Reconnaissance Orbiter mapping reveals a regional rock layer with near-infrared spectral characteristics that are consistent with the presence of magnesium carbonate in the Nili Fossae region. The carbonate is closely associated with both phyllosilicate-bearing and olivine-rich rock units and probably formed during the Noachian or early Hesperian era from the alteration of olivine by either hydrothermal fluids or near-surface water. The presence of carbonate as well as accompanying clays suggests that waters were neutral to alkaline at the time of its formation and that acidic weathering, proposed to be characteristic of Hesperian Mars, did not destroy these carbonates and thus did not dominate all aqueous environments