Origins and insights into the historic Judean date palm based on genetic analysis of germinated ancient seeds and morphometric studies

Resurrection of a diatom after 7000 years from anoxic Baltic Sea sediment

Dormancy is a widespread key life history trait observed across the tree of life. Many plankton species form dormant cell stages that accumulate in aquatic sediments and, under anoxic conditions, form chronological records of past species and population dynamics under changing environmental conditions. Here we report on the germination of a microscopic alga, the abundant marine diatom Skeletonema marinoi Sarno et Zigone, that had remained dormant for up to 6871 ± 140 years in anoxic sediments of the Baltic Sea and resumed growth when exposed to oxygen and light. Resurrected diatom strains, representing cohorts from six different time points of the past 6871 ± 140 years, are genetically differentiated, and fundamental physiological functions such as growth and photosynthesis have remained stable through time despite distinct environmental dynamics. Showing that resurrection and full functional recovery, in comparison to 3 ± 2 years of dormancy, is possible after millennial resting, we emphasize the relevance of dormancy and living sediment archives. For the future, sediment archives, together with the resurrection approach, would offer a powerful tool to trace adaptive traits over millennia under distinct climatic conditions and elucidate the underlying mechanisms.

Date palm (Phoenix dactylifera) bioactive constituents and their applications as natural multifunctional ingredients in health-promoting foods and nutraceuticals: A comprehensive review

Foods that support human health and longevity are becoming increasingly relevant as substitutes for or adjuncts to pharmacological drugs, either through direct consumption or incorporation into designer foods fortified with health-promoting ingredients. Date palm (Phoenix dactylifera L.) fruits, seeds, and pollen are a cornerstone of diverse food and medicine traditions. Their reported metabolic activities include anti-inflammatory, antioxidant, antihypertensive, antihyperlipidemic, antidiabetic, antitumor, antianemia, hepatoprotective, antibacterial, and antiviral effects. Beneficial effects on gut health and vascular health, as well as effectiveness in alleviating certain dysfunctions of the reproductive system, have also been noted. The genomic diversity of this versatile tree and the diverse agroecological conditions in which it grows lead to appreciable variations in the occurrence of protective nutrients and other high-value bioactive phytochemicals, including flavonoid and non-flavonoid phenolics, carotenoids, phytosterols, and oxylipins, whose potential remains underutilized in the food sector. As food ingredients, date fruits and their co-products can improve the sensory, nutritional, and nutraceutical qualities of a broad range of dietary items. Their high nutritional density can assist with the design of novel or improved products that meet the demand for healthier foods. This review summarizes the current state of evidence on the potentialities of date palm fruits and co-products in functional food development, focusing on the nutrients and extra-nutritional compounds of interest, their biofunctional activities, and factors that influence their abundance and bioactivity. Proofs of concept across food and beverage categories, new developments, and clinical evidence are discussed, followed by recommendations for addressing research gaps.

Developmental and Genetic Aspects of Desert Crops

Deserts are hostile environments to plant life due to exposure to abiotic stresses, including high temperature, heat, high light, low water availability, and poor soil quality. Desert plants have evolved to cope with these stresses, and for thousands of years humans have used these plants as sources of food, fiber, and medicine. Due to desertification, the amount of arable land is reduced every year; hence, the usage of these species as substitutes for some crops might become one of the solutions for food production and land remediation. Additionally, increasing our understanding of how these plants have adapted to their environment could aid in the generation of more resistant staple crops. In this review, we examine three desert plant species and discuss their developmental aspects, physiological adaptations, and genetic diversity and the related genomic resources available to date. We also address major environmental challenges and threats faced by these species as well as their potential use for improving food security through stimulating stress resistance in crops.

Biomolecular condensates in plant cells: Mediating and integrating environmental signals and development

In response to the spatiotemporal coordination of various biochemical reactions and membrane-encapsulated organelles, plants appear to provide another effective mechanism for cellular organization by phase separation that allows the internal compartmentalization of cells to form a variety of membrane-less organelles. Most of the research on phase separation has centralized in various non-plant systems, such as yeast and animal systems. Recent studies have shown a remarkable correlation between the formation of condensates in plant systems and the formation of condensates in these systems. Moreover, the last decade has made new advances in phase separation research in the context of plant biology. Here, we provide an overview of the physicochemical forces and molecular factors that drive liquid-liquid phase separation in plant cells and the biochemical characterization of condensates. We then explore new developments in phase separation research specific to plants, discussing examples of condensates found in green plants and detailing their role in plant growth and development. We propose that phase separation may be a conserved organizational mechanism in plant evolution to help plants respond rapidly and effectively to various environmental stresses as sessile organisms.

The property and function of proteins undergoing liquid-liquid phase separation in plants

A wide variety of membrane-less organelles in cells play an essential role in regulating gene expression, RNA processing, plant growth and development, and helping organisms cope with changing external environments. In biology, liquid-liquid phase separation (LLPS) usually refers to a reversible process in which one or more specific molecular components are spontaneously separated from the bulk environment, producing two distinct liquid phases: concentrated and dilute. LLPS may be a powerful cellular compartmentalisation mechanism whereby biocondensates formed via LLPS when biomolecules exceed critical or saturating concentrations in the environment where they are found will be generated. It has been widely used to explain the formation of membrane-less organelles in organisms. LLPS studies in the context of plant physiology are now widespread, but most of the research is still focused on non-plant systems; the study of phase separation in plants needs to be more thorough. Proteins and nucleic acids are the main components involved in LLPS. This review summarises the specific features and properties of biomolecules undergoing LLPS in plants. We describe in detail these biomolecules' structural characteristics, the mechanism of formation of condensates, and the functions of these condensates. Finally, We summarised the phase separation mechanisms in plant growth, development, and stress adaptation.

Characterization and analysis of a Commiphora species germinated from an ancient seed suggests a possible connection to a species mentioned in the Bible

A seed recovered during archaeological excavations of a cave in the Judean desert was germinated, with radiocarbon analysis indicating an age of 993 CE- 1202 calCE. DNA sequencing and phylogenetic analysis identified the seedling as belonging to the angiosperm genus Commiphora Jacq., sister to three Southern African Commiphora species, but unique from all other species sampled to date. The germinated seedling was not closely related to Commiphora species commonly harvested for their fragrant oleoresins including Commiphora gileadensis (L.) C.Chr., candidate for the locally extinct "Judean Balsam" or "Balm of Gilead" of antiquity. GC-MS analysis revealed minimal fragrant compounds but abundance of those associated with multi-target bioactivity and a previously undescribed glycolipid compound series. Several hypotheses are offered to explain the origins, implications and ethnobotanical significance of this unknown Commiphora sp., to the best of our knowledge the first identified from an archaeological site in this region, including identification with a resin producing tree mentioned in Biblical sources and possible agricultural relationship with the historic Judean Balsam.

Three-dimensional genome architecture persists in a 52,000-year-old woolly mammoth skin sample

Analyses of ancient DNA typically involve sequencing the surviving short oligonucleotides and aligning to genome assemblies from related, modern species. Here, we report that skin from a female woolly mammoth (†Mammuthus primigenius) that died 52,000 years ago retained its ancient genome architecture. We use PaleoHi-C to map chromatin contacts and assemble its genome, yielding 28 chromosome-length scaffolds. Chromosome territories, compartments, loops, Barr bodies, and inactive X chromosome (Xi) superdomains persist. The active and inactive genome compartments in mammoth skin more closely resemble Asian elephant skin than other elephant tissues. Our analyses uncover new biology. Differences in compartmentalization reveal genes whose transcription was potentially altered in mammoths vs. elephants. Mammoth Xi has a tetradic architecture, not bipartite like human and mouse. We hypothesize that, shortly after this mammoth's death, the sample spontaneously freeze-dried in the Siberian cold, leading to a glass transition that preserved subfossils of ancient chromosomes at nanometer scale.

Unraveling the diversity and cultural heritage of fruit crops through paleogenomics

Abundant and plentiful fruit crops are threatened by the loss of diverse legacy cultivars which are being replaced by a limited set of high-yielding ones. This article delves into the potential of paleogenomics that utilizes ancient DNA analysis to revive lost diversity. By focusing on grapevines, date palms, and tomatoes, recent studies showcase the effectiveness of paleogenomic techniques in identifying and understanding genetic traits crucial for crop resilience, disease resistance, and nutritional value. The approach not only tracks landrace dispersal and introgression but also sheds light on domestication events. In the face of major future environmental challenges, integrating paleogenomics with modern breeding strategies emerges as a promising avenue to significantly bolster fruit crop sustainability.

Seed Collection in Temperate Trees-Clean, Fast, and Effective Extraction of Populus Seeds for Laboratory Use and Long-term Storage

Seeds ensure the growth of a new generation of plants and are thus central to maintaining plant populations and ecosystem processes. Nevertheless, much remains to be learned about seed biology and responses of germinated seedlings to environmental challenges. Experiments aiming to close these knowledge gaps critically depend on the availability of healthy, viable seeds. Here, we report a protocol for the collection of seeds from plants in the genus Populus. This genus comprises trees with a wide distribution in temperate forests and with economic relevance, used as scientific models for perennial plants. As seed characteristics can vary drastically between taxonomic groups, protocols need to be tailored carefully. Our protocol takes the delicate nature of Populus seeds into account. It uses P. deltoides as an example and provides a template to optimize bulk seed extraction for other Populus species and plants with similar seed characteristics. The protocol is designed to only use items available in most labs and households and that can be sterilized easily. The unique characteristics of this protocol allow for the fast and effective extraction of high-quality seeds. Here, we report on seed collection, extraction, cleaning, storage, and viability tests. Moreover, extracted seeds are well suited for tissue culture and experiments under sterile conditions. Seed material obtained with this protocol can be used to further our understanding of tree seed biology, seedling performance under climate change, or diversity of forest genetic resources. Key features • Populus species produce seeds that are small, delicate, non-dormant, with plenty of seed hair. Collection of seed material needs to be timed properly. • Processing, seed extraction, seed cleaning, and storage using simple, sterilizable laboratory and household items only. Obtained seeds are pure, high quality, close to 100% viability. • Seeds work well in tissue culture and in experiments under sterile conditions. • Extractability, speed, and seed germination were studied and confirmed for Populus deltoides as an example. • Can also serve as template for bulk seed collection from other Populus species and plant groups that produce delicate seeds (with no or little modifications). Graphical overview.

Active food packaging films from alginate and date palm pit extract: Physicochemical properties, antioxidant capacity, and stability

Date palm pits are highly available and inexpensive palm date by-products, representing a valuable source of natural antioxidants, particularly phenolic compounds. Date palm pit extract (DPPE) was prepared from these waste products and characterized for its phenolic content and in vitro antioxidant activity. Profiling DPPE by liquid chromatography coupled with mass spectrometry (LC/MS) showed the presence of dimers and trimers of (epi)catechin as the main constituents. Alginate-based films with four increasing concentrations of DPPE (10%, 20%, 30%, and 40% w/w) were prepared by the casting method. DPPE incorporation reduced solubility values of alginate films by 37%-64% and their surface wettability by 72%-111%. The incorporation of 10% DPPE improved water vapor barrier properties and increased tensile strength (TS) and elongation at break (%E) of alginate films by more than 23%, 50%, and 45%, respectively. The film containing 40% DPPE showed the lowest loss of phenolic content (32%), DPPH (1,1-diphenyl-2-picrylhydrazyl) scavenging activity (38%), and ferric reducing antioxidant power (FRAP) (30%) after storage for 3 months.

HLA-A, -B, -C, -DRB1 and -DQB1 allele and haplotype frequencies in Lebanese and their relatedness to neighboring and distant populations

BACKGROUND

This study examined the origin of present-day Lebanese using high-resolution HLA class I and class II allele and haplotype distributions. The study subjects comprised 152 unrelated individuals, and their HLA class I and class II alleles and two-locus and five-locus haplotypes were compared with those of neighboring and distant communities using genetic distances, neighbor-joining dendrograms, correspondence, and haplotype analyses. HLA class I (A, B, C) and class II (DRB1, DQB1) were genotyped at a high-resolution level by PCR-SSP.

RESULTS

In total, 76 alleles across the five HLA loci were detected: A*03:01 (17.1%), A*24:02 (16.5%), B*35:01 (25.7%), C*04:01 (25.3%), and C*07:01 (20.7%) were the most frequent class I alleles, while DRB1*11:01 (34.2%) and DQB1*03:01 (43.8%) were the most frequent class II alleles. All pairs of HLA loci were in significant linkage disequilibrium. The most frequent two-locus haplotypes recorded were DRB1*11:01 ~ DQB1*03:01 (30.9%), B*35:01-C*04:01 (20.7%), B*35:01 ~ DRB1*11:01 (13.8%), and A*24:02 ~ B*35:01 (10.3%). Lebanese appear to be closely related to East Mediterranean communities such as Levantines (Palestinians, Syrians, and Jordanians), Turks, Macedonians, and Albanians. However, Lebanese appear to be distinct from North African, Iberian, and Sub-Saharan communities.

CONCLUSIONS

Collectively, this indicates a limited genetic contribution of Arabic-speaking populations (from North Africa or the Arabian Peninsula) and Sub-Saharan communities to the present-day Lebanese gene pool. This confirms the notion that Lebanese population are of mixed East Mediterranean and Asian origin, with a marked European component.

A prion-like protein regulator of seed germination undergoes hydration-dependent phase separation

Many organisms evolved strategies to survive desiccation. Plant seeds protect dehydrated embryos from various stressors and can lay dormant for millennia. Hydration is the key trigger to initiate germination, but the mechanism by which seeds sense water remains unresolved. We identified an uncharacterized Arabidopsis thaliana prion-like protein we named FLOE1, which phase separates upon hydration and allows the embryo to sense water stress. We demonstrate that biophysical states of FLOE1 condensates modulate its biological function in vivo in suppressing seed germination under unfavorable environments. We find intragenic, intraspecific, and interspecific natural variation in FLOE1 expression and phase separation and show that intragenic variation is associated with adaptive germination strategies in natural populations. This combination of molecular, organismal, and ecological studies uncovers FLOE1 as a tunable environmental sensor with direct implications for the design of drought-resistant crops, in the face of climate change.

Redox-related gene expression and sugar accumulation patterns are altered in the edible inflorescence produced by the cultivated form of pacaya palm (Chamaedorea tepejilote)

BACKGROUND AND AIMS

The pacaya palm is a dioecious neotropical palm species that is exploited in Latin America for its male inflorescence, which is edible when immature. It is cultivated, in a non-intensive manner, in Guatemala, where a morphotype occurs that produces much larger, more highly branched inflorescences compared with wild palms. We sought to identify molecular factors underlying this phenotypic divergence, which is likely to be a product of domestication.

METHODS

We performed RNA-seq-based studies on immature pacaya palm male inflorescences in order to identify genes that might be directly or indirectly affected in their expression in relation to domestication. We also measured the accumulation of a range of soluble sugar molecules to provide information on the biochemical status of the two different types of material.

KEY RESULTS

A total of 408 genes were found to display significantly different expression levels between the wild and cultivated morphotypes. Three different functional categories were found to be enriched in the gene set that was upregulated in the cultivated morphotype: redox balance; secondary metabolism; and transport. Several sugars were found to accumulate at higher levels in inflorescences of the cultivated morphotype, in particular myo-inositol, fructose and glucose.

CONCLUSIONS

The observed upregulation of redox-related genes in the cultivated morphotype is corroborated by the observation of higher myo-inositol accumulation, which has been shown to be associated with enhanced scavenging of reactive oxygen species in other plants and which may affect meristem activity.

The genomes of ancient date palms germinated from 2,000 y old seeds

Resurrection genomics is an alternative to ancient DNA approaches in studying the genetics and evolution of past and possibly extinct populations. By reviving biological material such as germinating ancient seeds from archaeological and paleontological sites, or historical collections, one can study genomes of lost populations. We applied this approach by sequencing the genomes of seven Judean date palms (Phoenix dactylifera) that were germinated from ∼2,000 y old seeds recovered in the Southern Levant. Using this genomic data, we were able to document that introgressive hybridization of the wild Cretan palm Phoenix theophrasti into date palms had occurred in the Eastern Mediterranean by ∼2,200 y ago and examine the evolution of date palm populations in this pivotal region two millennia ago.

Seven date palm seeds (Phoenix dactylifera L.), radiocarbon dated from the fourth century BCE to the second century CE, were recovered from archaeological sites in the Southern Levant and germinated to yield viable plants. We conducted whole-genome sequencing of these germinated ancient samples and used single-nucleotide polymorphism data to examine the genetics of these previously extinct Judean date palms. We find that the oldest seeds from the fourth to first century BCE are related to modern West Asian date varieties, but later material from the second century BCE to second century CE showed increasing genetic affinities to present-day North African date palms. Population genomic analysis reveals that by ∼2,400 to 2,000 y ago, the P. dactylifera gene pool in the Eastern Mediterranean already contained introgressed segments from the Cretan palm Phoenix theophrasti, a crucial genetic feature of the modern North African date palm populations. The P. theophrasti introgression fraction content is generally higher in the later samples, while introgression tracts are longer in these ancient germinated date palms compared to modern North African varieties. These results provide insights into crop evolution arising from an analysis of plants originating from ancient germinated seeds and demonstrate what can be accomplished with the application of a resurrection genomics approach.

Efficient utilization of date palm waste for the bioethanol production through Saccharomyces cerevisiae strain

Dates (Phoenix dactylifera L.) are rich in nutritional compounds, particularly in sugars. Sugars offer anaerobic fermentation, used for bioethanol production. Recently, researchers and industrialists finding ways to produce low-cost bioethanol on large scale using agricultural wastes. Date palm residual is the largest agricultural waste in Pakistan, which can be the cheapest source for bioethanol production, whereas the current study was designed to explore the possible utilization and the potential of date palm waste for bioethanol production through Saccharomyces cerevisiae grown in yeast extract, Bacto peptone, and d-glucose medium. The fermentation process resulted in the production of 15% (v/v) ethanol under the optimum condition of an incubation period of 72 hr and three sugars (glucose, fructose, and sucrose) were found in date waste. The functional group of ethanol (C2H5OH) was also found via Fourier-transform infrared spectroscopy (FTIR) analysis. Therefore, S. cerevisiae could be recommended for ethanol production due to short fermentation time at 25% inoculum in 30°C and reduced the processing cost. Common date varieties of low market value are a preferred substrate for the process of producing industrial ethanol. Additionally, proximate analysis of date fruit by near-infrared spectroscopy revealed moisture contents (16.84%), crude protein (0.3%), ash (9.8%), crude fat (2.6%), and neutral detergent fibers (13.4%). So, date fruit contains various nutrients for microbial growth for ethanol production.

Topological Interlocking and Geometric Stiffening as Complementary Strategies for Strong Plant Shells

Many organisms encapsulate their embryos in hard, protective shells. While birds and reptiles largely rely on mineralized shells, plants often develop highly robust lignocellulosic shells. Despite the abundance of hard plant shells, particularly nutshells, it remains unclear which fundamental properties drive their mechanical stability. This multiscale analysis of six prominent (nut)shells (pine, pistachio, walnut, pecan, hazelnut, and macadamia) reveals geometric and structural strengthening mechanisms on the cellular and macroscopic length scales. The strongest tissues, found in walnut and pistachio, exploit the topological interlocking of 3D-puzzle cells and thereby outperform the fiber-reinforced structure of macadamia under tensile and compressive loading. On the macroscopic scale, strengthening occurs via an increased shell thickness, spherical shape, small size, and a lack of extended sutures. These functional interrelations suggest that simple geometric modifications are a powerful and resource-efficient strategy for plants to enhance the fracture resistance of entire shells and their tissues. Understanding the interplay between structure, geometry, and mechanics in hard plant shells provides new perspectives on the evolutionary diversification of hard seed coats, as well as insights for nutshell-based material applications.