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Climate warming is causing quick changes in mean annual temperature and more severe drought period. These are major contributors of forest dieback, which is becoming more frequent and widespread, particularly in warm and drought-prone regions. Despite being a hot topic in non-woody plant sciences, the information about how heatwaves impact in tree molecular biology is still scarce. In this work we investigated how the transcriptome of Pinus radiata changes during initial stress response and stress acclimation. To this end, and considering this species is non sequenced, we generated a deep dataset employing Illumina technology. This approach allowed us to reconstruct 77335 contigs which were annotated following gene ontology, and to define 12164 and 13590 transcripts as down- and upregulated, respectively, across the three sampled experimental points. Enrichment analysis allowed to distinguish 9 down-regulated pathways, the most of them related to the reduction of apoplast, and water transport. While 22 were upregulated, which followed two different trends those pathways that peaks at short-term (acute response) from those which accumulated long-term (acclimation response) being most of them related to heat shock response, redox machinery and RNA processing. Additionally, the combination of transcriptome data with other available omics layers, allowed an exceptional understanding of the mechanisms behind heat stress response, involving complex interrelated processes from molecular to physiological level. Nucleolus and nucleoid activities seem to be a central core in acclimating process, producing specific RNA isoforms and other essential elements for anterograde-retrograde stress signaling as NAC proteins, Helicase RVB, RZ1 RNA chaperone, or ribosomal RPS4. These mechanisms are connected by elements already known in heat stress-response (redox, heat shock proteins or ABA-related). But also, novel candidates, as photosynthetic pigments, shikimate, or proline centric proteases activities, have been identified effectively networking biochemical responses to its potential regulatory element. This work provides a first deep overview about what molecular mechanisms underlying heat stress response and acclimation in pines, supporting the development of new breeding strategies to face the challenges that the climate change will impose to forests.

Apomixis was originally defined as the replacement of sexual reproduction by an asexual process that does not involve fertilization but, in angiosperms, it is often used in the more restricted sense of asexual reproduction through seeds. In ferns, apomixis combines the production of unreduced spores (diplospory) and the formation of sporophytes from somatic cells of the prothallium (apogamy). The genes that control the onset of apogamy in ferns are largely unknown. In this study, we describe the gametophyte transcriptome of the apogamous fern Dryopteris affinis ssp. affinis using an RNA-Seq approach to compare the gene expression profiles of one- and two-dimensional gametophytes, the latter containing apogamic centers. After collapsing highly similar de novo transcripts, we obtained 166,191 unigenes, of which 30% could be annotated using public databases. Multiple quality metrics indicate a good quality of the de novo transcriptome with a low level of fragmentation. Our data show a total of 10,679 genes (6% of all genes) to be differentially expressed between gametophytes of filamentous (one-dimensional) and prothallial (two-dimensional) architecture. 6,110 genes were up-regulated in two-dimensional relative to one-dimensional gametophytes, some of which are implicated in the regulation of meristem growth, auxin signaling, reproduction, and sucrose metabolism. 4,570 genes were down-regulated in two-dimensional versus one-dimensional gametophytes, which are enriched in stimulus and defense genes, as well as genes involved in epigenetic gene regulation and ubiquitin degradation. Our results provide insights into free-living gametophyte development, focusing on the filamentous-to-prothallus growth transition, and provide a useful resource for further investigations of asexual reproduction.

Due to the current climate change, many studies have described main drivers in abiotic stress. Recent findings suggest that alternative splicing (AS) has a critical role in controlling plant responses to high temperature. AS is a mechanism that allows organisms to create an assortment of RNA transcripts and proteins using a single gene. However, the most important roles of AS in stress could not be rigorously addressed because research has been focused on model species, covering only a narrow phylogenetic and lifecycle spectrum. Thus, AS degree of diversification among more dissimilar taxa in heat response is still largely unknown. To fill this gap, the present study employs a systems biology approach to examine how the AS landscape responds to and 'remembers' heat stress in conifers, a group which has received little attention even though their position can solve key evolutionary questions. Contrary to angiosperms, we found that potential intron retention may not be the most prevalent type of AS. Furthermore, our integrative analysis with metabolome and proteome data places splicing as the main source of variation during the response. Finally, we evaluated possible acquired long-term splicing memory in a diverse subset of events, and although this mechanism seems to be conserved in seed plants, AS dynamics are divergent. These discoveries reveal the particular way of remembering past temperature changes in long-lived plants and open the door to include species with unique features to determine the extent of conservation in gene expression regulation.

Ramón y Cajal Programme (RYC-2015-17871, Spanish Ministry of Economy and Competitiveness); Programa de Ayudas Predoctorales Severo Ochoa, Autonomous Community of Asturias, Spain; Spanish Ministry of Universities fellowship (FPU19/01142)

The recovery and maintenance of plant homeostasis under stressful environments are complex processes involving organelle crosstalk for a coordinated cellular response. Here, we revealed through nuclear and chloroplast subcellular proteomics, biochemical cell profiles and targeted transcriptomics how chloroplasts and nuclei developed their responses under increased temperatures in a long-lived species (Pinus radiata). Parallel to photosynthetic impairment and ROS production in the chloroplast, a DNA damage response was triggered in the nucleus followed by an altered chromatin conformation. In addition, in the nuclei, we found several proteins, such as HEMERA or WHIRLY, which change their locations from the chloroplasts to the nuclei carrying the stress message. Additionally, our data showed a deep rearrangement of RNA metabolism in both organelles, revealing microRNAs and AGO1 as potential regulators of the acclimation mechanisms. Altogether, our study highlights the synchronisation among the different stages required for thermotolerance acquisition in P. radiata, pointing out the role of chromatin conformation and post-transcriptional gene regulation in overcoming heat stress and assuring plant survival for the following years. This article is protected by copyright. All rights reserved.

Despite it being an important issue in the context of climate change, for most plant species it is not currently known how abiotic stresses affect nuclear proteomes and mediate memory effects. This study examines how Pinus radiata nuclei respond, adapt, ‘remember’, and ‘learn’ from heat stress. Seedlings were heat-stressed at 45 °C for 10 d and then allowed to recover. Nuclear proteins were isolated and quantified by nLC-MS/MS, the dynamics of tissue DNA methylation were examined, and the potential acquired memory was analysed in recovered plants. In an additional experiment, the expression of key gene genes was also quantified. Specific nuclear heat-responsive proteins were identified, and their biological roles were evaluated using a systems biology approach. In addition to heat-shock proteins, several clusters involved in regulation processes were discovered, such as epigenomic-driven gene regulation, some transcription factors, and a variety of RNA-associated functions. Nuclei exhibited differential proteome profiles across the phases of the experiment, with histone H2A and methyl cycle enzymes in particular being accumulated in the recovery step. A thermopriming effect was possibly linked to H2A abundance and over-accumulation of spliceosome elements in recovered P. radiata plants. The results suggest that epigenetic mechanisms play a key role in heat-stress tolerance and priming mechanisms., Heat stress followed by a recovery period leads to changes in the nuclear proteome of Pinus radiata that suggest that epigenetic mechanisms play a key role in tolerance and priming mechanisms.

Despite the importance of dormancy and dormancy cycling for plants’ fitness and life cycle phenology, a comprehensive characterization of the global and cellular epigenetic patterns across space and time in different seed dormancy states is lacking. Using Capsella bursa-pastoris (L.) Medik. (shepherd’s purse) seeds with primary and secondary dormancy, we investigated the dynamics of global genomic DNA methylation and explored the spatio-temporal distribution of 5-methylcytosine (5-mC) and histone H4 acetylated (H4Ac) epigenetic marks. Seeds were imbibed at 30 °C in a light regime to maintain primary dormancy, or in darkness to induce secondary dormancy. An ELISA-based method was used to quantify DNA methylation, in relation to total genomic cytosines. Immunolocalization of 5-mC and H4Ac within whole seeds (i.e., including testa) was assessed with reference to embryo anatomy. Global DNA methylation levels were highest in prolonged (14 days) imbibed primary dormant seeds, with more 5-mC marked nuclei present only in specific parts of the seed (e.g., SAM and cotyledons). In secondary dormant seeds, global methylation levels and 5-mC signal where higher at 3 and 7 days than 1 or 14 days. With respect to acetylation, seeds had fewer H4Ac marked nuclei (e.g., SAM) in deeper dormant states, for both types of dormancy. However, the RAM still showed signal after 14 days of imbibition under dormancy-inducing conditions, suggesting a central role for the radicle/RAM in the response to perceived ambient changes and the adjustment of the seed dormancy state. Thus, we show that seed dormancy involves extensive cellular remodeling of DNA methylation and H4 acetylation.

Background The exposure of microalgae and plants to low UV-C radiation dosages can improve their biomass composition and stress tolerance. Despite UV-C sharing these effects with UV-A/B but at much lower dosages, UV-C sensing and signal mechanisms are still mostly unknown. Thus, we have described and integrated the proteometabolomic and physiological changes occurring in Chlamydomonas reinhardtii—a simple Plantae model—into the first 24 h after a short and low-intensity UV-C irradiation in order to reconstruct the microalgae response system to this stress. Results The microalgae response was characterized by increased redox homeostasis, ROS scavenging and protein damage repair/avoidance elements. These processes were upregulated along with others related to the modulation of photosynthetic electron flux, carbon fixation and C/N metabolism. These changes, attributed to either direct UV-C-, ROS- or redox unbalances-associated damage, trigger a response process involving novel signaling intermediaries and effectors such as the translation modulator FAP204, a PP2A-like protein and a novel DYRK kinase. These elements were found linked to the modulation of Chlamydomonas biomass composition (starch accumulation) and proliferation, within an UV-C response probably modulated by different epigenetic factors. Conclusion Chosen multiomics integration approach was able to describe many fast changes, including biomass composition and ROS stress tolerance, as a response to a low-intensity UV-C stress. Moreover, the employed omics and systems biology approach placed many previously unidentified protein and metabolites at the center of these changes. These elements would be promising targets for the characterization of this stress response in microalgae and plants and the engineering of more productive microalgae strains.

The complexity of the plant cell proteome, exhibiting thousands of proteins whose abundance varies in several orders of magnitude, makes impossible to cover most of the plant proteins using standard shotgun-based approaches. Despite this general description of plant proteomes, the complexity is not a big issue (current protocols and instrumentation allow for the identification of several thousand proteins per injection), low or medium abundant proteins cannot be detected most of times, being necessary to fraction or perform targeted analyses in order to detect and quantify them. Among fractioning choices, cell fractioning in its different organelles is a good strategy for gaining not only a deeper coverage of the proteome but also the basis for understanding organelle function, protein dynamics, and trafficking within the cell, as nuclear and chloroplast communication. This approach is used routinely in many labs working with model species; however, the available protocols focusing on tree species are scarce. In this chapter, we provide a simple but robust protocol for isolating nuclei and chloroplasts in pine needles that is fully compatible with later mass spectrometry-based proteome analysis.

Microalgae are gaining attention in industry for their high value-added biomolecules and biomass production and for studying fundamental processes in biology. The introduction of novel approaches for understanding and modeling molecular networks at different omic levels is paramount for increasing the productivity of these organisms. However, the construction of these networks requires high quality datasets with, if possible, perfectly overlapping datasets. The employ of different materials for different biomolecule isolation protocols, even if they come from the same homogenate, is one of the commonest issues affecting quality. Hence, a new method has been developed, allowing for the combined extraction of different levels including total metabolites, or their pigments or lipid fractions along nucleic acids (DNA and RNA) and/or proteins from the same sample reducing biological and time variation between levels data.

Pinus radiata seedlings, the most widely planted pine species in the world, were exposed to temperatures within a range mimicking future scenarios based on current models of heat increase. The short-term heat response in P. radiata was studied in detail by exploring the metabolome, proteome and targeted transcriptome. The use of complementary mass spectrometry techniques, GC-MS and LC-Orbitrap-MS, together with novel bioinformatics tools allowed the reliable quantification of 2,075 metabolites and 901 protein groups. Integrative analyses of different functional levels and plant physiological status revealed a complex molecular interaction network of positive and negative correlations between proteins and metabolites involved in short-term heat response, including three main physiological functions as: 1) A hormone subnetwork, where fatty acids, flavonoids and hormones presented a key role; 2) An oxidoreductase subnetwork, including several dehydrogenase and peroxidase proteins; and 3) A heat shock protein subnetwork, with numerous proteins that contain a HSP20 domain, all of which were overexpressed at the transcriptional level. Integrated analysis pinpointed the basic mechanisms underlying the short-term physiological reaction of P. radiata during heat response. This approach was feasible in forest species and unmasked two novel candidate biomarkers of heat resistance, PHO1 and TRANSCRIPTION FACTOR APFI, and a MITOCHONDRIAL SMALL HEAT SHOCK PROTEIN, for use in future breeding programs.

The complexity of the plant cell proteome, exhibiting thousands of proteins whose abundance varies in several orders of magnitude, makes impossible to cover most of the plant proteins using standard shotgun-based approaches. Despite this general description of plant proteomes, the complexity is not a big issue (current protocols and instrumentation allow for the identification of several thousand proteins per injection), low or medium abundant proteins cannot be detected most of times, being necessary to fraction or perform targeted analyses in order to detect and quantify them. Among fractioning choices, cell fractioning in its different organelles is a good strategy for gaining not only a deeper coverage of the proteome but also the basis for understanding organelle function, protein dynamics, and trafficking within the cell, as nuclear and chloroplast communication. This approach is used routinely in many labs working with model species; however, the available protocols focusing on tree species are scarce. In this chapter, we provide a simple but robust protocol for isolating nuclei and chloroplasts in pine needles that is fully compatible with later mass spectrometry-based proteome analysis.

Microalgae are gaining attention in industry for their high value-added biomolecules and biomass production and for studying fundamental processes in biology. The introduction of novel approaches for understanding and modeling molecular networks at different omic levels is paramount for increasing the productivity of these organisms. However, the construction of these networks requires high quality datasets with, if possible, perfectly overlapping datasets. The employ of different materials for different biomolecule isolation protocols, even if they come from the same homogenate, is one of the commonest issues affecting quality. Hence, a new method has been developed, allowing for the combined extraction of different levels including total metabolites, or their pigments or lipid fractions along nucleic acids (DNA and RNA) and/or proteins from the same sample reducing biological and time variation between levels data.

The importance of UV stress and its side-effects over the loss of plant productivity in forest species demands a deeper understanding of how pine trees respond to UV irradiation. Although the response to UV stress has been characterized at system and cellular levels, the dynamics within the nuclear proteome triggered by UV is still unknown despite that they are essential for gene expression and regulation of plant physiology. To fill this gap this work aims to characterize the variations in the nuclear proteome as a response to UV irradiation by using state-of-the-art mass spectrometry-based methods combined with novel bioinformatics workflows. The combination of SEQUEST, de novo sequencing, and novel annotation pipelines allowed cover sensing and transduction pathways, endoplasmic reticulum-related mechanisms and the regulation of chromatin dynamism and gene expression by histones, histone-like NF-Ys, and other transcription factors previously unrelated to this stress source, as well as the role of alternative splicing and other mechanisms involved in RNA translation and protein synthesis. The determination of 33 transcription factors, including NF-YB13, Pp005698_3 (NF-YB) and Pr009668_2 (WD-40), which are correlated to stress responsive mechanisms like an increased accumulation of photoprotective pigments and reduced photosynthesis, pointing them as strong candidate biomarkers for breeding programs aimed to improve UV resistance of pine trees.The description of the nuclear proteome of Pinus radiata combining a classic approach based on the use of SEQUEST and the use of a mass accuracy precursor alignment (MAPA) allowed an unprecedented protein coverage. This workflow provided the methodological basis for characterizing the changes in the nuclear proteome triggered by UV irradiation, allowing the depiction of the nuclear events involved in stress response and adaption. The relevance of some of the discovered proteins will suppose a major advance in stress biology field, also providing a set of transcription factors that can be considered as strong biomarker candidates to select trees more tolerant to UV radiation in forest upgrade programs.

During its life, freshwater microalgae need to grow under varying water availabilities such as seasonal dryness of puddles or tidal variations. A vast knowledge of the physiological and molecular responses to osmotic stress is available for land plants, however these responses have been scarcely studied in microalgae. In this work we described the acclimation of Chlamydomonas reinhardtii to a mild osmotic stress during a 24 h time-course experiment. The microalgae stress-responses were reconstructed from the generated proteometabolomic datasets using a systems biology approach. Protein and metabolite dynamics showed a Chlamydomonas tolerance to osmotic stress which seems to rely on three strategies: the accumulation of osmolyte/osmoprotective sugars and glycerol, the increase of ROS scavenging mechanisms, and the alteration of cell physiology. These responses involved specific proteome and metabolome changes, probably tuned by several signaling proteins (MAPK, PP2Cs, PKL1, GUN4) and metabolites as 2-hydroxyglutarate which accumulated under stress. Moreover, the function of the plant orthologs of these proteins suggested the potential activation of brassinosteroid- and ABA-mediated pathways in a plant-like way and the activation of a HOG-like osmorelay resembling a yeast-like response. These pathways were also probably regulating a long-term acclimation mediated by epigenetic mechanisms, being promising targets for further osmotic response characterization or exploitation towards engineering strains accumulating glycerol or other industry-demanding biomolecules.

Trees are sessile and long-lived organism so they have to rapidly adapt to dynamic and unfavorable environments (drought, soil salinity, heat, …) for ensure their survival. Acclimation is mostly related to epigenetic regulation mechanisms that act responding to environmental stimuli and thus regulating gene expression during leaf development, floral transition, bud dormancy, and climate change induced abiotic stress response. Also, environmental stresses have been related to the transgenerational inheritance of epigenetic marks, called epigenetic memory. Epigenetic variation complements natural genetic variation as a source of phenotypic and functional diversity in plants, resulting in a phenotypic plasticity including also traits of transgenerational inheritance. This chapter provide an overview about how epigenetic mechanisms act, the memory role and new epi-variates definition that combined will help us to create new biotechnological tools for forest trees productivity improvement.

The SnRK (Snf1-Related protein Kinase) gene family plays an important role in energy sensing and stress-adaptive responses in plant systems. In this study, Chlamydomonas CKIN family (SnRK in Arabidopsis) was defined after a genome-wide analysis of all sequenced Chlorophytes. Twenty-two sequences were defined as plant SnRK orthologs in Chlamydomonas and classified into two subfamilies: CKIN1 and CKIN2. While CKIN1 subfamily is reduced to one conserved member and a close protein (CKIN1L), a large CKIN2 subfamily clusters both plant-like and algae specific CKIN2s. The responsiveness of these genes to abiotic stress situations was tested by RT-qPCR. Results showed that almost all elements were sensitive to osmotic stress while showing different degrees of sensibility to other abiotic stresses, as occurs in land plants, revealing their specialization and the family pleiotropy for some elements. The regulatory pathway of this family may differ from land plants since these sequences shows unique regulatory features and some of them are sensitive to ABA, despite conserved ABA receptors (PYR/PYL/RCAR) and regulatory domains are not present in this species. Core Chlorophytes and land plant showed divergent stress signalling, but SnRKs/CKINs share the same role in cell survival and stress response and adaption including the accumulation of specific biomolecules. This fact places the CKIN family as well-suited target for bioengineering-based studies in microalgae (accumulation of sugars, lipids, secondary metabolites), while promising new findings in stress biology and specially in the evolution of ABA-signalling mechanisms.

Histone H4 acetylation at Lysine 16 (H4K16ac) is a key epigenetic mark involved in gene regulation, DNA repair and chromatin remodeling, and though it is known to be essential for embryonic development, its role during adult life is still poorly understood. Here we show that this lysine is massively hyperacetylated in peripheral neutrophils. Genome-wide mapping of H4K16ac in terminally differentiated blood cells, along with functional experiments, supported a role for this histone post-translational modification in the regulation of cell differentiation and apoptosis in the hematopoietic system. Furthermore, in neutrophils, H4K16ac was enriched at specific DNA repeats. These DNA regions presented an accessible chromatin conformation and were associated with the cleavage sites that generate the 50 kb DNA fragments during the first stages of programmed cell death. Our results thus suggest that H4K16ac plays a dual role in myeloid cells as it not only regulates differentiation and apoptosis, but it also exhibits a non-canonical structural role in poising chromatin for cleavage at an early stage of neutrophil cell death., Plan Nacional de I+D+I co-funding FEDER [PI15/00892 and PI18/01527 to M.F.F. and A.F.F.; PI16/01318 and PI14/01244 to C.L.]; ISCIII-Subdireccion General de Evaluacion y Fomento de la Investigacion, and Plan Nacional de I+D+I 2008–2011/FEDER [CP11/00131 to A.F.F.]; IUOPA (to G.F.B. and M.I.S.); Fundacion Cientifica de la AECC (to R.G.U.); Ministry of Economy and Competitiveness Juan de la Cierva postdoctoral fellowships [FJCI-2015-26965 to J.R.T., IJCI-2015- 23316 to V.L.]; Fundacion Ramon Areces (to M.F.F); FICYT (to E.G.T., M.G.G., A.C.); Asturias Regional Government [GRUPIN14-052 to M.F.F.]; Gobierno del Principado de Asturias, PCTI-Plan de Ciencia, Tecnologia e Innovacion co-funding Fondos FEDER (grant number IDI/2018/146 to M.F.F. and IDI/2018/144 to C.L.); Deutsche Forschungsgemeinschaft (DFG) [SFB960 to A.V.G., R.D.]; European Research Council [CoG-2014-646903]; Spanish Ministry of Economy and Competitiveness [SAF-SAF2013-43065 to P.M.]; Asociacion Española Contra el Cancer [AECC-CI-2015]; FERO Foundation, and the ISCIII [PI14-01191 to C.B.]; P.M. acknowledges financial support from The Obra Social La Caixa Fundacio Josep Carreras and The Generalitat de Catalunya (SGR330). P.M. an investigator from the Spanish Cell Therapy cooperative network (TERCEL). The IUOPA is supported by the Obra Social Liberbank-Cajastur, Spain. Funding for open access charge: Plan Nacional de I+D+I co-funding FEDER [PI18/01527].

A major problem in forest clonal productivity is the loss of morphogenetic capability with the increasing age of plants. However, despite of the importance of loss of morphogenetic competence, very little research has been done about the underlying mechanisms involved in this process. For this reason, a gene expression analysis using dot blot technique was performed in needles and stems of 1- and 3-year old Pinus radiata rootstock plants with a proved decrease in morphogenetic competence. Needles of one year old rootstock plants showed a higher number of up-regulated in genes mainly corresponding to photosynthesis and protein synthesis, degradation and modification, reflecting a higher number of active pathways in younger hedges, contrary to the older ones. Gene expression profiles found in stems are in agreement with those found in needles, indicating more active pathways in younger rootstock plants than in older ones. Several transcripts regulating transcription and translation were up-regulated in young competent tissues. Three-year-old stems presented an increase in the expression of an ethylene response factor, involved in plant organ senescence, indicating that pathways involved in senescence and ageing might inhibit the adventitious root formation, as in the older cuttings.

Adventitious organogenesis from zygotic embryos is one of the most reliable techniques to propagate clonal Pinus radiata individuals. Regulation of gene expression has an important role to generate a correct caulogenic pattern, and genomic DNA methylation is amongst the main studied regulatory mechanisms in animals and plants. The aim of this work is to evaluate the role of DNA methylation and histone H4 acetylation during different cell reprogramming processes. Embryo macromorphological responses to each growth regulator were correlated to DNA methylation and acetylated H4 histone content over time. Immunodetection of 5-mdC and AcH4 in whole embryos revealed differences in the tissue depending on the growth regulator. Adventitious shoot induction by benzyladenine is associated with a DNA hypomethylation. The distribution along the tissue of the methylation signal suggests a possible inhibition of growth and elongation in the embryos. However, a hypomethylation in the cotyledons during adventitious shoot induction could indicate an active gene expression during the organogenic process. On the other hand, alteration of embryo growth induced by indole butyric acid and 2,4-dichlorophenoxyacetic acid occurs along a wide change in DNA methylation and H4 histone acetylation content and distribution. These results show that the action of the different growth regulators is epigenetically regulated in both apical meristems.

Systems biology has emerged in the last years as a comprehensive set of tools which provides rich biological information by integrating different cell organization levels (genome, epigenome, transcripts, proteins, and metabolites) and providing not only the relationships and correlations among them but also giving the possibility of modeling how and why cells and tissues are plastic to different environments. To perform this characterization, several analytical methods (NGS, mass spectrometry) and statistical and modeling tools must be used. Contrary to classic targeted approaches, the untargeted analyses of a plant system far from introducing noise or scattering the focus of the research can provide new candidates, pathways, or counterintuitive mechanisms otherwise undetectable. In this chapter, we briefly describe methodology and applications of systems biology by using three different studies: natural variation of the metabolome of Pinus pinaster and its relation to different geographic origins and wood quality traits and how Pinus radiata adapt to thermal or ultraviolet stresses. These examples illustrate how systems biology can contribute toward the full understanding of the biological processes mediating tree stress adaption and development, and forest ecology, besides constituting a powerful tool for breeders toward the selection of specific donors for specific environments, or model how new mixtures of genotypes will impact over forestry demanding traits.

Long-lived conifers are vulnerable to climate change because classical evolutionary processes are slow in developing adaptive responses. Therefore, the capacity of a genotype to adopt different phenotypes is important. Gene expression is the primary mechanism that converts genome-encoded information into phenotypes, and DNA methylation is employed in the epigenetic regulation of gene expression. We investigated variations in global DNA methylation and gene expression between three Scots pine (Pinus sylvestris L.) populations located in northern and southern Finland using mature seeds. Gene expression levels were studied in six DNA methyltransferase (DNMT) genes, which were characterized in this study, and in 19 circadian clock genes regulating adaptive traits. In embryos, expression diversity was found for three DNMT genes, which maintain DNA methylation. The expression of two DNMT genes was strongly correlated with climate variables, which suggests a role for DNA methylation in local adaptation. For adaptation-related genes, expression levels showed between-population variation in 11 genes in megagametophytes and in eight genes in embryos, and many of these genes were linked to climate factors. Altogether, our results suggest that differential DNA methylation and gene expression contribute to local adaptation in Scots pine populations and may enhance the fitness of trees under rapidly changing climatic conditions.

The gametophyte of ferns is a cellular monolayer structure, whose more important function is to form the gametes, responsible of sexual fusion that will lead to sporophyte generation. In most cases, as sporophyte develops, the gametophyte is about to disappear, reflecting to have a role purely involved on reproduction. Omics technologies based on comprehensive biochemical and molecular characterizations of an organism, tissue, or cell type and next-generation omics approaches facilitate the analyses of non-model organisms owing to the rapid generation of large amounts of de novo systems biology data, making them attractive options for studying plant development and evolution.

Clonal propagation of Quercus suber via somatic embryogenesis is an alternative to conventional tree propagation methods; however, complete maturation of somatic embryos is considered the major bottleneck for mass propagation of Quercus species. During somatic embryogenesis, embryo development and maturation are controlled by signaling pathways that integrate information from genetic and epigenetic programs as well as hormonal signals. Therefore, in this study genes were identified related to epigenetic regulation and the abscisic acid (ABA) pathway during development and maturation of cork oak somatic embryos. A total of eight expressed sequence tags were obtained of genes encoding a 9-cis-epoxycarotenoid dioxygenase (NCED), two histone deacetylases (HDA6 and HDA19), two histone monoubiquitinases (HUB1 and HUB2), a histone H3 kinase (AUR3) as well as genes related to chromatin remodeling processes PICKLE and VP1/ABSCISIC ACID INSENSITIVE 3-LIKE 1 (VAL1). The analysis of the expression patterns of selected genes during different developmental stages indicated that QsNCED3 may play a role in ABA synthesis during embryogenesis. The change in the expression levels for all seven genes associated with epigenetic regulation showed that QsHUB1 and QsHUB2 may have a role in ABA signalling while QsHDA6 and QsHDA19 could act in different pathways than in Arabidopsis. Furthermore, expression levels of QsAUR3 indicated that histone phosphorylation is an early epigenetic mark in Q. suber somatic embryos while QsPICKLE and QsVAL1 may be necessary for the correct development of cork oak somatic embryos.

Global DNA methylation was classically considered the relative percentage of 5-methylcysine (5mC) with respect to total cytosine (C). Early approaches were based on the use of high-performance separation technologies and UV detection. However, the recent development of protocols using mass spectrometry for the detection has increased sensibility and permitted the precise identification of peak compounds based on their molecular masses. This allows work to be conducted with much less genomic DNA starting material and also to quantify 5-hydroxymethyl-cytosine (5hmC), a recently identified form of methylated cytosine that could play an important role in active DNA demethylation. Here, we describe the protocol that we currently use in our laboratory to analyze 5mC and 5hmC by mass spectrometry. The protocol, which is based on the method originally developed by Le and colleagues using Ultra Performance Liquid Chromatography (UPLC) and mass spectrometry (triple Quadrupole (QqQ)) detection, allows for the rapid and accurate quantification of relative global 5mC and 5hmC levels starting from just 1 μg of genomic DNA, which allows for the rapid and accurate quantification of relative global 5mC and 5hmC levels.

The integrative omics approach is crucial to identify the molecular mechanisms underlying high-temperature response in non-model species. Based on future scenarios of heat increase, Pinus radiata plants were exposed to a temperature of 40°C for a period of 5 days, including recovered plants (30 days after last exposure to 40°C) in the analysis. The analysis of the metabolome using complementary mass spectrometry techniques (GC-MS and LC-Orbitrap-MS) allowed the reliable quantification of 2,287 metabolites. The analysis of identified metabolites and highlighter metabolic pathways across heat time exposure reveal the dynamism of the metabolome in relation to high-temperature response in P. radiata, identifying the existence of a turning point (on day 3) at which P. radiata plants changed from an initial stress response program (shorter-term response) to an acclimation one (longer-term response). Furthermore, the integration of metabolome and physiological measurements, which cover from the photosynthetic state to hormonal profile, suggests a complex metabolic pathway interaction network related to heat-stress response. Cytokinins (CKs), fatty acid metabolism and flavonoid and terpenoid biosynthesis were revealed as the most important pathways involved in heat-stress response in P. radiata, with zeatin riboside (ZR) and isopentenyl adenosine (iPA) as the key hormones coordinating these multiple and complex interactions. On the other hand, the integrative approach allowed elucidation of crucial metabolic mechanisms involved in heat response in P. radiata, as well as the identification of thermotolerance metabolic biomarkers (L-phenylalanine, hexadecanoic acid, and dihydromyricetin), crucial metabolites which can reschedule the metabolic strategy to adapt to high temperature.

Background The use of enriched stable isotopes is of outstanding importance in chemical metrology as it allows the application of isotope dilution mass spectrometry (IDMS). Primary methods based on IDMS ensure the quality of the analytical measurements and traceability of the results to the international system of units. However, the synthesis of isotopically labelled molecules from enriched stable isotopes is an expensive and a difficult task. Either chemical and biochemical methods to produce labelled molecules have been proposed, but so far, few cost-effective methods have been described. Results The aim of this study was to use the microalgae Chlamydomonas reinhardtii to produce, at laboratory scale, 15N-labelled amino acids with a high isotopic enrichment. To do that, a culture media containing 15NH4Cl was used. No kinetic isotope effect (KIE) was observed. The labelled proteins biosynthesized by the microorganism were extracted from the biomass and the 15N-labelled amino acids were obtained after a protein hydrolysis with HCl. The use of the wall deficient strain CC503 cw92 mt+ is fit for purpose, as it only assimilates ammonia as nitrogen source, avoiding isotope contamination with nitrogen from the atmosphere or the reagents used in the culture medium, and enhancing the protein extraction efficiency compared to cell-walled wild type Chlamydomonas. The isotopic enrichment of the labelled amino acids was calculated from their isotopic composition measured by gas chromatography mass spectrometry (GC–MS). The average isotopic enrichment for the 16 amino acids characterized was 99.56 ± 0.05% and the concentration of the amino acids in the hydrolysate ranged from 18 to 90 µg/mL. Conclusions Previously reported biochemical methods to produce isotopically labelled proteins have been applied in the fields of proteomics and fluxomics. For these approaches, low amounts of products are required and the isotopic enrichment of the molecules has never been properly determined. So far, only 13C-labelled fatty acids have been isolated from labelled microalga biomass as valuable industrial products. In this study, we propose Chlamydomonas reinhardtii CC503 as a feasible microorganism and strain to produce labelled biomass from which a standard containing sixteen 15N-labelled amino acids could be obtained. Electronic supplementary material The online version of this article (doi:10.1186/s12934-017-0759-9) contains supplementary material, which is available to authorized users.

Performing proteomic studies on non-model organisms with little or no genomic information is still difficult. However, many specific processes and biochemical pathways occur only in species that are poorly characterized at the genomic level. For example, many plants can reproduce both sexually and asexually, the first one allowing the generation of new genotypes and the latter their fixation. Thus, both modes of reproduction are of great agronomic value. However, the molecular basis of asexual reproduction is not well understood in any plant. In ferns, it combines the production of unreduced spores (diplospory) and the formation of sporophytes from somatic cells (apogamy). To set the basis to study these processes, we performed transcriptomics by next-generation sequencing (NGS) and shotgun proteomics by tandem mass spectrometry in the apogamous fern D. affinis ssp. affinis. For protein identification we used the public viridiplantae database (VPDB) to identify orthologous proteins from other plant species and new transcriptomics data to generate a "species-specific transcriptome database" (SSTDB). In total 1,397 protein clusters with 5,865 unique peptide sequences were identified (13 decoy proteins out of 1,410, protFDR 0.93% on protein cluster level). We show that using the SSTDB for protein identification increases the number of identified peptides almost four times compared to using only the publically available VPDB. We identified homologs of proteins involved in reproduction of higher plants, including proteins with a potential role in apogamy. With the increasing availability of genomic data from non-model species, similar proteogenomics approaches will improve the sensitivity in protein identification for species only distantly related to models.

This report is intended to compare proteomic profiles between female and male gametophytes of Blechnum spicant L. For this purpose, female gametophytes were obtained from spores germinated on Murashige and Skoog medium (1962), and the male ones by culturing 30-day-old gametophytes on the same medium supplemented with extract derived from mature gametophytes, which exhibits anteridiogen effect. Proteins were extracted using the phenolic method, and after two-dimensional gel electrophoresis, 581 spots were detected in Coomassie stained gels within the 3-11 pH range and 10-100 kDa Mr ranges. Quantitative and qualitative differences in spot intensity between both types of gametophytes were found. The induction of male gametophytes by antheridiogens was correlated to a global increase in stress and defence-related pathways, which affect flavonoid signaling and cell division, while reducing protein biosynthesis, photosynthesis, and other energy-related pathways, reflecting how stressed are the gametophytes during the induction process. This is the first proteomic study that examines proteins associated to sexual development in the gametophyte of the fern B. spìcant.

Cork oak (Quercus suber L.) is a research priority in the Mediterranean area and because of cork oaks' distribution these stands are experiencing daily stress. Based on projections of intensifying climate change and considering the key role of exploring the recovery abilities, cork oak seedlings were subjected to a cumulative temperature increase from 25 degrees C to 55 degrees C and subsequent recovery. CO2 assimilation rate, chlorophyll fluorescence, anthocyanins, proline and lipid peroxidation were used to evaluate plant performance, while the relative abundance of seven genes encoding for proteins of cork oak with a putative role in thermal/stress regulation (POX1, POX2, HSP10.4, HSP17a.22, CHS, MTL and RBC) was analyzed by qPCR (quantitative Polymerase Chain Reaction). A temperature change to 35 degrees C showed abundance alterations in the tested genes; at 45 degrees C, the molecular changes were associated with an antioxidant response, possibly modulated by anthocyanins. At 55 degrees C, HSP17a.22, MTL and proline accumulation were evident. After recovery, physiological balance was restored, whereas POX1, HSP10.4 and MTL abundances were suggested to be involved in increased thermotolerance. The data presented here are expected to pinpoint some pathways changes occurring during such stress and further recovery in this particular Mediterranean species. (C) 2013 Elsevier GmbH. All rights reserved.

Globally expected changes in environmental conditions, especially the increase of UV irradiation, necessitate extending our knowledge of the mechanisms mediating tree species adaptation to this stress. This is crucial for designing new strategies to maintain future forest productivity. Studies focused on environmentally realistic dosages of UV irradiation in forest species are scarce. Pinus spp. are commercially relevant trees and not much is known about their adaptation to UV. In this work, UV treatment and recovery of Pinus radiata plants with dosages mimicking future scenarios, based on current models of UV radiation, were performed in a time-dependent manner. The combined metabolome and proteome analysis were complemented with measurements of + physiological parameters and gene expression. Sparse PLS analysis revealed complex molecular interaction networks of molecular and physiological data. Early responses prevented phototoxicity by reducing photosystem activity and the electron transfer chain together with the accumulation of photoprotectors and photorespiration. Apart from the reduction in photosynthesis as consequence of the direct UV damage on the photosystems, the primary metabolism was rearranged to deal with the oxidative stress while minimizing ROS production. New protein kinases and proteases related to signaling, coordination, and regulation of UV stress responses were revealed. All these processes demonstrate a complex molecular interaction network extending the current knowledge on UV-stress adaptation in pine.

Globally expected changes in environmental conditions, especially the increase of UV irradiation, necessitate extending our knowledge of the mechanisms mediating tree species adaptation to this stress. This is crucial for designing new strategies to maintain future forest productivity. Studies focused on environmentally realistic dosages of UV irradiation in forest species are scarce. Pinus spp. are commercially relevant trees and not much is known about their adaptation to UV. In this work, UV treatment and recovery of Pinus radiata plants with dosages mimicking future scenarios, based on current models of UV radiation, were performed in a time-dependent manner. The combined metabolome and proteome analysis were complemented with measurements of + physiological parameters and gene expression. Sparse PLS analysis revealed complex molecular interaction networks of molecular and physiological data. Early responses prevented phototoxicity by reducing photosystem activity and the electron transfer chain together with the accumulation of photoprotectors and photorespiration. Apart from the reduction in photosynthesis as consequence of the direct UV damage on the photosystems, the primary metabolism was rearranged to deal with the oxidative stress while minimizing ROS production. New protein kinases and proteases related to signaling, coordination, and regulation of UV stress responses were revealed. All these processes demonstrate a complex molecular interaction network extending the current knowledge on UV-stress adaptation in pine.

Use of meta-topolin (mT) [6-(3-hydroxybenzylamino) purine] to scale up the plantain clone ‘CEMSA ¾’ in temporary immersion systems (TIS), when compared with conventional micropropagation protocols, has been shown to improve production and quality of microplants. To evaluate the impact of those innovations on plant field performance, in vitro plants of ‘CEMSA ¾’ were subjected to either an additional multiplication cycle using TIS or semi-solid medium (SS) in the presence of 4.44 μM mT or N 6 -benzyladenine (BA). Growth and yield components in the microplants grown in field – plant crop – and in the developed plants of the following field generation – first ratoon – were evaluated. Also (epi)genomic traits were studied by flow cytometry, fluorimetry-based AFLP and HPLC analyses of global genomic DNA methylation. Neither in vitro microprogation systems – TIS and SS – nor cytokinins – mT and BA – had any factorial effect on yield productivity of the plant crop. In the first ratoon, significant differences in yield appeared, with TIS-BA plants being more productive than those generated from TIS-mT. For most of the measured variables, the plant crop had higher values than the first ratoon, but true-to-type and each off-type phenotype of the plant crop was always inherited by their corresponding offspring of the first ratoon. The proportion of true-to-type plants was higher for SS-BA and TIS-mT culture conditions. Irrespective of micropropagation protocol and phenotype, in the plant crop, average genomic DNA content was maintained and global genomic methylation levels were similar. Nevertheless, dwarf individuals showed more AFLP polymorphisms with respect to mother plants than the rest of the micropropagated plants, and a dwarfism-related AFLP marker is proposed. On the basis of the results obtained and previous reports, the innovative TIS-mT protocol was deemed to be the most suitable plantain multiplication technique among those tested.

The ability to control the timing of flowering is a key strategy for planning production in ornamental species such as the azalea; however, this requires a thorough understanding of floral induction pathways. DNA methylation is one of the main mechanisms involved in controlling the functional state of chromatin and gene expression in response to environmental and developmental signals. This work investigated the promotion of flowering in azaleas by the manipulation of environmental factors, using DNA methylation levels as a marker of floral bud development. The results showed that the change of long-day (LD) to short-day (SD) photoperiod is the primary factor responsible for floral induction in azaleas, whereas the existence of the previous cold period as well as the physiological memory are factors which improve floral production. Furthermore, for blooming to take place, 1300 units of growing degree days under an LD were necessary. The promotion of flowering in azaleas by alterations of photoperiod and temperature induced DNA methylation changes. The demethylation observed after the change from LD to SD is linked to a change in cell fate which is necessary for floral transition to take place and seems to be associated with the floral signal.

The floral transition includes a complex system of factors that interact and involve various biochemical signals, including plant growth regulators. The physiological signals involved in the control of the floral transition have been sparsely studied and mainly in plant species whose genetics are poorly known. In this work, the role of polyamines, gibberellins, and cytokinins was investigated by analyzing their endogenous content in vegetative and floral buds of azalea. The results showed that there is a clear distinction between floral and vegetative buds with respect to the levels of these plant hormones, with floral buds containing higher amounts of conjugated polyamines, gibberellins (GAs) from the non-13-hydroxylation pathway (GA9, GA7, and GA4), and cytokinins (particularly isopentenyl-type species), and vegetative buds containing higher amounts of free polyamines and gibberellins from the early 13-hydroxylation pathway and fewer cytokinins. In conclusion, there is a specific pattern of endogenous hormone profiles in both vegetative and floral bud development in azalea, which may be relevant for future research on the control of flowering by exogenous hormone applications.

In vitro physiology and carbon metabolism can be affected by the sink–source relationship. The effect of different sucrose concentrations (10, 30, and 50 g L−1), light intensities (80 and 150 μmol m−2 s−1), and CO2 levels (375 and 1,200 μmol mol−1) were tested during plantain micropropagation in temporary immersion bioreactors. Activities of pyruvate kinase, phosphoenol pyruvate carboxylase, and the photosynthesis rate were recorded. From the morphological and practical point of view, the best results were obtained when plants were cultured with 30 g L−1 sucrose, 80 μmol m−2 s−1 light intensity, and 1,200 μmol mol−1 CO2 concentration. This treatment improved leaf and root development, reduced respiration during in vitro culture, and increased starch level at the end of the hardening phase. In addition to that, the number of competent plants was increased from 80.0% to 91.0% at the end of the in vitro phase and the survival percentage from 95.71% to 99.80% during ex vitro hardening.

Embryogenic cell lines initiated from immature zygotic embryos of Pinus nigra Arn. ssp. Austriaca were characterized in terms of macromorphological traits (colour, bipolar structures formation, germination ability) and their embryogenic potential was defined as high, medium or null. Quantification of global genomic DNA methylation revealed the existence of specific DNA methylation levels for the determinated embryogenic potentials. The line considered as effectively embryogenic, i.e., with the ability of develop the whole embryogenic program and producing plants, showed the lowest methylation levels. There was also proved the existence of an inverse relationship between total contents of free PAs and embryogenic potential, being the highest contents of free putrescine and spermidine in the non-embryogenic line and the lowest in the effectively embryogenic one. Relationships among DNA methylation levels, profiles of free individual polyamine contents and embryogenic potentials based on the ability to produce well-formed somatic embryos with effective plant conversion are discussed.

This study analysed the changes in the endogenous levels of total and individual polyamines (PAs) during the different rooting phases in Pinus caribaea microshoots: induction, induction-initiation and functional root system emergence. The analysis, performed using high-resolution liquid chromatography, demonstrated that during the inductive phase there is a drop in total PA content in all the fractions, with an increase in the degradation product diaminopropane. In the induction-initiation phase PAs are present in all the fractions. The microshoots with root nodules always presented higher Putrescine (Put) levels, whereas those that did not have them had similar spermidine and Put levels, while maintaining elevated spermine levels. The comparative analysis of microshoots with and without a rooting response indicates that high PA levels are maintained when root manifestation does not occur, coinciding with basal callus formation.

Pinus radiata is one of the most economically important forest tree species, with a worldwide production of around 370 million m (3) of wood per year. Current selection of elite trees to be used in conservation and breeding programes requires the physiological and molecular characterization of available populations. To identify key proteins related to tree growth, productivity and responses to environmental factors, a proteomic approach is being utilized. In this paper, we present the first report of the 2-DE protein reference map of physiologically mature P. radiata needles, as a basis for subsequent differential expression proteomic studies related to growth, development, biomass production and responses to stresses. After TCA/acetone protein extraction of needle tissue, 549 +/- 21 well-resolved spots were detected in Coommassie-stained gels within the 5-8 pH and 10-100 kDa M(r) ranges. The analytical and biological variance determined for 450 spots were of 31 and 42%, respectively. After LC/MS/MS analysis of in-gel tryptic digested spots, proteins were identified by using the novel Paragon algorithm that tolerates amino acid substitution in the first-pass search. It allowed the confident identification of 115 out of the 150 protein spots subjected to MS, quite unusual high percentage for a poor sequence database, as is the case of P. radiata. Proteins were classified into 12 or 18 groups based on their corresponding cell component or biological process/pathway categories, respectively. Carbohydrate metabolism and photosynthetic enzymes predominate in the 2-DE protein profile of P. radiata needles.