Ecotype formation and prophage domestication during gut bacterial evolution.

How much bacterial evolution occurs in our intestines and which factors control it are currently burning questions. The formation of new ecotypes, some of which capable of coexisting for long periods of time, is highly likely in our guts. Horizontal gene transfer driven by temperate phages that can perform lysogeny is also widespread in mammalian intestines. Yet, the roles of mutation and especially lysogeny as key drivers of gut bacterial adaptation remain poorly understood. The mammalian gut contains hundreds of bacterial species, each with many strains and ecotypes, whose abundance varies along the lifetime of a host. A continuous high input of mutations and horizontal gene transfer events mediated by temperate phages drives that diversity. Future experiments to study the interaction between mutations that cause adaptation in microbiomes and lysogenic events with different costs and benefits will be key to understand the dynamic microbiomes of mammals. Also see the video abstract here: https://youtu.be/Zjqsiyb5Pk0.

Analyzing the response of rice to tefuryltrione herbicide: Haplotype variation and evolutionary dynamics of the HIS1 gene.

Weeds pose multifaceted challenges in rice cultivation, leading to substantial economic losses through reduced yield and poor grain quality. Harnessing the natural genetic diversity in germplasm collections becomes crucial for identifying novel herbicide resistance loci in crops. A comprehensive analysis was conducted on 475 rice accessions from the KRICE depository, assessing their response to TFT (tefuryltrione) and probing the underlying HIS1 (HPPD INHIBITOR SENSITIVE 1) genotypic variations. The HIS1 gene, responsible for detoxifying benzobicyclon (BBC) and imparting broad-spectrum herbicide resistance, holds significant promise in rice breeding. This study explores the genetic landscape of HIS1 within Korean rice collection (KRICE), aiming to unveil genetic variations, haplotype diversity, and evolutionary relationships across diverse rice ecotypes. The indica ecotype showed the highest nucleotide diversity, while the wild and temperate japonica groups exhibited low diversity, hinting at selective sweeps and possible population expansion. Negative Tajima's D values in temperate japonica and wild groups indicate an excess of low-frequency mutations, potentially resulting from selective sweeps. In contrast, with positive Tajima's D values, admixture, indica, and aus groups suggest balancing selection. Furthermore, haplotype analysis uncovered 42 distinct haplotypes within KRICE, with four shared haplotypes between cultivated and wild accessions, four specific to cultivated accessions, and 34 specific to wild types. Phenotypic assessments of these haplotypes revealed that three haplotypes, viz., Hap_1 (predominant in japonica), Hap_2 (predominant in indica), and Hap_3 (specific to indica), displayed significant differences from aus-specific Hap_4 and indica-specific Hap_5. This study offers insights into genetic diversity, selective pressures, and ecotype-specific responses, ultimately paving the way for developing HPPD-inhibiting herbicide-resistant rice cultivars.

Environmental correlates of adaptive diversification in postglacial freshwater fishes.

Determining how environmental conditions contribute to divergence among populations and drive speciation is fundamental to resolving mechanisms and understanding outcomes in evolutionary biology. Postglacial freshwater fish species in the Northern Hemisphere are ideal biological systems to explore the effects of environment on diversification in morphology, ecology, and genetics (ecomorph divergences) within lakes. To date, various environmental factors have been implicated in the presence of multiple ecomorphs within particular lakes or regions. However, concerted evidence for generalizable patterns in environmental variables associated with speciation across geographical regions and across species and genera has been lacking. Here, we aimed to identify key biotic and abiotic factors associated with ecological divergence of postglacial freshwater fish species into multiple sympatric ecomorphs, focusing on species in the well-studied, widespread, and co-distributed genera Gasterosteus, Salvelinus, and Coregonus (stickleback, charr, and whitefish, respectively). We found that the presence of multiple sympatric ecomorphs tended to be associated with increasing lake surface area, maximum depth, and nutrient availability. In addition, predation, competition, and prey availability were suggested to play a role in divergence into multiple ecomorphs, but the effects of biotic factors require further study. Although we identified several environmental factors correlated with the presence of multiple ecomorphs, there were substantial data gaps across species and regions. An improved understanding of these systems may provide insight into both generalizable environmental factors involved in speciation in other systems, and potential ecological and evolutionary responses of species complexes when these variables are altered by environmental change.

miR394 enhances WUSCHEL-induced somatic embryogenesis in Arabidopsis thaliana.

Many plant species can give rise to embryos from somatic cells after a simple hormone treatment, illustrating the remarkable developmental plasticity of differentiated plant cells. However, many species are recalcitrant to somatic embryo formation for unknown reasons, which poses a significant challenge to agriculture, where somatic embryogenesis is an important tool to propagate desired genotypes. The micro-RNA394 (miR394) promotes shoot meristem maintenance in Arabidopsis thaliana, but the underlying mechanisms have remained elusive. We analyzed whether miR394 affects indirect somatic embryogenesis and determined the transcriptome of embryogenic callus upon miR394-enhanced somatic embryogenesis. We show that ectopic miR394 expression enhances somatic embryogenesis in the recalcitrant Ler accession when co-expressed with the transcription factor WUSCHEL (WUS) and that miR394 acts in this process through silencing the target LEAF CURLING RESPONSIVENESS (LCR). Furthermore, we show that higher endogenous miR394 levels are required for the elevated embryogenic potential of the Columbia accession compared with Ler, providing a mechanistic explanation for this natural variation. Our transcriptional analysis provides a framework for miR394 function in regulating pluripotency by expanding WUS-mediated direct transcriptional repression.

Tidal gradients, fine-scale homing and a potential cryptic ecotype of wild spawning pink salmon (Oncorhynchus gorbuscha).

The homing behaviour of salmon is a remarkable natural phenomenon, critical for shaping the ecology and evolution of populations yet the spatial scale at which it occurs is poorly understood. This study investigated the spatial scale and mechanisms driving homing as depicted by spawning site-choice behaviour in pink salmon (Oncorhynchus gorbuscha) in Prince William Sound, Alaska. Molecular pedigree analyses of over 30,000 adult spawners in four streams revealed that pink salmon exhibit fine-scale site fidelity within a stream, returning to within <100 m of their parents. Homing behaviours were driven in part by a salinity gradient between intertidal and freshwater environments, with individuals incubated in freshwater environments more than twice as likely to spawn upstream of tidal influence than those incubated in the intertidal. Our findings challenge the traditional view that pink salmon populations are genetically and phenotypically homogenous due to their short freshwater residency as juveniles and high rates of dispersal as returning adults (i.e. straying). This study has important implications for rates of inbreeding, local adaptation and gene flow within populations, and is particularly relevant to the management of salmon hatcheries, given the high incidence of hatchery-origin pink salmon, reared in freshwater hatchery environments, that stray into wild populations of Prince William Sound.

Movement diversity and partial sympatry of coastal and Northeast Arctic cod ecotypes at high latitudes.

Movement diversity within species represent an important but often neglected, component of biodiversity that affects ecological and genetic interactions, as well as the productivity of exploited systems. By combining individual tracking data from acoustic telemetry with novel genetic analyses, we describe the movement diversity of two Atlantic cod Gadus morhua ecotypes in two high-latitude fjord systems: the highly migratory Northeast Arctic cod (NEA cod) that supports the largest cod fishery in the world, and the more sedentary Norwegian coastal cod, which is currently in a depleted state. As predicted, coastal cod displayed a higher level of fjord residency than NEA cod. Of the cod tagged during the spawning season, NEA cod left the fjords permanently to a greater extent and earlier compared to coastal cod, which to a greater extent remained resident and left the fjords temporarily. Despite this overall pattern, horizontal movements atypical for the ecotypes were common with some NEA cod remaining within the fjords year-round and some coastal cod displaying a low fjord fidelity. Fjord residency and exit timing also differed with spawning status and body size, with spawning cod and large individuals tagged during the feeding season more prone to leave the fjords and earlier than non-spawning and smaller individuals. While our results confirm a lower fjord dependency for NEA cod, they highlight a movement diversity within each ecotype and sympatric residency between ecotypes, previously undetected by population-level monitoring. This new knowledge is relevant for the management, which should base their fisheries advice for these interacting ecotypes on their habitat use and seasonal movements.

Sympatric co-existence of two ecotypes of Impatiens noli-tangere (Balsaminaceae) with different morphology and flowering phenology.

In angiosperms, intraspecific variation of flowering phenology may affect reproductive isolation and, consequently, speciation. This study focused on Impatiens noli-tangere (Balsaminaceae), which is distributed over broad latitudinal and altitudinal ranges in Japan. We aimed to reveal the phenotypic mixture of two ecotypes of I. noli-tangere with different flowering phenology and morphological traits in a narrow contact zone. Previous studies have shown that I. noli-tangere has early- and late-flowering types. The early-flowering type makes buds in June and is distributed at high-elevation sites. The late-flowering type makes buds in July and is distributed at low-elevation sites. In this study, we analyzed the flowering phenology of individuals at an intermediate elevation site where the early- and late-flowering types grow in sympatry (contact zone). We found no individuals showing intermediate flowering phenology at the contact zone, and early- and late-flowering types were clearly distinguishable. We also found that the differences in many other phenotypic traits between the early- and late-flowering types were maintained, including the number of flowers produced (total number of chasmogamous and cleistogamous flowers), leaf morphology (aspect ratio, number of serrations), seed traits (aspect ratio), and flower bud formation positions on the plant. This study showed that these two flowering ecotypes maintain many different traits in sympatry.

Functional Quality, Antioxidant Capacity and Essential Oil Percentage in Different Mint Species Affected by Salinity Stress.

Saline stress is responsible for significant reductions in the growth of plants, and it globally leads to limitations in the performance of crops, especially in drought-affected areas. However, a better understanding of the mechanisms involved in the resistance of plants to environmental stress can lead to a better plant breeding and selection of cultivars. Mint is one of the most important medicinal plants, and it has important properties for industry, and for the medicinal and pharmacy fields. The effects of salinity on the biochemical and enzymatic properties of 18 ecotypes of mint from six different species, that is, Mentha piperita, Mentha mozafariani, Mentha rotundifolia, Mentha spicata, Mentha pulegium and Mentha longifolia, have been examined in this study. The experimental results showed that salinity increased with increasing in stress integrity influenced the enzymatic properties, proline content, electrolyte leakage, and the hydrogen peroxide, malondialdehyde, and essential oil contents. Cluster analysis and principal component analysis were conducted, and they grouped the studied species on the basis of their biochemical characteristics. According to the obtained biplot results, M. piperita and M. rotundifolia showed better stress tolerance than the other varieties, and M. longifolia was identified as being salt sensitive. Generally, the results showed that H2 O2 and malondialdehyde had a positive connection with each other and showed a reverse relationship with all the enzymatic and non-enzymatic antioxidants. Finally, it was found that the M. spicata, M. rotundifolia and M. piperita ecotypes could be used for future breeding projects to improve the salinity tolerance of other ecotypes.

Effects of cadmium and pyrene on earthworm-associated bacterial communities: Unveiling new perspectives for soil pollution management.

Earthworms are considered to be excellent bioindicators of soil pollution. In recent years, there has been increasing interest in examining the effects of soil pollution on earthworm-associated microbiomes, with a particular focus on the gut microbiomes. However, relatively little effort has been invested in comprehensively investigating other microbiomes associated with earthworms and their responses to soil pollution. To fill this gap, we systematically studied the effects of Cd, pyrene, and combined pollution on the bacterial community in different vermicompartments, i.e., burrow wall, gut, and cast, in both epigeic Eisenia fetida and anecic Metaphire guillelmi, using a 2D-terraria incubator and high-throughput sequencing techniques. The results showed that bacterial alpha diversity followed the order of burrow wall > cast > gut, and this did not vary with soil pollution or earthworm ecotypes. Moreover, the dominant phyla in the vermicompartments were similar across different pollution treatments. Principal coordinate analysis (PCoA) revealed that the bacterial communities in different vermicompartments and ecotypes of earthworm were separated from each other, whereas they were grouped together in polluted treatments and unpolluted conditions. These results imply that even in polluted soil, vermicompartment and earthworm ecotypes remain the most significant factors affecting earthworm-associated microbiomes. However, the impacts of soil pollution on the bacterial composition in each vermicompartment were still evident. A comprehensive analysis revealed that the gut bacterial communities are more sensitive to soil contamination than casts and burrow wall in different ecotypes. Additionally, linear discriminant analysis of effect size (LefSe) identified several bacteria in Gemmatimonadota, the Firmicutes phylum in the burrow walls, and Patescibacteria (phyla) in the gut as potential biomarkers for pyrene contamination in soil. This research provides a comprehensive understanding of the effects of soil pollution on earthworm-associated microbiomes, thereby enhancing our understanding of earthworm ecotoxicology and soil pollution management.

Bioactive Compounds and Sensory Analysis of Freeze-Dried Prickly Pear Fruits from an Inter-Andean Valley in Peru.

Prickly pear fruits are seasonal and have shades ranging from pale green to deep purple. Their pigments are associated with bioactive compounds, being sensitive to thermal transformation processes for their conservation. The objective of this research was to evaluate the bioactive compounds and the sensory analysis of freeze-dried prickly pear fruits from an inter-Andean valley in Peru. The prickly pear fruits of the morada, anaranjada, and blanca ecotypes came from an inter-Andean valley in Peru at 2972 m altitude. The sliced fruits were freeze-dried at -40 °C and 0.25 mTorr, and the total polyphenol content (TPC), vitamin C, and antioxidant activity (AA) were determined, as well as the color L* a* b*, color index (CI*), FTIR spectra, and mineral content. In the same way, sensory analysis of preferences with nine scales was applied. It was observed that in the freeze-dried fruits, TPC, AA, and vitamin C increased significantly (p-value < 0.05), and their corresponding functional groups increased in intensity in their corresponding FTIR spectra; furthermore, trace elements such as Cu, Fe, Se, Zn, Si, and Mn were identified. On the other hand, freeze-drying provided deeper colors to the fruits, which most panelists said they "very much liked" during the sensory analysis, although the texture was not very well accepted, with most panelists reporting being "indifferent" towards it. The freeze-drying technique allows the bioactive and sensory attributes of prickly pear fruits from inter-Andean valleys to be preserved, making it a potential fruit for export and conservation due to its seasonality.

Evolution of different rice ecotypes and genetic basis of flooding adaptability in Deepwater rice by GWAS.

BACKGROUND: Rice is the world's second largest food crop and accelerated global climate change due to the intensification of human activities has a huge impact on rice. Research on the evolution of different rice ecotypes is essential for enhancing the adaptation of rice to the unpredictable environments. RESULTS: The sequencing data of 868 cultivated and 140 wild rice accessions were used to study the domestication history and signatures of adaptation in the distinct rice ecotypes genome. The different populations had formed distinct rice ecotypes by phylogenetic analyses and were domesticated independently in the two subspecies of rice, especially deepwater and upland rice. The domestication history of distinct rice ecotypes was confirmed and the four predicted admixture events mainly involved gene flow between wild rice and cultivated rice. Importantly, we identified numerous selective sweeps that have occurred during the domestication of different rice ecotypes and one candidate gene (LOC_Os11g21804) for deepwater based on transcriptomic evidence. In addition, many regions of genomic differentiation between the different rice ecotypes were identified. Furthermore, the main reason for the increase in genetic diversity in the ecotypes of xian (indica) rice was the high proportion of alternative allele frequency in new mutations. Genome-wide association analysis revealed 28 QTLs associated with flood tolerance which contained 12 related cloned genes, and 20 candidate genes within 13 deepwater QTLs were identified by transcriptomic and haplotype analyses. CONCLUSIONS: These results enhanced our understanding of domestication history in different rice ecotypes and provided valuable insights for genetic improvement and breeding of rice in the current changing environments.

Genetic basis of maturity time is independent from that of flowering time and contributes to ecotype differentiation in common buckwheat (Fagopyrum esculentum Moench).

BACKGROUND: Common buckwheat is considered a quantitative short-day plant and is classified into the autumn (highly photoperiod sensitive), summer (weakly photoperiod sensitive), and intermediate ecotype. Understanding ecotype differentiation is essential for adaptive expansion and maximizing yield. The genetic analysis for ecotype has focused on photoperiod-dependent flowering time, whereas post-flowering traits such as seed set and maturity time might also regulate ecotype differentiation. RESULTS: A field experiment revealed that ecotype differentiation is mainly defined by the timing of seed set and maturation, whereas flowering time is less relevant. Thus, we focused on maturity time as a trait that defines the ecotype. To detect QTLs for maturity time, we developed two F2 populations derived from early × late-maturing accessions and intermediate × late-maturing accessions. Using genotyping by random amplicon sequencing-direct analysis, we generated a high-density linkage map. QTL analysis detected two major QTLs for maturity time, one in each F2 population. We also detected QTLs for flowering time at loci different from maturity time QTLs, which suggests that different genetic mechanisms regulate flowering and maturity. Association analysis showed that both QTLs for maturity time were significantly associated with variations in the trait across years. CONCLUSIONS: Maturity time appeared to be more suitable for explaining ecotype differentiation than flowering time, and different genetic mechanisms would regulate the timing of flowering and maturation. The QTLs and QTL-linked markers for maturity time detected here may be useful to extend the cultivation area and to fine-tune the growth period to maximize yield in buckwheat.

Stomatal morphological variation contributes to global ecological adaptation and diversification of Brassica napus.

MAIN CONCLUSION: Stomatal density and guard cell length of 274 global core germplasms of rapeseed reveal that the stomatal morphological variation contributes to global ecological adaptation and diversification of Brassica napus. Stomata are microscopic structures of plants for the regulation of CO2 assimilation and transpiration. Stomatal morphology has changed substantially in the adaptation to the external environment during land plant evolution. Brassica napus is a major crop to produce oil, livestock feed and biofuel in the world. However, there are few studies on the regulatory genes controlling stomatal development and their interaction with environmental factors as well as the genetic mechanism of adaptive variation in B. napus. Here, we characterized stomatal density (SD) and guard cell length (GL) of 274 global core germplasms at seedling stage. It was found that among the significant phenotypic variation, European germplasms are mostly winter rapeseed with high stomatal density and small guard cell length. However, the germplasms from Asia (especially China) are semi-winter rapeseed, which is characterized by low stomatal density and large guard cell length. Through selective sweep analysis and homology comparison, we identified several candidate genes related to stomatal density and guard cell length, including Epidermal Patterning Factor2 (EPF2; BnaA09g23140D), Epidermal Patterning Factor Like4 (EPFL4; BnaC01g22890D) and Suppressor of LLP1 (SOL1 BnaC01g22810D). Haplotype and phylogenetic analysis showed that natural variation in EPF2, EPFL4 and SOL1 is closely associated with the winter, spring, and semi-winter rapeseed ecotypes. In summary, this study demonstrated for the first time the relation between stomatal phenotypic variation and ecological adaptation in rapeseed, which is useful for future molecular breeding of rapeseed in the context of evolution and domestication of key stomatal traits and global climate change.

Fine-scale genetic diversity and putative ecotypes of oxymonad protists coinhabiting the hindgut of Reticulitermes speratus.

The hindgut of lower termites is generally coinhabited by multiple morphologically identifiable protist species. However, it is unclear how many protist species truly coexist in this miniaturized environment, and moreover, it is difficult to define the fundamental unit of protist diversity. Species delineation of termite gut protists has therefore been guided without a theory-based concept of species. Here, we focused on the hindgut of the termite Reticulitermes speratus, where 10 or 11 morphologically distinct oxymonad cell types, that is, morphospecies, coexist. We elucidated the phylogenetic structure of all co-occurring oxymonads and addressed whether their diversity can be explained by the "ecotype" hypothesis. Oxymonad-specific 18S rRNA gene amplicon sequencing analyses of whole-gut samples, combined with single-cell 18S rRNA sequencing of the oxymonad morphospecies, identified 210 one-nucleotide-level variants. The phylogenetic analysis of these variants revealed the presence of microdiverse clusters typically within 1% sequence divergence. Each known oxymonad morphospecies comprised one to several monophyletic or paraphyletic microdiverse clusters. Using these sequence data sets, we conducted computational simulation to predict the rates of ecotype formation and periodic selection, and to demarcate putative ecotypes. Our simulations suggested that the oxymonad genetic divergence is constrained primarily by strong selection, in spite of limited population size and possible bottlenecks during intergenerational transmission. A total of 33 oxymonad ecotypes were predicted, and most of the putative ecotypes were consistently detected among different colonies and host individuals. These findings provide a possible theoretical basis for species diversity and underlying mechanisms of coexistence of termite gut protists.

Environmental contributions to the evolution of trait differences in Geum triflorum: Implications for restoration.

PREMISE: How the environment influences the distribution of trait variation across a species' range has important implications for seed transfer during restoration. Evolution across environments could influence fitness when individuals are transferred into new environments. Here, we evaluate the role the environment has had on the distribution of genetic variance for traits important to adaptation. METHODS: In a common garden experiment, we quantified trait differentiation for populations of Geum triflorum sourced from three distinct ecoregions and evaluated the ability of climate to predict trait variation. Populations were sourced from the Manitoba and Great Lake alvar ecoregions that experience predictable extremes in seasonal water availability and the prairie ecoregion which exhibits unpredictable changes in water availability. RESULTS: Plants sourced from alvar ecoregions exhibited smaller but more stomata and greater intrinsic water-use efficiency relative to prairie plant populations, supporting the evolution of ecotypic differences. Estimates of standing genetic variance and heritable genetic variation for quantitative traits suggest alvar populations have greater adaptive potential. However, low evolvability suggests all populations likely have limited capacity to evolve in response to environmental change. CONCLUSIONS: These results highlight the importance of the environment in influencing the evolution and distribution of genetic differences across populations used as seed sources for restoration. Additionally, these data may inform recommendations for seed transfer across novel environments and our expectations of populations' adaptive potential.

A SNP marker to discriminate the european brook lamprey (Lampetra planeri), river lamprey (L. fluviatilis) and their hybrids.

BACKGROUND: The European River lamprey Lampetra fluviatilis and the brook lamprey L. planeri are two closely related species that are also considered as partially reproductively isolated ecotypes. At the larval stage, they cannot be distinguished morphologically or genetically by mitochondrial DNA. We aimed at developing a molecular tool to identify early life stages of L. fluviatilis and L. planeri. METHODS AND RESULTS: We first identified Single Nucleotide Polymorphism (SNP) markers with distinct alleles between L. fluviatilis and L. planeri based on RADseq data from 186 individuals collected in France. Then, we developed a quantitative PCR protocol to genotype a species-specific SNP, which was tested on 270 samples including larvae and adults from both species and 17 sites from Western Europe. Results were consistent with morphological identification in all cases except for samples from the Rhône drainage and the Loch Lomond in Scotland. CONCLUSIONS: This marker allows the identification of larval stages of L. fluviatilis, L. planeri as well as hybrids. The two cases where the marker was not diagnostic might be explained by an isolated and distinct L. planeri lineage in the Rhône drainage, and high levels of admixture among L. fluviatilis, L. planeri and the lake-parasitic form in Loch Lomond.

QTL × environment interactions underlie adaptive divergence in switchgrass across a large latitudinal gradient.

Local adaptation is the process by which natural selection drives adaptive phenotypic divergence across environmental gradients. Theory suggests that local adaptation results from genetic trade-offs at individual genetic loci, where adaptation to one set of environmental conditions results in a cost to fitness in alternative environments. However, the degree to which there are costs associated with local adaptation is poorly understood because most of these experiments rely on two-site reciprocal transplant experiments. Here, we quantify the benefits and costs of locally adaptive loci across 17° of latitude in a four-grandparent outbred mapping population in outcrossing switchgrass (Panicum virgatum L.), an emerging biofuel crop and dominant tallgrass species. We conducted quantitative trait locus (QTL) mapping across 10 sites, ranging from Texas to South Dakota. This analysis revealed that beneficial biomass (fitness) QTL generally incur minimal costs when transplanted to other field sites distributed over a large climatic gradient over the 2 y of our study. Therefore, locally advantageous alleles could potentially be combined across multiple loci through breeding to create high-yielding regionally adapted cultivars.

Ecotype Division and Chemical Diversity of Cynomorium songaricum from Different Geographical Regions.

Cynomorium songaricum is an important endangered plant with significant medicinal and edible values. However, the lack of resources and quality variation have limited the comprehensive developments and sustainable utilization of C. songaricum. Here, we evaluated the chemical and genetic traits of C. songaricum from the highly suitable habitat regions simulated with species distribution models. The PCA and NJ tree analyses displayed intraspecific variation in C. songaricum, which could be divided into two ecotypes: ecotype I and ecotype II. Furthermore, the LC-MS/MS-based metabolomic was used to identify and analyze the metabolites of two ecotypes. The results indicated that a total of 589 compounds were detected, 236 of which were significantly different between the two ecotypes. Specifically, the relative content and the kind of flavonoids were more abundant in ecotype I, which were closely associated with the medicinal activities. In contrast, amino acids and organic acids were more enriched in ecotype II, which may provide better nutritional quality and unique flavor. In summary, our findings demonstrate the ecotype division and chemical diversity of C. songaricum in China from different geographical regions and provide a reference for the development of germplasm and directed plant breeding of endangered medicinal plants.

A Tandem Mass Tags (TMTs) labeling approach highlights differences between the shoot proteome of two Arabidopsis thaliana ecotypes, Col-0 and Ws.

Arabidopsis has become a powerful model to study morphogenesis, plant growth, development but also plant response to environmental conditions. Over 1000 Arabidopsis genomes are available and show natural genetic variations. Among them, the main reference accessions Wassilewskija (Ws) and Columbia (Col-0), originally growing at contrasted altitudes and temperatures, are widely studied, but data contributing to their molecular phenotyping are still scarce. A global quantitative proteomics approach using isobaric stable isotope labeling (Tandem Mass Tags, TMT) was performed on Ws and Col-0. Plants have been hydroponically grown at 16 h/8 h (light/dark cycle) at 23°C day/19°C night for three weeks. A TMT labeling of the proteins extracted from their shoots has been performed and showed a differential pattern of protein abundance between them. These results have allowed identifying several proteins families possibly involved in the differential responses observed for Ws and Col-0 during plant development and upon environmental changes. In particular, Ws and Col-0 mainly differ in photosynthesis, cell wall-related proteins, plant defense/stress, ROS scavenging enzymes/redox homeostasis and DNA/RNA binding/transcription/translation/protein folding.

European oak chemical diversity - from ecotypes to herbivore resistance.

Climate change is increasing insect pressure and forcing plants to adapt. Although chemotypic differentiation and phenotypic plasticity in spatially separated tree populations are known for decades, understanding their importance in herbivory resistance across forests remains challenging. We studied four oak forest stands in Germany using nontarget metabolomics, elemental analysis, and chemometrics and mapped the leaf metabolome of herbivore-resistant (T-) and herbivore-susceptible (S-) European oaks (Quercus robur) to Tortrix viridana, an oak pest that causes severe forest defoliation. Among the detected metabolites, we identified reliable metabolic biomarkers to distinguish S- and T-oak trees. Chemotypic differentiation resulted in metabolic shifts of primary and secondary leaf metabolism. Across forests, T-oaks allocate resources towards constitutive chemical defense enriched of polyphenolic compounds, e.g. the flavonoids kaempferol, kaempferol and quercetin glucosides, while S-oaks towards growth-promoting substances such as carbohydrates and amino-acid derivatives. This extensive work across natural forests shows that oaks' resistance and susceptibility to herbivory are linked to growth-defense trade-offs of leaf metabolism. The discovery of biomarkers and the developed predictive model pave the way to understand Quercus robur's susceptibility to herbivore attack and to support forest management, contributing to the preservation of oak forests in Europe.