The first initiative of DNA barcoding of ornamental plants from Egypt and potential applications in horticulture industry

Abstract: DNA barcoding relies on short and standardized gene regions to identify species. The agricultural and horticultural applications of barcoding such as for marketplace regulation and copyright protection remain poorly explored. This study examines the effectiveness of the standard plant barcode markers (matK and rbcL) for the identification of plant species in private and public nurseries in northern Egypt. These two markers were sequenced from 225 specimens of 161 species and 62 plant families of horticultural importance. The sequence recovery was similar for rbcL (96.4%) and matK (84%), but the number of specimens assigned correctly to the respective genera and species was lower for rbcL (75% and 29%) than matK (85% and 40%). The combination of rbcL and matK brought the number of correct generic and species assignments to 83.4% and 40%, respectively. Individually, the efficiency of both markers varied among different plant families; for example, all palm specimens (Arecaceae) were correctly assigned to species while only one individual of Asteraceae was correctly assigned to species. Further, barcodes reliably assigned ornamental horticultural and medicinal plants correctly to genus while they showed a lower or no success in assigning these plants to species and cultivars. For future, we recommend the combination of a complementary barcode (e.g. ITS or trnH-psbA) with rbcL + matK to increase the performance of taxa identification. By aiding species identification of horticultural crops and ornamental palms, the analysis of the barcode regions will have large impact on horticultural industry

Seaweed Extracts Enhance Salam Turfgrass Performance during Prolonged Irrigation Intervals and Saline Shock

The negative effects of the ongoing climate change include unusual prolonged droughts and increased salinity pressures on the agricultural lands. Consequently, crops are facing unprecedented environmental pressure, and this calls for more research toward controlling such major stresses. The current study investigates the effects of seaweed extract sprays of Ascophyllum nodosum (5 and 7 mL·L−1; 6 day intervals) on Paspalum vaginatum Salam' during prolonged irrigation intervals (2 and 6 day) and saline growing conditions (1 and 49.7 dS·m−1) for 6 weeks in containers under greenhouse conditions. Control plants showed reduced turf quality, photochemical efficiency, root length and dry weight, total non-structural carbohydrates, and K and Ca compositions. Seaweed extracts increased turf quality, leaf photochemical efficiency, root length and dry weight, total non-structural carbohydrates, K, Ca, and proline in treated plants during prolonged irrigation intervals as well as saline shock conditions. There were also increases in the antioxidant defensive mechanisms such as catalase (CAT), superoxide dismutase (SOD) and ascorbate peroxidase (APX) activities and non-enzymatic antioxidants as well as reduced lipid peroxidation. The application of SWE at 7 mL·L−1 showed higher performance in treated plants during prolonged irrigation intervals as well as saline conditions. Our findings imply that several mechanisms including drought tolerance, osmotic adjustment and antioxidant defense system may interact to enhance the performance of plants in the face of environmental stress following SWE treatments

Evaluation of Silicon Supplementation for Drought Stress under Water-Deficit Conditions: An Application of Sustainable Agriculture

Drought is a key abiotic stress that confines agriculture development worldwide. Silicon (Si) is commonly considered to be a valuable element for resistance against drought and for sustainable agriculture. To investigate the morpho-physiological and biochemical characteristics of Gerbera jamesonii plants, a pot experiment was conducted under greenhouse conditions and exposed to water stress (60% FC) and well-watered (100% FC) conditions. Foliar application of Si was carried out after ten days (48 days after sowing) of drought treatment and was repeated weekly, while well-water was regarded as control. Water deficiency significantly abridged the morphological attributes, pigments, and stress-related metabolites and negatively affected the photosynthetic apparatus in drought-stressed gerbera plants. However, Si supplementation by 40 mg L-1 produced increased leaf area (31%), stem length (25%), flower diameter (22%), plant fresh biomass (17%), total chlorophyll (48%), and concentration of carotenoids (54%) in water-stressed plants. Similarly, the accretion of a total free amino acid (41%) and the activities of peroxidase, catalase, superoxide dismutase, ascorbate peroxidase, glycinebetaine, total soluble proteins, total free proline, and malondialdehyde were enhanced by 44%, 31%, 53%, 33%, 330%, 61%, 51%, and 66%, respectively, under drought stress in comparison with control conditions. Meanwhile, the photosynthetic rate (89%), the transpiration rate (12%), and stomatal conductance (55%) were significantly enhanced in water-deficit gerbera leaves with Si supplementation. This study proposes that the foliar application of Si is a viable and convenient method of improving the performance of elegant gerbera flower plants in regions of the world that are facing severe water deficiency

Bioactivities of Traditional Medicinal Plants in Alexandria

In traditional folklore, medicinal herbs play a vital role in the prevention and treatment of microbial diseases. In the present study, the phenolic profiles of the medicinal plants Asparagus aethiopicus L., Citrullus colocynthis L., Senna alexandrina L., Kalanchoe delagoensis L., Gasteria pillansii L., Cymbopogon citratus, Brassica juncea, and Curcuma longa L. were determined by high-performance liquid chromatography with a diode-array detector method. The results revealed rich sources of important compounds such as robinin in the fruits and leaves of A. aethiopicus; caffeic acid in the tubers of A. aethiopicus and quercitrin in the leaves of G. pillansii. Further, relatively high antioxidant, antibacterial, and antifungal activities were observed in C. colocynthis fruit coat, S. alexandrina pods, and A. aethiopicus leaves, respectively. The relatively higher the bioactivities of plants extracts associated with the phenols in these plants, in particular, the more abundant the phenols. Therefore, it was concluded that the fruit coat of C. colocynthis, pods of S. alexandrina, and leaves of A. aethiopicus might be excellent sources of natural products. These plant extracts also have a wide spectrum of antimicrobial activities that could be used in the pharmaceutical industries and to control diseases

Treatment of Sweet Pepper with Stress Tolerance-Inducing Compounds Alleviates Salinity Stress Oxidative Damage by Mediating the Physio-Biochemical Activities and Antioxidant Systems

Salinity stress occurs due to the accumulation of high levels of salts in soil, which ultimately leads to the impairment of plant growth and crop loss. Stress tolerance-inducing compounds have a remarkable ability to improve growth and minimize the effects of salinity stress without negatively affecting the environment by controlling the physiological and molecular activities in plants. Two pot experiments were carried out in 2017 and 2018 to study the influence of salicylic acid (1 mM), yeast extract (6 g L−1), and proline (10 mM) on the physiological and biochemical parameters of sweet pepper plants under saline conditions (2000 and 4000 ppm). The results showed that salt stress led to decreasing the chlorophyll content, relative water content, and fruit yields, whereas electrolyte leakage, malondialdehyde (MDA), proline concentration, reactive oxygen species (ROS), and the activities of antioxidant enzymes increased in salt-stressed plants. The application of salicylic acid (1 mM), yeast extract (6 g L−1), and proline (10 mM) markedly improved the physiological characteristics and fruit yields of salt-stressed plants compared with untreated stressed plants. A significant reduction in electrolyte leakage, MDA, and ROS was also recorded for all treatments. In conclusion, our results reveal the important role of proline, SA, and yeast extracts in enhancing sweet pepper growth and tolerance to salinity stress via modulation of the physiological parameters and antioxidants machinery. Interestingly, proline proved to be the best treatment.</jats:p

Mosaic Origins of a Complex Chimeric Mitochondrial Gene in Silene vulgaris

Chimeric genes are significant sources of evolutionary innovation that are normally created when portions of two or more protein coding regions fuse to form a new open reading frame. In plant mitochondria astonishingly high numbers of different novel chimeric genes have been reported, where they are generated through processes of rearrangement and recombination. Nonetheless, because most studies do not find or report nucleotide variation within the same chimeric gene, evolution after the origination of these chimeric genes remains unstudied. Here we identify two alleles of a complex chimera in Silene vulgaris that are divergent in nucleotide sequence, genomic position relative to other mitochondrial genes, and expression patterns. Structural patterns suggest a history partially influenced by gene conversion between the chimeric gene and functional copies of subunit 1 of the mitochondrial ATP synthase gene (atp1). We identified small repeat structures within the chimeras that are likely recombination sites allowing generation of the chimera. These results establish the potential for chimeric gene divergence in different plant mitochondrial lineages within the same species. This result contrasts with the absence of diversity within mitochondrial chimeras found in crop species

Plastome-wide rearrangements and gene losses in carnivorous Droseraceae

The plastid genomes of four related carnivorous plants (Drosera regia, Drosera erythrorhiza, Aldrovanda vesiculosa and Dionaea muscipula) were sequenced to examine changes potentially induced by the transition to carnivory. The plastid genomes of the Droseraceae show multiple rearrangements, gene losses and large expansions or contractions of the inverted repeat. All the ndh genes are lost or non-functional, as well as in some of the species, clpP1, ycf1, ycf2 and some tRNA genes. Uniquely amongst land plants, the trnK gene has no intron. Carnivory in the Droseraceae coincides with changes in plastid gene content similar to those induced by parasitism and mycoheterotrophy, suggesting parallel changes in chloroplast function due to the similar switch from autotrophy to (mixo-) heterotrophy. A molecular phylogeny of the taxa based on all shared plastid genes indicates that the ‘snap-traps’ of Aldrovanda and Dionaea have a common origin

Phylogeny and Biogeography of the Carnivorous Plant Family Sarraceniaceae

The carnivorous plant family Sarraceniaceae comprises three genera of wetland-inhabiting pitcher plants: Darlingtonia in the northwestern United States, Sarracenia in eastern North America, and Heliamphora in northern South America. Hypotheses concerning the biogeographic history leading to this unusual disjunct distribution are controversial, in part because genus- and species-level phylogenies have not been clearly resolved. Here, we present a robust, species-rich phylogeny of Sarraceniaceae based on seven mitochondrial, nuclear, and plastid loci, which we use to illuminate this family's phylogenetic and biogeographic history. The family and genera are monophyletic: Darlingtonia is sister to a clade consisting of Heliamphora+Sarracenia. Within Sarracenia, two clades were strongly supported: one consisting of S. purpurea, its subspecies, and S. rosea; the other consisting of nine species endemic to the southeastern United States. Divergence time estimates revealed that stem group Sarraceniaceae likely originated in South America 44–53 million years ago (Mya) (highest posterior density [HPD] estimate = 47 Mya). By 25–44 (HPD = 35) Mya, crown-group Sarraceniaceae appears to have been widespread across North and South America, and Darlingtonia (western North America) had diverged from Heliamphora+Sarracenia (eastern North America+South America). This disjunction and apparent range contraction is consistent with late Eocene cooling and aridification, which may have severed the continuity of Sarraceniaceae across much of North America. Sarracenia and Heliamphora subsequently diverged in the late Oligocene, 14–32 (HPD = 23) Mya, perhaps when direct overland continuity between North and South America became reduced. Initial diversification of South American Heliamphora began at least 8 Mya, but diversification of Sarracenia was more recent (2–7, HPD = 4 Mya); the bulk of southeastern United States Sarracenia originated co-incident with Pleistocene glaciation, <3 Mya. Overall, these results suggest climatic change at different temporal and spatial scales in part shaped the distribution and diversity of this carnivorous plant clade

IBD risk loci are enriched in multigenic regulatory modules encompassing putative causative genes.

GWAS have identified >200 risk loci for Inflammatory Bowel Disease (IBD). The majority of disease associations are known to be driven by regulatory variants. To identify the putative causative genes that are perturbed by these variants, we generate a large transcriptome data set (nine disease-relevant cell types) and identify 23,650 cis-eQTL. We show that these are determined by ∼9720 regulatory modules, of which ∼3000 operate in multiple tissues and ∼970 on multiple genes. We identify regulatory modules that drive the disease association for 63 of the 200 risk loci, and show that these are enriched in multigenic modules. Based on these analyses, we resequence 45 of the corresponding 100 candidate genes in 6600 Crohn disease (CD) cases and 5500 controls, and show with burden tests that they include likely causative genes. Our analyses indicate that ≥10-fold larger sample sizes will be required to demonstrate the causality of individual genes using this approach