Species pool, local assembly processes: Disentangling the mechanisms determining bacterial α- and ß-diversity during forest secondary succession.

Across ecology, and particularly within microbial ecology, there is limited understanding how the generation and maintenance of diversity. Although recent work has shown that both local assembly processes and species pools are important in structuring microbial communities, the relative contributions of these mechanisms remain an important question. Moreover, the roles of local assembly processes and species pools are drastically different when explicitly considering the potential for saturation or unsaturation, yet this issue is rarely addressed. Thus, we established a conceptual model that incorporated saturation theory into the microbiological domain to advance the understanding of mechanisms controlling soil bacterial diversity during forest secondary succession. Conceptual model hypotheses were tested by coupling soil bacterial diversity, local assembly processes and species pools using six different forest successional chronosequences distributed across multiple climate zones. Consistent with the unsaturated case proposed in our conceptual framework, we found that species pool consistently affected α-diversity, even while local assembly processes on local richness operate. In contrast, the effects of species pool on ß-diversity disappeared once local assembly processes were taken into account, and changes in environmental conditions during secondary succession led to shifts in ß-diversity through mediation of the strength of heterogeneous selection. Overall, this study represents one of the first to demonstrate that most local bacterial communities might be unsaturated, where the effect of species pool on α-diversity is robust to the consideration of multiple environmental influences, but ß-diversity is constrained by environmental selection.

Cavitation fatigue in conifers: a study on eight European species.

After drought-induced embolism and repair, tree xylem may be weakened against future drought events (cavitation fatigue). As there are few data on cavitation fatigue in conifers available, we quantified vulnerability curves (VCs) after embolism/repair cycles on eight European conifer species. We induced 50% and 100% loss of conductivity (LC) with a cavitron, and analyzed VCs. Embolism repair was obtained by vacuum infiltration. All species demonstrated complete embolism repair and a lack of any cavitation fatigue after 50% LC . After 100% LC, European larch (Larix decidua), stone pine (Pinus cembra), Norway spruce (Picea abies), and silver fir (Abies alba) remained unaffected, while mountain pine (Pinus mugo), yew (Taxus baccata), and common juniper (Juniperus communis) exhibited 0.4-0.9 MPa higher vulnerability to embolism. A small cavitation fatigue observed in Scots pine (Pinus sylvestris) was probably biased by incomplete embolism repair, as indicated by a correlation of vulnerability shifts and conductivity restoration. Our data demonstrate that cavitation fatigue in conifers is species-specific and depends on the intensity of preceding LC. The lack of fatigue effects after moderate LC, and relevant effects in only three species after high LC, indicate that conifers are relatively resistant against cavitation fatigue. This is remarkable considering the complex and delicate conifer pit architecture and may be important considering climate change projections.

Characterization of gelsevirine metabolites in rat liver S9 by accurate mass measurements using high-performance liquid chromatography/quadrupole-time-of-flight mass spectrometry.

RATIONALE: Gelsemium elegans Benth. belongs to the family Loganiaceae and is widely distributed in northern America, east Asia, and southeast Asia. It has attracted wide attention for its diverse biological effects and complex architectures. Gelsevirine is one of the major components in G. elegans. Compared with other alkaloids from G. elegans, gelsevirine exhibits equally potent anxiolytic effects but with less toxicity. However, the metabolism of gelsevirine has not been clearly elucidated. METHODS: The metabolism of gelsevirine was investigated using liver S9 fractions derived from rat liver homogenates by centrifugation at 9000 g. A rapid and accurate high-performance liquid chromatography/quadrupole-time-of-flight mass spectrometry (HPLC/QqTOF-MS) method was applied to characterize the gelsevirine metabolites. RESULTS: We discovered a total number of four metabolites of gelsevirine. The metabolic pathways of gelsevirine consisted of hydrogenation, N-demethylenation and oxidation in rat liver S9. CONCLUSIONS: This is the first study on the metabolism of gelsevirine. We proposed possible metabolic pathways of gelsevirine. These findings may warrant future studies of the in vivo metabolism of gelsemine in animals.

Strigolactones Promote Leaf Elongation in Tall Fescue through Upregulation of Cell Cycle Genes and Downregulation of Auxin Transport Genes in Tall Fescue under Different Temperature Regimes.

Strigolactones (SLs) have recently been shown to play roles in modulating plant architecture and improving plant tolerance to multiple stresses, but the underlying mechanisms for SLs regulating leaf elongation and the influence by air temperature are still unknown. This study aimed to investigate the effects of SLs on leaf elongation in tall fescue (Festuca arundinacea, cv. 'Kentucky-31') under different temperature regimes, and to determine the interactions of SLs and auxin in the regulation of leaf growth. Tall fescue plants were treated with GR24 (synthetic analog of SLs), naphthaleneacetic acid (NAA, synthetic analog), or N-1-naphthylphthalamic acid (NPA, auxin transport inhibitor) (individually and combined) under normal temperature (22/18 °C) and high-temperature conditions (35/30 °C) in controlled-environment growth chambers. Exogenous application of GR24 stimulated leaf elongation and mitigated the heat inhibition of leaf growth in tall fescue. GR24-induced leaf elongation was associated with an increase in cell numbers, upregulated expression of cell-cycle-related genes, and downregulated expression of auxin transport-related genes in elongating leaves. The results suggest that SLs enhance leaf elongation by stimulating cell division and interference with auxin transport in tall fescue.

Genome-Wide Identification of Direct Targets of the TTG1-bHLH-MYB Complex in Regulating Trichome Formation and Flavonoid Accumulation in Arabidopsis Thaliana.

Extensive studies have shown that the MBW complex consisting of three kinds of regulatory proteins, MYB and basic helix-loop-helix (bHLH) transcription factors and a WD40 repeat protein, TRANSPARENT TESTA GLABRA1 (TTG1), acts in concert to promote trichome formation and flavonoid accumulation in Arabidopsis thaliana. TTG1 functions as an essential activator in these two biological processes. However, direct downstream targets of the TTG1-dependent MBW complex have not yet been obtained in the two biological processes at the genome-wide level in A. thaliana. In the present study, we found, through RNA sequencing and quantitative real-time PCR analysis, that a great number of regulatory and structural genes involved in both trichome formation and flavonoid accumulation are significantly downregulated in the young shoots and expanding true leaves of ttg1-13 plants. Post-translational activation of a TTG1-glucocorticoid receptor fusion protein and chromatin immunoprecipitation assays demonstrated that these downregulated genes are directly or indirectly targeted by the TTG1-dependent MBW complex in vivo during trichome formation and flavonoid accumulation. These findings further extend our understanding of the role of TTG1-dependent MBW complex in the regulation of trichome formation and flavonoid accumulation in A. thaliana.

Sedoheptulose-1,7-Bisphosphatase is Involved in Methyl Jasmonate- and Dark-Induced Leaf Senescence in Tomato Plants.

Leaf senescence represents the final stage of leaf development and is regulated by diverse internal and environmental factors. Jasmonates (JAs) have been demonstrated to induce leaf senescence in several species; however, the mechanisms of JA-induced leaf senescence remain largely unknown in tomato plants (Solanum lycopersicum). In the present study, we tested the hypothesis that sedoheptulose-1,7-bisphosphatase (SBPase), an enzyme functioning in the photosynthetic carbon fixation in the Calvin⁻Benson cycle, was involved in methyl jasmonate (MeJA)- and dark-induced leaf senescence in tomato plants. We found that MeJA and dark induced senescence in detached tomato leaves and concomitantly downregulated the expression of SlSBPASE and reduced SBPase activity. Furthermore, CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9)-mediated mutagenesis of SlSBPASE led to senescence-associated characteristics in slsbpase mutant plants, including loss of chlorophyll, repressed photosynthesis, increased membrane ion leakage, and enhanced transcript abundance of senescence-associated genes. Collectively, our data suggest that repression of SBPase by MeJA and dark treatment plays a role in JA- and dark-induced leaf senescence.

Knockout of SlSBPASE Suppresses Carbon Assimilation and Alters Nitrogen Metabolism in Tomato Plants.

Sedoheptulose-1,7-bisphosphatase (SBPase) is an enzyme in the Calvin⁻Benson cycle and has been documented to be important in carbon assimilation, growth and stress tolerance in plants. However, information on the impact of SBPase on carbon assimilation and nitrogen metabolism in tomato plants (Solanum lycopersicum) is rather limited. In the present study, we investigated the role of SBPase in carbon assimilation and nitrogen metabolism in tomato plants by knocking out SBPase gene SlSBPASE using clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) gene editing technology. Compared with wild-type plants, slsbpase mutant plants displayed severe growth retardation. Further analyses showed that knockout of SlSBPASE led to a substantial reduction in SBPase activity and as a consequence, ribulose-1,5-bisphosphate (RuBP) regeneration and carbon assimilation rate were dramatically inhibited in slsbpase mutant plants. It was further observed that much lower levels of sucrose and starch were accumulated in slsbpase mutant plants than their wild-type counterparts during the photoperiod. Intriguingly, mutation in SlSBPASE altered nitrogen metabolism as demonstrated by changes in levels of protein and amino acids and activities of nitrogen metabolic enzymes. Collectively, our data suggest that SlSBPASE is required for optimal growth, carbon assimilation and nitrogen metabolism in tomato plants.

Exogenous Melatonin Mitigates Methyl Viologen-Triggered Oxidative Stress in Poplar Leaf.

As a ubiquitous molecule, melatonin plays a crucial role in tolerance to multiple stresses in plants. In the present work, we report the role of exogenous melatonin in relieving oxidative stress induced by methyl viologen (MV) in poplar (Populus alba × Populus glandulosa) leaf. Leaf discs pretreated with melatonin exhibited increased tolerance to MV-mediated oxidative stress. It was observed that melatonin pretreatment effectively reduced membrane damage and lipid oxidation as demonstrated by decreased relative electrolyte leakage and malonaldehyde content in poplar leaf discs. Exogenous melatonin also stimulated activities of antioxidant enzymes, including superoxide dismutase (SOD), catalase (CAT), peroxidase (POD), and ascorbate peroxidase (APX), and enhanced accumulation of non-enzymatic antioxidants of AsA and GSH in leaf discs exposed to MV. In addition, pretreatment of melatonin prompted expression of genes for those antioxidant enzymes. Notably, exogenous melatonin increased expression of P5CS, a key gene for proline biosynthesis, under MV treatment. It was further observed that pretreatment with melatonin boosted activity of P5CS as well as accumulation of proline in leaf discs under MV-mediated oxidative stress. Collectively, this work provides evidence for the ameliorative effect of melatonin on MV-induced oxidative stress in poplar leaf.

Exogenous Melatonin Improves Tolerance to Water Deficit by Promoting Cuticle Formation in Tomato Plants.

The plant cuticle, composed of cutin and waxes, is a hydrophobic layer coating the aerial organs of terrestrial plants and playing a critical role in limiting water loss. While melatonin has been recently demonstrated to be involved in responses to drought stress in plants, its relationship with cuticle formation is not known. In the present work, we report the effects of melatonin on the formation of cuticle in tomato leaves subjected to water deficit. Preliminary analysis by light microscope showed that tomato leaves pretreated with exogenous melatonin might have thicker cutin than tomato leaves without melatonin pretreatment under water deficit condition. Chemical characterization showed that exogenous application of melatonin increased the level of cuticular waxes in tomato leaves under water deficit. Consistent with the change in cuticular waxes was the increased abundance of wax-associated gene transcripts. Further, assessment of water loss and chlorophyll leaching in tomato leaves revealed the association of cuticle deposition with reduced leaf permeability, which is important in restricting water loss in water deficit-stressed tomato plants. These results suggest a role for melatonin in regulating leaf cuticle formation and non-stomatal water loss in leaves.

Sodium Hydroxide Pinpoint Pressing Permeation Method for the Animal Modeling of Sick Sinus Syndrome.

Sodium hydroxide pinpoint pressing permeation (SHPPP) was investigated in order to build a rat model of sick sinus syndrome (SSS), which is easy to operate and control the degree of damage, with fewer complications and applicable for large and small animals.Thirty healthy Wistar rats (15 males and 15 females, weighing 250-350 g) were randomly divided into 3 groups, namely a formaldehyde thoracotomy wet compressing group (FTWC), formaldehyde pinpoint pressing permeation group (FPPP) group, and SHPPP group. The number of surviving rats, heart rate (HR), sinoatrial node recovery time (SNRT), corrected SNRT (CSNRT), and sinoatrial conduction time (SACT) were recorded 3 days, one week, and two weeks after modeling.The achievement ratio of modeling was 10% in the FTWC group, 40% in the FPPP group, and 70% in the SHPPP group, and the differences were statistically significant (χ(2) = 7.250, P = 0.007). Meanwhile, the HR was reduced by about 37% in these 3 groups 3 days after modeling, while the reduction was maintained only in SHPPP (P > 0.05) and the HR was re-elevated in the FTWC and FPPP groups 2 weeks after modeling (P < 0.05). Additionally, the SNRT, cS-NRT, and SACT were significantly prolonged compared with pre-modeling in all 3 groups (P < 0.01).SHPPP was the best method with which to build an SSS model with stable and lasting low HR and high success rate of modeling, which might be helpful for further studies on the SSS mechanisms and drugs.

Water relations of Robinia pseudoacacia†L.: do vessels cavitate and refill diurnally or are R-shaped curves invalid in Robinia?

Since 2005, an unresolved debate has questioned whether R-shaped vulnerability curves (VCs) might be an artefact of the centrifuge method of measuring VCs. VCs with R-shape show loss of stem conductivity from approximately zero tension, and if true, this suggests that some plants either refill embolized vessels every night or function well with a high percentage of vessels permanently embolized. The R-shaped curves occur more in species with vessels greater than half the length of the segments spun in a centrifuge. Many have hypothesized that the embolism is seeded by agents (bubbles or particles) entering the stem end and travelling towards the axis of rotation in long vessels, causing premature cavitation. VCs were measured on Robinia pseudoacacia L. by three different techniques to yield three different VCs; R-shaped: Cavitron P50 = 0.30 MPa and S-shaped: air injection P50 = 1.48 MPa and bench top dehydration P50 = 3.57 MPa. Stem conductivity measured in the Cavitron was unstable and is a function of vessel length when measured repeatedly with constant tension, and this observation is discussed in terms of stability of air bubbles drawn into cut-open vessels during repeated Cavitron measurement of conductivity; hence, R-shaped curves measured in a Cavitron are probably invalid.

Recalcitrant vulnerability curves: methods of analysis and the concept of fibre bridges for enhanced cavitation resistance.

Vulnerability curves (VCs) generally can be fitted to the Weibull equation; however, a growing number of VCs appear to be recalcitrant, that is, deviate from a Weibull but seem to fit dual Weibull curves. We hypothesize that dual Weibull curves in Hippophae rhamnoides L. are due to different vessel diameter classes, inter-vessel hydraulic connections or vessels versus fibre tracheids. We used dye staining techniques, hydraulic measurements and quantitative anatomy measurements to test these hypotheses. The fibres contribute 1.3% of the total stem conductivity, which eliminates the hypothesis that fibre tracheids account for the second Weibull curve. Nevertheless, the staining pattern of vessels and fibre tracheids suggested that fibres might function as a hydraulic bridge between adjacent vessels. We also argue that fibre bridges are safer than vessel-to-vessel pits and put forward the concept as a new paradigm. Hence, we tentatively propose that the first Weibull curve may be accounted by vessels connected to each other directly by pit fields, while the second Weibull curve is associated with vessels that are connected almost exclusively by fibre bridges. Further research is needed to test the concept of fibre bridge safety in species that have recalcitrant or normal Weibull curves.

Chromosome-level genome assembly of Platycarya strobilacea.

Platycarya strobilacea belongs to the walnut family (Juglandaceae), is commonly known as species endemic to East Asia, and is an ecologically important, wind pollinated, woody deciduous tree. To facilitate this ancient tree for the ecological value and conservation of this ancient tree, we report a new high-quality genome assembly of P. strobilacea. The genome size was 677.30 Mb, with a scaffold N50 size of 45,791,698 bp, and 98.43% of the assembly was anchored to 15 chromosomes. We annotated 32,246 protein-coding genes in the genome, of which 96.30% were functionally annotated in six databases. This new high-quality assembly of P. strobilacea provide valuable resource for the phylogenetic and evolutionary analysis of the walnut family and angiosperm.

Metabolomic profiling for identification of potential biomarkers in the protective effects of modified Sinisan against liver injury in dimethylnitrosamine treated rats.

Metabolomics is a new platform based on the comprehensive analysis of low molecular weight metabolites and provides a powerful approach to discover biomarkers in biological systems. Modified Sinisan (MSNS), a traditional Chinese medicine formula, displayed bright prospects in the prevention and therapy of liver injury. However, its molecular mechanism of hepatoprotective effects remains unclear. This paper was designed to explore the effects and potential mechanisms of MSNS against dimethylnitrosamine-induced liver injury. Global metabolic profiling was performed by ultra-performance liquid chromatography/electrospray ionization quadrupole time-of-flight mass spectrometry (UPLC/ESI-Q-TOF-MS) in conjunction with multivariate data analysis and pathway analysis. Eleven serum biomarkers were identified and pathway analysis results showed that phenylalanine, tyrosine and tryptophan biosynthesis, phenylalanine metabolism, tryptophan metabolism, retinol metabolism, tyrosine metabolism were perturbed by liver injury. More importantly, MSNS has showed satisfactory pharmacological effect on liver injury through partially regulating the perturbed pathways, correlates well to the biochemical and histopathological detection results. The present study proved that the robust metabolomics approach is promising for unraveling hepatoprotective effects of MSNS and these findings provide new insights into mechanisms of the liver injury, and its pathophysiologic processes.

Ultrasound promotes germination of aging Pinus tabuliformis seeds is associated with altered lipid metabolism.

Seed germination is an essential biological process for establishing new organisms of higher plants, it is especially significant for those aged seeds stored in gene banks for years. In this study, we investigated ultrasound treatment induced germination for aged Pinus tabuliformis seeds, which has been used in large scale aircraft sowing based afforestation in North China over 30 years' ago without knowing possible mechanisms. We showed certain strength of ultrasound could increase the germination rate of aged seeds for about 3 times compare with control. Interestingly, although our transcriptome and lipidome analysis showed the differences between control and ultrasound treatments can be observed 1 day after germination by partial least squares discriminant analysis (PLSDA) analysis, majority (75 % or 69 %) of the significantly altered genes or lipids were commonly shared between them. Further analysis for the commonly altered lipids between both treatments showed ultrasound provoked the variations of lipids during germination process. Our investigation also revealed large amount of ultrasound-related genes and lipids that might be involved in germination promotion process. We hypothesis ultrasound provokes seed lipidome which further increases seed germination of Pinus tabuliformis. Our study provides new insides into the role of ultrasound induced lipidome change in seed germination. Moreover, we provide a new method to improve germination of aged seeds which might benefit preservation of seeds in gene banks.

Pan-genome and transcriptome analyses provide insights into genomic variation and differential gene expression profiles related to disease resistance and fatty acid biosynthesis in eastern black walnut (Juglans nigra).

Walnut (Juglans) species are used as nut crops worldwide. Eastern black walnut (EBW, Juglans nigra), a diploid, horticultural important woody species is native to much of eastern North America. Although it is highly valued for its wood and nut, there are few resources for understanding EBW genetics. Here, we present a high-quality genome assembly of J. nigra based on Illumina, Pacbio, and Hi-C technologies. The genome size was 540.8 Mb, with a scaffold N50 size of 35.1 Mb, and 99.0% of the assembly was anchored to 16 chromosomes. Using this genome as a reference, the resequencing of 74 accessions revealed the effective population size of J. nigra declined during the glacial maximum. A single whole-genome duplication event was identified in the J. nigra genome. Large syntenic blocks among J. nigra, Juglans regia, and Juglans microcarpa predominated, but inversions of more than 600 kb were identified. By comparing the EBW genome with those of J. regia and J. microcarpa, we detected InDel sizes of 34.9 Mb in J. regia and 18.3 Mb in J. microcarpa, respectively. Transcriptomic analysis of differentially expressed genes identified five presumed NBS-LRR (NUCLEOTIDE BINDING SITE-LEUCINE-RICH REPEAT) genes were upregulated during the development of walnut husks and shells compared to developing embryos. We also identified candidate genes with essential roles in seed oil synthesis, including FAD (FATTY ACID DESATURASE) and OLE (OLEOSIN). Our work advances the understanding of fatty acid bioaccumulation and disease resistance in nut crops, and also provides an essential resource for conducting genomics-enabled breeding in walnut.

Photosynthesis and Fine Root Growth Dynamics of Soybean in Walnut-Soybean Agroforestry System.

Agroforestry system is regarded as a promising practice in sustainable agricultural management. However, the effects of long-term tree-based intercropping on crop remain poorly understood, especially in the Loess Plateau (China). In this study, the impacts of photosynthetic and respiration rate were determined by the portable photosynthesis system (Li-6400), and the effects of the root growth dynamics of soybean in the walnut-soybean intercropping system were measured by soil auger and WinRHIZO root analysis system, in the Loess Plateau. The results showed that soybean reached the highest net photosynthetic rate during flowering period, with the net photosynthetic rate of intercropped soybean, which was 20.40 µmol·m-2·s-1, significantly higher than that of its monocropped counterpart. Soybean biomass reached the maximum during the pod-bearing period, with intercropped soybean biomass being 25.49 g, significantly higher than that of its monocropped counterpart. The mean diameter and increased density of soybean fine roots reduced along with increased soil depth. Both the diameter (0.43 mm) and increased density (930 cm/dm3) of intercropped soybean fine roots were evidently higher than those of monocropped soybean (0.35 mm, 780 cm/dm3). With increasing cropping years, fine roots of intercropped soybean tended to be mainly distributed in soil at a depth between 0 and 20 cm from the fifth year. Collectively, compared with soybean monoculture, walnut-soybean agroforestry system is more conducive to soybean growth in the Loess Plateau.

SlMYC2 mediates jasmonate-induced tomato leaf senescence by promoting chlorophyll degradation and repressing carbon fixation.

Leaf senescence occurs as the last developmental phase of leaf. The initiation and progression of leaf senescence is highly regulated by a plethora of internal developmental signals and environmental stimuli. Being an important class of phytohormones, jasmonates (JAs) are shown to induce premature leaf senescence in tomato (Solanum lycopersicum), nevertheless, the underlying mechanisms remain enigmatic. Here, we report that tomato MYC2, a key factor in the JA signal transduction, functions in JA-induced tomato leaf senescence by promoting chlorophyll degradation and inhibiting photosynthetic carbon fixation. We found that exogenous application of MeJA reduced chlorophyll content, decreased carbon assimilation rates and disrupted membrane integrity. We further demonstrated using SlMYC2-RNAi tomato plants that SlMYC2 enhanced the expression of SlPAO, which encodes a chlorophyll degradation enzyme, but suppressed the expression of SlRCA and SlSBPASE, both of which are required for photosynthesis and growth in plants. Dual-luciferase assay confirmed that SlMYC2 activated the transcription of SlPAO, but inhibited the transcription of SlRCA and SlSBPASE. Furthermore, repression of SlRCA led to typical features associated with leaf senescence in tomato. Taken together, these results favor that tomato MYC2 acts positively in the regulation of JA-dependent tomato leaf senescence. The results extend our mechanistic understanding of JA-induced senescence in an important horticultural crop.

Jasmonate and Melatonin Act Synergistically to Potentiate Cold Tolerance in Tomato Plants.

Both jasmonic acid (JA) and melatonin (MT) have been demonstrated to play positive roles in cold tolerance, however, whether and how they crosstalk in the cold responses in plants remain elusive. Here, we report that JA and MT act synergistically in the cold tolerance in tomato plants (Solanum lycopersicum). It was found that JA and MT were both substantially accumulated in response to cold stress and foliar applications of methyl jasmonate (MeJA) and MT promoted cold tolerance as evidenced by increased Fv/Fm, decreased relative electrolyte leakage (EL) and declined H2O2 accumulation in tomato plants. Inhibition of MT biosynthesis attenuated MeJA-induced cold tolerance, while inhibition of JA biosynthesis reduced MT accumulation in tomato plants under cold conditions. Furthermore, qRT-PCR analysis showed that the expressions of two MT biosynthetic genes, SlSNAT and SlAMST, were strongly induced by MeJA, whereas suppression of SlMYC2, a master JA signaling regulator, abated the expressions of SlSNAT and SlAMST under cold stress. Additionally, suppression of SlMYC2 reduced MT accumulation, decreased Fv/Fm and increased EL in cold-stressed tomato plants. Interestingly, exogenous MT promoted JA accumulation, while inhibition of MT biosynthesis significantly reduced JA accumulation in tomato plants under the cold condition. Taken together, these results suggest that JA and MT act cooperatively in cold tolerance and form a positive feedback loop, amplifying the cold responses of tomato plants. Our findings might be translated into the development of cold-resistant tomato cultivars by genetically manipulating JA and MT pathways.

Whole genome based insights into the phylogeny and evolution of the Juglandaceae.

BACKGROUND: The walnut family (Juglandaceae) contains commercially important woody trees commonly called walnut, wingnut, pecan and hickory. Phylogenetic relationships and diversification within the Juglandaceae are classic and hot scientific topics that have been elucidated by recent fossil, morphological, molecular, and (paleo) environmental data. Further resolution of relationships among and within genera is still needed and can be achieved by analysis of the variation of chloroplast, mtDNA, and nuclear genomes. RESULTS: We reconstructed the backbone phylogenetic relationships of Juglandaceae using organelle and nuclear genome data from 27 species. The divergence time of Juglandaceae was estimated to be 78.7 Mya. The major lineages diversified in warm and dry habitats during the mid-Paleocene and early Eocene. The plastid, mitochondrial, and nuclear phylogenetic analyses all revealed three subfamilies, i.e., Juglandoideae, Engelhardioideae, Rhoipteleoideae. Five genera of Juglandoideae were strongly supported. Juglandaceae were estimated to have originated during the late Cretaceous, while Juglandoideae were estimated to have originated during the Paleocene, with evidence for rapid diversification events during several glacial and geological periods. The phylogenetic analyses of organelle sequences and nuclear genome yielded highly supported incongruence positions for J. cinerea, J. hopeiensis, and Platycarya strobilacea. Winged fruit were the ancestral condition in the Juglandoideae, but adaptation to novel dispersal and regeneration regimes after the Cretaceous-Paleogene boundary led to the independent evolution of zoochory among several genera of the Juglandaceae. CONCLUSIONS: A fully resolved, strongly supported, time-calibrated phylogenetic tree of Juglandaceae can provide an important framework for studying classification, diversification, biogeography, and comparative genomics of plant lineages. Our addition of new, annotated whole chloroplast genomic sequences and identification of their variability informs the study of their evolution in walnuts (Juglandaceae).