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The complete plastome sequences of invasive weed Parthenium hysterophorus: genome organization, evolutionary significance, structural features, and comparative analysis. Lubna, S Asaf, R Jan, S Asif, S Bilal, AL Khan, AN Al-Rawahi, KM Kim, Scientific Reports 14 (1), 4006

Microbiome structure variation and soybean’s defense responses during flooding stress and elevated CO2

L Coffman, W Ahmad, AL Khan

Frontiers in Plant Science 14, 1295674

The silicon regulates microbiome diversity and plant defenses during cold stress in Glycine max L.

W Ahmad, L Coffman, AD Weerasooriya, AL Khan

Frontiers in Plant Science 14, 1280251


Comparative plastome genomics, taxonomic delimitation and evolutionary divergences of Tetraena hamiensis var. qatarensis and Tetraena simplex (Zygophyllaceae). W Ahmad, S Asaf, A Al-Rawahi, A Al-Harrasi, AL Khan. Scientific Reports 13 (1), 7436


Silicon-Induced Morphological, Biochemical and Molecular Regulation in Phoenix dactylifera L. under Low-Temperature Stress. S Bilal, T Khan, S Asaf, NA Khan, S Saad Jan, M Imran, A Al-Rawahi, . International Journal of Molecular Sciences 24 (7), 6036


Unraveling the mutualistic interaction between endophytic Curvularia lunata CSL1 and tomato to mitigate cadmium (Cd) toxicity via transcriptomic insights. S Asaf, R Jan, MA Khan, AL Khan, S Asif, S Bilal, W Ahmad, M Waqas, . Science of The Total Environment 861, 160542


Diversity, Lifestyle, Genomics, and Their Functional Role of Cochliobolus, Bipolaris, and Curvularia Species in Environmental Remediation and Plant Growth . NA Khan, S Asaf, W Ahmad, R Jan, S Bilal, I Khan, AL Khan, KM Kim, . Journal of Fungi 9 (2), 254


Genome-wide annotation and expression analysis of WRKY and bHLH transcriptional factor families reveal their involvement under cadmium stress in tomato. I Khan, S Asaf, R Jan, S Bilal, ALK Lubna, KM Kim, A Al-Harrasi. Frontiers in Plant Science 14, 45



Genome and Transcriptome-Wide Analysis of OsWRKY and OsNAC Gene Families in Oryza sativa and Their Response to White-Backed Planthopper Infestation. I Khan, R Jan, S Asaf, AL Khan, S Bilal, KM Kim, A Al-Harrasi. International Journal of Molecular Sciences 23 (23), 15396


Melatonin and nitric oxide: Dual players inhibiting hazardous metal toxicity in soybean plants via molecular and antioxidant signaling cascades. M Imran, AL Khan, BG Mun, S Bilal, S Shaffique, EH Kwon, SM Kang, . Chemosphere 308, 136575


Uncovering the first complete plastome genomics, comparative analyses, and phylogenetic dispositions of endemic medicinal plant Ziziphus hajarensis (Rhamnaceae). S Asaf, W Ahmad, A Al-Harrasi, AL Khan. BMC Genomics 23 (1), 1-16


Complete chloroplast genome sequencing and comparative analysis of threatened dragon trees Dracaena serrulata and Dracaena cinnabari. W Ahmad, S Asaf, A Khan, A Al-Harrasi, A Al-Okaishi, AL Khan. Scientific Reports 12 (1), 16787


Silicon-Induced Tolerance against Arsenic Toxicity by Activating Physiological, Anatomical and Biochemical Regulation in Phoenix dactylifera (Date Palm). T Khan, S Bilal, S Asaf, SS Alamri, M Imran, AL Khan, A Al-Rawahi, IJ Lee, . Plants 11 (17), 2263


Genome Structure and Evolutionary History of Frankincense producing Boswellia sacra. AL Khan, A Al-Harrasi, JP Wang, S Asaf, JJM Riethoven, T Shehzad, . iScience, 104574

Complete mitochondrial genome of endangered Arabian tahr (Arabitragus jayakari) and phylogenetic placement. AN Al-Rawahi, ZS Alalawi, S Asaf, AL Khan, A Khan, H Al-Rawahi, . Mitochondrial DNA Part B 7 (6), 1189-1190


Silicon-and Boron-Induced Physio-Biochemical Alteration and Organic Acid Regulation Mitigates Aluminum Phytotoxicity in Date Palm Seedlings. S Bilal, A Khan, M Imran, AL Khan, S Asaf, A Al-Rawahi, MSA Al-Azri, . Antioxidants 11 (6), 1063


The Plastome Sequences of Triticum sphaerococcum (ABD) and Triticum turgidum subsp. durum (AB) Exhibit Evolutionary Changes, Structural Characterization . S Asaf, R Jan, AL Khan, W Ahmad, S Asif, A Al-Harrasi, KM Kim, IJ Lee. International Journal of Molecular Sciences 23 (5), 2783


Unraveling the Genome Sequence of Plant Growth Promoting Aspergillus niger (CSR3) Provides Insight into the Synthesis of Secondary Metabolites and Its Comparative Genomics. S Asaf, R Jan, AL Khan, S Bilal, S Asif, A Al-Harrasi, KM Kim. Journal of Fungi 8 (2), 107


Microbiome Variation Across Populations of Desert Halophyte Zygophyllum qatarensis. AL Khan, LD Lopes, S Bilal, S Asaf, KM Crawford, V Balan, A Al-Rawahi, . Frontiers in plant science 13


Utilization of Spectral Indices for High-Throughput Phenotyping. R Tayade, J Yoon, L Lay, AL Khan, Y Yoon, Y Kim. Plants 11 (13), 1712



Decoding first complete chloroplast genome of toothbrush tree (Salvadora persica L.): insight into genome evolution, sequence divergence and phylogenetic relationship within . AL Khan, S Asaf, A Al-Rawahi, A Al-Harrasi. BMC genomics 22 (1), 1-16


Transcriptomics of tapping and healing process in frankincense tree during resin production. AL Khan, S Asaf, M Numan, NM AbdulKareem, M Imran, JJM Riethoven, . Genomics 113 (6), 4337-4351


The dynamic history of gymnosperm plastomes: Insights from structural characterization, comparative analysis, phylogenomics, and time divergence. S Asaf, AL Khan, R Jan, A Khan, A Khan, KM Kim, IJ Lee. The Plant Genome, e20130

Selected texts


Plant growth promoting bacteria as an alternative strategy for salt tolerance in plants: a review

"Approximately 5.2 billion hectare agriculture land are affected by erosion, salinity and soil degradation. Salinity stress has significantly affecting the fertile lands, and therefore possesses a huge impact on the agriculture and economy of a country. Salt stress has severe effects on the growth and development of plants as well as reducing its yield. Plants are inherently equipped with stress tolerance ability to responds the specific type of stress. Plants retained specific mechanisms for salt stress mitigation, such as hormonal stimulation, ion exchange, antioxidant enzymes and activation of signaling cascades on their metabolic and genetic frontiers that sooth the stressed condition. Additional to the plant inherent mechanisms, certain plant growth promoting bacteria (PGPB) also have specialized mechanism that play key role for salt stress tolerance and plant growth promotion. These bacteria triggers plants to produce different plant growth hormones like auxin, cytokinine and gibberellin as well as volatile organic compounds. These bacteria also produces growth regulators like siderophore, which fix nitrogen, solubilize organic and inorganic phosphate. Considering the importance of PGPB in compensation of salt tolerance in plants, the present study has reviewed the different aspect and mechanism of bacteria that play key role in promoting plants growth and yield. It can be concluded that PGPB can be used as a cost effective and economical tool for salinity tolerance and growth promotion in plants."


Inoculation of abscisic acid-producing endophytic bacteria enhances salinity stress tolerance in Oryza sativa

"Salinity hinders plant growth and results in reduced crop yield. The use of plant growth-promoting endophytic bacteria is an eco-friendly strategy to counteract such stresses and confer tolerance to the host. Endophytic bacteria have been recognized for their active role in auxin production; however, little is known about their ability to produce abscisic acid (ABA). In recent studies, the bacterial endophyte Bacillus amyloliquefaciens RWL-1 has been found to produce ABA, and as such, has the potential to increase plant resistance to salinity stress. Results showed that RWL-1 produced varying concentrations of ABA (0.32 ± 0.015–0.14 ± 0.030 ng mL−1) under normal and saline conditions. The ability of RWL-1 to produce ABA was reduced in response to increasing salinity; however, it maintained its growth by up-regulating production of essential amino acids (glutamic acid and proline). To further investigate the potential of this endophytic bacterium, a plant-microbe interaction experiment was conducted which showed that RWL-1 inoculation significantly increased growth attributes of rice plants as compared to non-inoculated control plants under salinity stress. Micrographs also revealed active symbiosis of RWL-1 with plant roots under normal and salinity stress conditions. The essential amino acids (glutamic acid, aspartic acid, phenylalanine, proline, and cysteine) were significantly up-regulated by RWL-1 inoculation under salinity stress. In addition, the stress-sensitive endogenous ABA levels were significantly reduced, whereas the levels of endogenous salicylic acid were significantly higher in RWl-1-inoculated plants than in control plants exposed to the same level of salinity stress. The current findings suggest that the phytohormone-producing abilities of endophytic bacteria can increase plant resistance to salinity, in turn improving agricultural productivity."


Silicon regulates antioxidant activities of crop plants under abiotic-induced oxidative stress: a review

"Silicon (Si) is the second most abundant element in soil, where its availability to plants can exhilarate to 10% of total dry weight of the plant. Si accumulation/transport occurs in the upward direction, and has been identified in several crop plants. Si application has been known to ameliorate plant growth and development during normal and stressful conditions over past two-decades. During abiotic (salinity, drought, thermal, and heavy metal etc) stress, one of the immediate responses by plant is the generation of reactive oxygen species (ROS), such as singlet oxygen (1O2), superoxide (), hydrogen peroxide (H2O2), and hydroxyl radicals (OH), which cause severe damage to the cell structure, organelles, and functions. To alleviate and repair this damage, plants have developed a complex antioxidant system to maintain homeostasis through non-enzymatic (carotenoids, tocopherols, ascorbate, and glutathione) and enzymatic antioxidants [superoxide dismutase (SOD), catalase (CAT), and ascorbate peroxidase (APX)]. To this end, the exogenous application of Si has been found to induce stress tolerance by regulating the generation of ROS, reducing electrolytic leakage, and malondialdehyde (MDA) contents, and immobilizing and reducing the uptake of toxic ions like Na, under stressful conditions. However, the interaction of Si and plant antioxidant enzyme system remains poorly understood, and further in-depth analyses at the transcriptomic level are needed to understand the mechanisms responsible for the Si-mediated regulation of stress responses."


Indole acetic acid and ACC deaminase from endophytic bacteria improves the growth of Solarium lycopersicum

"Endophytic bacteria are ubiquitous in all plant species contributing in host plant's nutrient uptake and helping the host to improve its growth. Moringa peregrina which is a medicinal plant, growing in arid region of Arabia, was assessed for the presence of endophytic bacterial strains."


Bacterial endophyte Sphingomonas sp. LK11 produces gibberellins and IAA and promotes tomato plant growth

"Plant growth promoting endophytic bacteria have been identified as potential growth regulators of crops. Endophytic bacterium, Sphingomonas sp. LK11, was isolated from the leaves of Tephrosia apollinea. The pure culture of Sphingomonas sp. LK11 was subjected to advance chromatographic and spectroscopic techniques to extract and isolate gibberellins (GAs). Deuterated standards of [17, 17-2H2]-GA4, [17, 17-2H2]-GA9 and [17, 17-2H2]-GA20 were used to quantify the bacterial GAs. The analysis of the culture broth of Sphingomonas sp. LK11 revealed the existence of physiologically active gibberellins (GA4: 2.97 ± 0.11 ng/ml) and inactive GA9 (0.98 ± 0.15 ng/ml) and GA20 (2.41 ± 0.23). The endophyte also produced indole acetic acid (11.23 ± 0.93 μM/ml). Tomato plants inoculated with endophytic Sphingomonas sp. LK11 showed significantly increased growth attributes (shoot length, chlorophyll contents, shoot, and root dry weights) compared to the control. This indicated that such phyto-hormones-producing strains could help in increasing crop growth."


Gibberellin secreting rhizobacterium, Pseudomonas putida H-2-3 modulates the hormonal and stress physiology of soybean to improve the plant growth under saline and drought conditions

"The physiological changes in tolerant soybean plants under salt and drought stress conditions with Pseudomonas putida H-2-3 were investigated. A bacterial isolate H-2-3 was isolated from soil and identified as Pseudomonas putida H-2-3 by 16S rDNA sequences. The treatment of P. putida H-2-3 significantly increased the length, fresh and dry weight of shoot and chlorophyll content in gibberellins (GAs) deficient mutant Waito-c rice seedlings over the control, it might be the presence of GA1, GA4, GA9 and GA20. The soybean plant growth was retarded in salt (120 mM sodium chloride) and drought (15% polyethylene glycol) stress conditions at 10 days treatments, while P. putida H-2-3 effectively enhanced the shoot length and fresh weight of plants suffered at salt and drought stress. The chlorophyll content was lower in abiotic stress conditions and bacterial inoculant P. putida H-2-3 mitigated the stress effects by an evidence of higher quantity of chlorophyll content in plants exposed to salt and drought. The stress hormonal analysis revealed that individual treatment of P. putida H-2-3, salt and drought significantly enhanced the abscisic acid and salicylic acid content than their control. P. putida H-2-3 applied to salt and drought stressed plants showed a lower level of abscisic acid and salicylic acid and a higher level of jasmonic acid content. Under stress condition induced by salt and drought in plants expressed higher level of total polyphenol, superoxide dismutase and radical scavenging activity and no significant changes in flavonoids. The bio-inoculant, P. putida H-2-3 modulated those antioxidants by declining superoxide dismutase, flavonoids and radical scavenging activity. P. putida H-2-3 induced tolerance against abiotic stress was confirmed by a reduction of Na content in abiotic stressed plants. The results suggest that P. putida H-2-3 application reprograms the chlorophyll, stress hormones and antioxidants expression in abiotic stress affected soybean plant and improves their growth under stress environment."


Plant growth-promoting rhizobacteria reduce adverse effects of salinity and osmotic stress by regulating phytohormones and antioxidants in Cucumis sativus

"We assessed the role of plant growth-promoting rhizobacteria (PGPR) strains viz. Burkholdera cepacia SE4, Promicromonospora sp. SE188 and Acinetobacter calcoaceticus SE370 in counteracting salinity and drought stress to cucumber plants. The control plants had stunted growth, while PGPR-treated plants had significantly higher biomass and chlorophyll contents under salinity and drought stress. The ameliorative effects of PGPR-application were also evidenced by the increased water potential and decreased electrolytic leakage. The PGPR-applied plants had reduced sodium ion concentration, while the potassium and phosphorus were abundantly present as compared to control under stress. Oxidative stress was mitigated by PGPR through reduced activities of catalase, peroxidase, polyphenol oxidase, and total polyphenol as compared to control. The control plants showed up-regulation of stress-responsive abscisic acid as compared to PGPR application, while salicylic acid and gibberellin 4 were significantly higher in PGPR. In conclusion, the PGPR application might be used in marginalized agricultural lands to increase crop productivity."


"Silicon (Si) application has been known to enhance the tolerance of plants against abiotic stresses. However, the protective mechanism of Si under heavy metals contamination is poorly understood. The aim of this study was to assess the role of Si in counteracting toxicity due to cadmium (Cd) and copper (Cu) in rice plants (Oryza sativa). Si significantly improved the growth and biomass of rice plants and reduced the toxic effects of Cd/Cu after different stress periods. Si treatment ameliorated root function and structure compared with non-treated rice plants, which suffered severe root damage. In the presence of Si, the Cd/Cu concentration was significantly lower in rice plants, and there was also a reduction in lipid peroxidation and fatty acid desaturation in plant tissues. The reduced uptake of metals in the roots modulated the signaling of phytohormones involved in responses to stress and host defense, such as abscisic acid, jasmonic acid, and salicylic acid. Furthermore, the low concentration of metals significantly down regulated the mRNA expression of enzymes encoding heavy metal transporters (OsHMA2 and OsHMA3) in Si-metal-treated rice plants. Genes responsible for Si transport (OsLSi1 and OsLSi2), showed a significant up-regulation of mRNA expression with Si treatment in rice plants. The present study supports the active role of Si in the regulation of stresses from heavy metal exposure through changes in root morphology."


Endophytic fungi produce gibberellins and indoleacetic acid and indoleacetic acid and promotes host-plant growth during stress

"We isolated and examined two endophytic fungi for their potential to secrete phytohormones viz. gibberellins (GAs) and indoleacetic acid (IAA) and mitigate abiotic stresses like salinity and drought. The endophytic fungi Phoma glomerata LWL2 and Penicillium sp. LWL3 significantly promoted the shoot and allied growth attributes of GAs-deficient dwarf mutant Waito-C and Dongjin-beyo rice. Analysis of the pure cultures of these endophytic fungi showed biologically active GAs (GA1, GA3, GA4 and GA7) in various quantities. The cultures of P. glomerata and Penicillium sp. also contained IAA. The culture application and endophytic-association with host-cucumber plants significantly increased the plant biomass and related growth parameters under sodium chloride and polyethylene glycol induced salinity and drought stress as compared to control plants. The endophytic symbiosis resulted in significantly higher assimilation of essential nutrients like potassium, calcium and magnesium as compared to control plants during salinity stress. Endophytic-association reduced the sodium toxicity and promoted the host-benefit ratio in cucumber plants as compared to non-inoculated control plants. The symbiotic-association mitigated stress by compromising the activities of reduced glutathione, catalase, peroxidase and polyphenol oxidase. Under stress conditions, the endophyte-infection significantly modulated stress through down-regulated abscisic acid, altered jasmonic acid, and elevated salicylic acid contents as compared to control. In conclusion, the two endophytes significantly reprogrammed the growth of host plants during stress conditions."


Endophytic fungal association via gibberellins and indoleacetic acid secretion can improve plant growth potential in abiotic stress: An example of Paecilomyces formosus LHL10

"Endophytic fungi are little known for exogenous secretion of phytohormones and mitigation of salinity stress, which is a major limiting factor for agriculture production worldwide. Current study was designed to isolate phytohormone producing endophytic fungus from the roots of cucumber plant and identify its role in plant growth and stress tolerance under saline conditions."

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