Abdul Latif Khan

• M.Phil, PhD
• Assistant Professor at University of Houston

We investigated the effects of silicon (Si) application on rice plants (Oryza sativa L.) and its responses in the regulation of jasmonic acid (JA) during wounding stress. Endogenous JA was significantly higher in wounded rice plants than in non-wounded. In contrast, Si treatment significantly reduced JA synthesis as compared to non-Si applications...

This chapter highlights the role of chemically engineered nanoparticles (NPs) in achieving sustainable and resilient agriculture. Chemically engineered NPs are derived from metals, carbon, polymers, silica, and composites. These engineered NPs offer effective solutions for making agriculture more productive and resilient to stresses. Metal-based NP...

Global climate change, rapid increase in human population, and ecological stress limit crop production. Conventional strategies failed to mitigate the adverse effects on crops. A relatively new branch of nanoparticle research, termed “green synthesized nanoparticles” (GNPs), uses plant extract instead of hazardous chemicals that affect non-targeted...

Microbes like bacteria and fungi are crucial for host plant growth and development. However, environmental factors and host genotypes can influence microbiome composition and diversity in plants such as industrial hemp (Cannabis sativa L.). Herein, we evaluated the endophytic and rhizosphere microbial communities of two cannabidiol (CBD; Sweet Sens...

Bacillus pumilus plays an essential role in agricultural applications as a beneficial microbe and for sustainable agriculture production. However, the underlying mechanisms of B. pumilus strains remain unclear as to how they are beneficial for plants as stress tolerant and growth promoters. Bacillus pumilus was isolated from the rhizosphere soil of...

Parthenium hysterophorus , a globally widespread weed, poses a significant threat to agricultural ecosystems due to its invasive nature. We investigated the chloroplast genome of P. hysterophorus in this study. Our analysis revealed that the chloroplast genome of P. hysterophorus spans a length of 151,881 base pairs (bp). It exhibits typical quadri...

Microorganisms like bacteria and fungi are crucial for host medicinal plant growth and development. However, environmental factors and host genotypes can influence microbiome composition and diversity in plants such as industrial hemp ( Cannabis sativa L.), which can help us understand how they cope with climatic stresses and pathogenic attacks. We...

Introduction With current trends in global climate change, both flooding episodes and higher levels of CO2 have been key factors to impact plant growth and stress tolerance. Very little is known about how both factors can influence the microbiome diversity and function, especially in tolerant soybean cultivars. This work aims to (i) elucidate the i...

Rice (Oryza sativa) is a research model for monocotyledonous plants. Rice is also one of the major staple foods and the primary crop for more than half of the world’s population. Increasing industrial activities and the use of different fertilizers and pesticides containing heavy metals (HMs) contribute to the contamination of agriculture fields. H...

Salinity stress, a significant global abiotic stress, is caused by various factors such as irrigation with saline water, fertilizer overuse, and drought conditions, resulting in reduced agricultural production and sustainability. In this study, we investigated the use of halotolerant bacteria from coastal regions characterized by high salinity as a...

Plant-microbe interactions play a crucial role in shaping plant growth and development, as well as in mediating plant responses to biotic and abiotic stresses. In this study, we used RNA-seq data to examine the expression profiles of SlWRKY, SlGRAS, and SlERF genes during the symbiotic association of Curvularia lunata SL1 with tomato (Solanum lycop...

The Zygophyllum and Tetraena genera are intriguingly important ecologically and medicinally. Based on morphological characteristics, T. hamiensis var. qatarensis, and T. simplex were transferred from Zygophyllum to Tetraena with the least genomic datasets available. Hence, we sequenced the T. hamiensis and T. simplex and performed in-depth comparat...

Climate changes abruptly affect optimum growth temperatures, leading to a negative influence on plant physiology and productivity. The present study aimed to investigate the extent of low-temperature stress effects on date palm growth and physiological indicators under the exogenous application of silicon (Si). Date palm seedlings were treated with...

Cochliobolus, Bipolaris, and Curvularia genera contain various devastating plant pathogens that cause severe crop losses worldwide. The species belonging to these genera also perform a variety of diverse functions, including the remediation of environmental contaminations, beneficial phytohormone production, and maintaining their lifestyle as epiph...

The WRKY and bHLH transcription factors have been implicated in the regulation of gene expression during various physiological processes in plants, especially in plant stress responses. However, little information about the heavy metal-responsive SlWRKY and SlbHLH in tomato (Solanum lycopersicum) is available. We performed a genome-wide investigati...

In this study, endophytic fungus Curvularia lunata strain SL1 was used to explore its bioremediation potential and growth restoration of tomato (Solanum lycopersicum) under cadmium (Cd) stress. Our findings demonstrate that SL1 establishes a symbiotic relationship with tomato plants, which modulates the antioxidant system, secondary metabolites, an...

Dracaena (Asparagaceae family) tree is famous for producing "dragon blood"—a bioactive red-colored resin. Despite its long history of use in traditional medicine, little knowledge exists on the genomic architecture, phylogenetic position, or evolution. Hence, in this study, we sequenced the whole chloroplast (cp) genomes of D. serrulata and D. cinn...

Melatonin (MT), a ubiquitous signaling molecule, is known to improve plant growth. Its regulatory function alongside nitric oxide (NO) is known to induce heavy metal (Cd and Pb) stress tolerance, although the underlying mechanisms remain unknown. Here, we observed that the combined application of MT and NO remarkably enhanced plant biomass by reduc...

Arsenic is a toxic metal abundantly present in agricultural, industrial, and pesticide effluents. To overcome arsenic toxicity and ensure safety for plant growth, silicon (Si) can play a significant role in its mitigation. Here, we aim to investigate the influence of silicon on date palm under arsenic toxicity by screening antioxidants accumulation...

The Arabian tahr (Arabitragus jayakari) endemic to mountains of northern Oman and the United Arab Emirates, however, the species is faced with significant threats to its population. Because of its small and dwindling population, it is listed as Endangered. Here, we sequenced and assembled the mitochondrial (mt) genome of A. jayakari into 16,485 bp...

Boswellia sacra Flueck (family Burseraceae) tree is wounded to produce frankincense. We report its de novo assembled genome (667.8 Mb) comprising 18,564 high-confidence protein-encoding genes. Comparing conserved single-copy genes across eudicots suggest >97% gene space assembly of B. sacra genome. Evolutionary history shows B. sacra gene-duplicati...

Microbial symbionts play a significant role in plant health and stress tolerance. However, few studies exist that address rare species of core-microbiome function during abiotic stress. In the current study, we compared the microbiome composition of succulent dwarf shrub halophyte Zygophyllum qatarensis Hadidi across desert populations. The results...

The mechanism and course of Triticum plastome evolution is currently unknown; thus, it remains unclear how Triticum plastomes evolved during recent polyploidization. Here, we report the complete plastomes of two polyploid wheat species, Triticum sphaerococcum (AABBDD) and Triticum turgidum subsp. durum (AABB), and compare them with 19 available and...

Background Ziziphus hajarensis is an endemic plant species well-distributed in the Western Hajar mountains of Oman. Despite its potential medicinal uses, little is known regarding its genomic architecture, phylogenetic position, or evolution. Here we sequenced and analyzed the entire chloroplast (cp) genome of Z. hajarensis to understand its geneti...

Frankincense tree (Boswellia sacra Fluek) has been poorly known on how it responds to tapping and wound-recovery process at molecular levels. Here, we used RNA-sequencing analysis to profile transcriptome of B. sacra after 30 min, 3 h and 6 h of post-tapping. Results showed 5525 differentially expressed genes (DEGs) that were related to terpenoid b...

Gymnosperms are among the most endangered groups of plant species; they include ginkgo, pines (Conifers I), cupressophytes (Conifers II), cycads, and gnetophytes. The relationships among the five extant gymnosperm groups remain equivocal. We analyzed 167 available gymnosperm plastomes and investigated their diversity and phylogeny. We found that pl...

Global warming is impacting the growth and development of economically important but sensitive crops, such as soybean (Glycine max L.). Using pleiotropic signaling molecules, melatonin can relieve the negative effects of high temperature by enhancing plant growth and development as well as modulating the defense system against abiotic stresses. How...

Melatonin is an indolamine bioactive molecule that regulates a wide range of physiological processes during plant growth and enhances abiotic stress tolerance. Here we examined the putative role of exogenous melatonin application (foliar or root zone) in improving drought stress tolerance in soybean seedlings. Pre-treatment of soybean seedlings wit...

Mangroves (Avicennia marina) growing in intertidal areas are often exposed to diesel spills, adversely damaging the ecosystem. Herein, we showed for the first time that mangrove seedlings’ associations with bacteria could reprogram host-growth, physiology, and ability to degrade diesel. We found four bacterial strains [Sphingomonas sp.-LK11, Rhodoc...

Date palm (Phoenix dactylifera L.)Date palm (Phoenix dactylifera) is a major fruitFruit crop of arid regions, domesticated ~7000 years ago in the Near and Middle East. With the advancement of next-generation sequencingNext Generation Sequencing (NGS) technology, genomicGenomics data of date palm have increased rapidly and yielded new insights into...

Drought stress retards plant growth and yield. Melatonin and nitric oxide (NO) have demonstrated their potential role against abiotic stresses; however, the underlying molecular mechanism by which they interact and extend drought stress tolerance has not been fully elucidated. Herein, the current study was performed to establish the optimum benefic...

Background Salvadora persica L. (Toothbrush tree – Miswak; family-Salvadoraceae) grows in the arid-land ecosystem and possesses economic and medicinal importance. The species, genus and the family have no genomic datasets available specifically on chloroplast (cp) genomics and taxonomic evolution. Herein, we have sequenced the complete chloroplast...

This review is not intended to describe the triterpenes isolated from the Boswellia genus, since this information has been covered elsewhere. Instead, the aim is to provide insights into the biosynthesis of triterpenes in Boswellia. This genus, which has 24 species, displays fascinating structural diversity and produces a number of medicinally impo...

Tef (Eragrostis tef (Zucc.) Trotter) is a staple food crop for 70% of the Ethiopian population and is currently cultivated in several countries for grain and forage production. It is one of the most nutritious grains, and is also more resilient to marginal soil and climate conditions than major cereals such as maize, wheat and rice. However, tef is...

Phoenix dactylifera (date palm) is a well-known nutritious and economically important fruit tree found in arid regions of the Middle East and North Africa. Being diploid, it has extremely high divergence in gender, where sex differentiation in immature date palms (Phoenix dactylifera L.) has remained an enigma in recent years. Herein, new robust in...

Avicennia marina (family Acanthaceae) is a halotolerant woody shrub that grows wildly and cultivated in the coastal regions. Despite its importance, the species suffers from lack of genomic datasets to improve its taxonomy and phylogenetic placement across the related species. Here, we have aimed to sequence the plastid genome of A. marina and its...

Background: SARS-CoV-2 has been proven lethal to human health affecting almost every corner of the world. The objectives of this study were to add context to the global data and international genomic consortiums, and to give insight into the efficiency of the contact tracing system in Oman. Methods: We combined epidemiological data and whole-gen...

Background The tRNAs act as a bridge between the coding mRNA and incoming amino acids during protein translation. The anti-codon of tRNA recognizes the codon of the mRNA and deliver the amino acid into the protein translation chain. However, we did not know about the exact abundance of anti-codons in the genome and whether the frequency of abundanc...

Oxalis corniculata L. (family Oxalidaceae) is a small creeper wood sorrel plant that grows well in moist climates. Despite being medicinally important, little is known about the genomics of this species. Here, we determined the complete chloroplast genome sequence of O. corniculata for the first time and compared it with other members of family Oxa...

Background The tRNAs act as a bridge between the coding mRNA and incoming amino acids during protein translation. The anti-codon of tRNA recognizes the codon of the mRNA and deliver the amino acid into the protein translation chain. However, we did not know about the exact abundance of anti-codons in the genome and whether the frequency of abundanc...

Background The tRNAs act as a bridge between the coding mRNA and incoming amino acids during protein translation. The anti-codon of tRNA recognizes the codon of the mRNA and deliver the amino acid into the protein translation chain. However, we did not know about the exact abundance of anti-codons in the genome and whether the frequency of abundanc...

Date palm (Phoenix dactylifera L.) and its fruit possess sociocultural, health and economic importance in Middle East. The date palm plantations are prone to Dubas bug (DB; Ommatissus lybicus DeBergevin; Homoptera: Tropiduchidae) attacks that severely damages the tree’s growth and reduces fruit production. However, the transcriptome related dataset...

Background: Incidences of heat stress due to the changing global climate can negatively affect the growth and yield of temperature-sensitive crops such as soybean variety, Pungsannamul. Increased temperatures decrease crop productivity by affecting biochemical, physiological, molecular, and morphological factors either individually or in combinati...

Background: Abiotic stresses (e.g., heat or limited water and nutrient availability) limit crop production worldwide. With the progression of climate change, the severity and variation of these stresses are expected to increase. Exogenous silicon (Si) has shown beneficial effects on plant growth; however, its role in combating the negative effects...

Date palm is one of the most economically vital fruit crops in North African and Middle East countries, including Oman. A controlled experiment was conducted to investigate the integrative effects of silicon (Si) and gibberellic acid (GA 3) on date palm growth and heat stress. The exogenous application of Si and GA 3 significantly promoted plant gr...

Genus Prosopis (family Fabaceae) are shrubby trees, native to arid and semi-arid regions of Asia, Africa, and America and known for nitrogen fixation. Here, we have sequenced the complete chloroplast (cp) genomes of two Prosopis species (P. juliflora and P. cineraria) and compared them with previously sequenced P. glandulosa, Adenanthera microsperm...

Heat stress is one of the major abiotic stresses that impair plant growth and crop productivity. Plant growth-promoting endophytic bacteria (PGPEB) and humic acid (HA) are used as bio-stimulants and ecofriendly approaches to improve agriculture crop production and counteract the negative effects of heat stress. Current study aimed to analyze the ef...

• Salt stress negatively affects growth and development of the plants. However, it is hypothesized that plant growth‐promoting endophytic bacteria greatly alleviate the adverse effects of salinity and can promote growth and development of the plants. In the present research, we aimed to isolate endophytic bacteria from halotolerant plants and evalu...

NAC (NAM, ATAF1,2, and CUC2) transcription factors are one of the largest transcription factor families found in the plants and are involved in diverse developmental and signalling events. Despite the availability of comprehensive genomic information from diverse plant species, the basic genomic, biochemical, and evolutionary details of NAC TFs hav...

Endophytic fungi have been a focus of attention for producing diverse classes of bioactive metabolites but little is known about endophytic fungi Aureobasidium pullulan, isolated from the bark of frankincense producing tree (Boswellia sacra). Extensive chromatographic methods resulted in the isolation of two known diketopeprazin (1 and 2) along wit...

Melatonin is a multifunctional signaling molecule that is ubiquitously distributed in different parts of a plant and responsible for stimulating several physio-chemical responses to adverse environmental conditions. In this review, we show that, although plants are able to biosynthesize melatonin, the exogenous application of melatonin to various c...

Agricultural land is extensively affected by salinity stress either due to natural phenomena or by agricultural practices. Saline stress possesses two major threats to crop growth: osmotic stress and oxidative stress. The response of these changes is often accompanied by variety of symptoms, such as the decrease in leaf area and internode length an...

In the current study, we aimed to elucidate the plant growth-promoting characteristics of Pseudomonas psychrotolerans CS51 under heavy metal stress conditions (Zn, Cu, and Cd) and determine the genetic makeup of the CS51 genome using the single-molecule real-time (SMRT) sequencing technology of Pacific Biosciences. The results revealed that inocula...

Plantago ovata (Plantaginaceae) is an economically and medicinally important species, however, least is known about its genomics and evolution. Here, we report the first complete plastome genome of P. ovata and comparison with previously published genomes of related species from Plantaginaceae. The results revealed that P. ovata plastome size was 1...

The use of plant growth-promoting rhizobacteria is economically viable and environmentally safe for mitigating various plant stresses. Abiotic stresses such as flood and drought are a serious threat to present day agriculture. In the present study, the indole-3-acetic acid-producing rhizobacterium R. sphaeroides KE149 was selected, and its effect o...

Euphorbia is one of the largest genera in the Euphorbiaceae family, comprising 2000 species possessing commercial, medicinal, and ornamental importance. However, there are very little data available on their molecular phylogeny and genomics, and uncertainties still exist at a taxonomic level. Herein, we sequence the complete chloroplast (cp) genome...

Chloroplasts are unique organelles within plant cells and are ultimately responsible for sustaining life forms on the earth due to their ability to conduct photosynthesis. Multiple functional genes within the chloroplast are responsible for a variety of metabolic processes that occur in the chloroplast. Considering its fundamental role in sustainin...

The species belonging to the Sphingomonas genus possess multifaceted functions ranging from remediation of environmental contaminations to producing highly beneficial phytohormones, such as sphingan and gellan gum. Recent studies have shown an intriguing role of Sphingomonas species in the degradation of organometallic compounds. However, the actua...

Alkalinity is a known threat to crop plant growth and production, yet the role of exogenous silicon (Si) and salicylic acid (SA) application has been largely unexplored. Here, we sought to understand the beneficial impacts of Si and SA on tomato seedlings during high-pH (9.0) stress. Results showed that Si- and SA-treated plants displayed higher bi...

Transfer RNAs (tRNAs) play important roles to decode the genetic information contained in mRNA in the process of translation. The tRNA molecules possess conserved nucleotides at specific position to regulate the unique function. However, several nucleotides at different position of the tRNA undergo modification to maintain proper stability and func...

Vachellia and Senegalia are the most important genera in the subfamily Mimosoideae (Fabaceae). Recently, species from both genera were separated from the long-characterized Acacia due to their macro-morphological characteristics. However, this morpho-taxonomic differentiation struggles to discriminate some species, for example, Vachellia nilotica a...

Salinity stress hinders the growth potential and productivity of crop plants by influencing photosynthesis, disturbing the osmotic and ionic concentrations, producing excessive oxidants and radicals, regulating endogenous phytohormonal functions, counteracting essential metabolic pathways, and manipulating the patterns of gene expression. In respon...

Chloroplasts are unique organelles within plant cells and are ultimately responsible for sustaining life forms on the earth due to their ability to conduct photosynthesis. Multiple functional genes within the chloroplast are responsible for a variety of metabolic processes that occur in the chloroplast. Considering its fundamental role in sustainin...

This study aimed to investigate the bioremediation efficiency of phytohormone-producing endophytic Bacillus amyloliquefaciens RWL-1 isolated from rice seeds. In this study, we tested RWL-1 against various heavy metals (Cu, Cr, Pb, and Cd). Among the tested heavy metals, RWL-1 showed highest tolerance for Cu stress and we observed alterations in gro...

Wild and medicinal plants producing resin and ladle with phenolic and polysaccharides have been found a major hurdle to extract high quality of genomic DNA. These contaminants co-precipitate with DNA and inhibit enzymatic modification of DNA. Previously reported protocols yielded highly viscous DNA regimen that were not amicable to down-stream anal...

Background: Salinity is one of the major abiotic constraints that hinder health and quality of crops. Conversely, halotolerant plant growth-promoting rhizospheric (PGPR) bacteria are considered biologically safe for alleviating salinity stress. Results: We isolated halotolerant PGPR strains from the rhizospheric soil of Artemisia princeps, Cheno...

Short-term water submergence to soybean ( Glycine max L.) create hypoxic conditions hindering plant growth and productivity. Nitric oxide (NO) is considered a stress-signalling and stress-evading molecule, however, little is known about its role during flooding stress. We elucidated the role of sodium nitroprusside (SNP) and S-nitroso L-cysteine (C...

Oxidative stress is often considered detrimental for cellular processes and damaging for the lipid bi-layer. Counteracting such stresses with the aid of nature-based chemical constituents can be an ideal therapeutic approach. The current study aimed to investigate the chemical constituents of resins derived from the well-known Aloe vera and less kn...

Salinity stress adversely affects the growth and productivity of different crops. In the present study, we isolated the rhizospheric bacteria Arthrobacter woluwensis AK1 from Pohang beach, South Korea and determined its plant growth-promoting potential under NaCl salt stress (0, 100, and 200 mM). AK1 has phosphate-solubilizing activity and produce...

Teucrium is one of the most economically and ecologically important genera in the Lamiaceae family; however, it is currently the least well understood at the plastome level. In the current study, we sequenced the complete chloroplast (cp) genomes of T. stocksianum subsp. stenophyllum R.A.King (TSS), T. stocksianum subsp. stocksianum Boiss. (TS) and...

Plant endophytes play vital role in plant growth promotion as well as in abiotic and biotic stress tolerance. They also mediate biotransformation of complex organic materials to simpler and useful by-product. Therefore, the role of plant endophyte in plant growth promotion and stress tolerance has gained considerable attention in recent days. Sphin...

In the current study, we aimed to elucidate the bioremediating potential of endophytic fungi during various heavy metals stresses to the cucumber (Cucumis sativus) plants. Preliminary screening showed that endophyte (Aureobasidium. pullulans BSS6) produced IAA and extra-cellular enzymes (phosphatase, cellulase and glucosidase). Therefore, BSS6 was...

This study investigates the stress-mitigating effects of endophytic Penicillium funiculosum LHL06 on soybean roots via modulation of physio-biochemical, molecular, and proteomic responses to combined heavy metal (Ni, Cu, Pb, Cr, and Al) toxicity. Preliminary screening revealed that LHL06 can tolerate and remediate combined heavy metal contamination...

Boswellia sacra has been studied with attention to the rhizosphere microbiota in its root zone. The current chapter discusses the bacterial and fungal rhizosphere communities living with both cultivated and wild B. sacra tree populations studied using next-generation sequencing approaches. The results revealed that Ascomycota and Basidiomycota were...

Endophytes (bacteria or fungi) are a major class of plant symbionts that live within their hosts. These endosymbionts provide a diverse hub of bioactive secondary metabolites, phytohormones, extracellular enzymes and essential nutrients. In return, the host provides a protective habitat and access to the nutrients needed to reproduce and grow durin...