Muhammad Taimoor Shakeel | The Islamia University of Bahawalpur (original) (raw)

Papers by Muhammad Taimoor Shakeel

Southern tomato amalgavirus (STV) is a cryptic pathogen that is abundant in tomato production fie... more Southern tomato amalgavirus (STV) is a cryptic pathogen that is abundant in tomato production fields and intensifies the resurgence of tomato yellow stunt disease (ToYSD), together with other phytoviruses. Here, we mapped the geographical and genomic diversity, phylogenetics, and evolutionary dynamics of STV. We found that STV prevailed across China and Pakistan, with a maximum average rate of infection of 43.19% in Beijing, China, and 40.08% in Punjab, Pakistan. Subsequently, we amplified, cloned, and annotated the complete genome sequences of STV isolates from Solanum lycopersicum L. in China (OP548653 and OP548652) and Pakistan (MT066231) using Sanger and next-generation sequencing (NGS). These STV isolates displayed close evolutionary relationships with others from Asia, America, and Europe. Whole-genome-based molecular diversity analysis showed that STV populations had 33 haplotypes with a gene diversity (Hd) of 0.977 and a nucleotide diversity (π) of 0.00404. The genetic variability of RNA-dependent RNA-polymerase (RdRp) was higher than that of the putative coat protein (CP) p42. Further analysis revealed that STV isolates were likely to be recombinant but with a lower-to-moderate level of confidence. With a variable distribution pattern of positively and negatively selected sites, negative selection pressure predominantly acted on p42 and RdRp. These findings elaborated on the molecular variability and evolutionary trends among STV populations across major tomato-producing regions of the world.

Tomato yellows disease (TYD) is a serious problem in tomato crops worldwide, in which two crinivi... more Tomato yellows disease (TYD) is a serious problem in tomato crops worldwide, in which two criniviruses are implicated: Tomato infectious chlorosis virus (TICV) and Tomato chlorosis virus (ToCV). During the growing season 2014-2015, survey of tomato-growing greenhouses conducted in different geographical locations of Riyadh region in Saudi Arabia in order to identify the criniviruses implicated in TYD. In total, 228 leaf samples were collected from tomato plants showing typical TYD symptoms, as well as 98 from other symptomatic crops and 283 arable weeds belonging to 38 species in 22 different families. Nucleic acids extracts prepared from the samples were tested by nested RT-PCR for the simultaneous detection of TICV and ToCV. In addition, 34 adult whiteflies were collected from the surveyed tomato greenhouses and analyzed using real time PCR. Results revealed that ToCV was the only virus associated with TYD as detected in 328 (53%) of a total of 609 tested samples (including all hosts tested), while it showed an expanded host range, as it was reported for the first time in bean, bitter gourd, eggplant and pepper in Saudi Arabia. In addition, ToCV was detected in 14 weed species belonging to 8 families. TICV was not detected in any of the tested samples. All collected whiteflies were identified as Bemisia tabaci biotype B (MEAM1), an efficient vector of ToCV. Sequencing analysis of 40 selected sequences of ToCV from different hosts clustered Saudi Arabian isolates into two subgroups. Almost all Saudi Arabian isolates shared high nucleotide identity among themselves (98.0-100%) while 97.1-100% with those published in NCBI.

ITS MH879769, EndoPG MK168643, RPB2 ON568191, and GAPDH ON568192) showed 99-100% similarity with ... more ITS MH879769, EndoPG MK168643, RPB2 ON568191, and GAPDH ON568192) showed 99-100% similarity with references LC440581, KP789546, and KP124767, and KP124156 respectively. Pathogenicity test was conducted on 50 healthy fruits, surface disinfected as reported above, sprayed with 10 5 conidia/mL suspension, and incubated at 26 ± 1 °C. Control fruit (n = 50) were sprayed with distilled water. Four days post-inoculation the fruits exhibited brown spot symptoms. ALT-16 was recovered from infected fruits and morphologically identified. The strain was deposited at the Fungal Culture Collection, University of Agriculture, Faisalabad, Pakistan. Previously, we reported A. alternata causing postharvest brown spot of mandarin in Pakistan (Moosa et al. 2021; Liaquat et al. 2021) reported preharvest brown spot of lemon caused by A. alternata, using the 18S rRNA region for identification. However, to our knowledge, this is the first record of A. alternata causing postharvest brown spot of lemon in Pakistan, identified using a multilocus approach.

During the spring season of 2014, a total of 148 melon and watermelon leaf samples were collected... more During the spring season of 2014, a total of 148 melon and watermelon leaf samples were collected from symptomatic and asymptomatic plants in the western and southwestern regions of Saudi Arabia and were tested for the presence of Watermelon chlorotic stunt virus (WmCSV) and other suspected cucurbit viruses by double antibody sandwich enzyme-linked immunosorbent assays. Ninety-eight samples were found to be positive for the presence of WmCSV, nine samples were positive for the presence of Cucurbit yellow stunting disorder virus (CYSDV), and 22 showed a mixed infection with both WmCSV and CYSDV. No other cucurbit viruses were detected in any of the samples. Host range experiments revealed that eight out of fourteen tested plant species were susceptible to WmCSV. PCR products of approximately 1.2 kb were obtained after amplification using primers specifically targeting the coat protein region of WmCSV. Positive PCR results were confirmed by dot blot hybridization. Coat protein gene sequences from eleven WmCSV isolates indicated that the highest identity was between the 104WMA-SA isolate from the Wadi Baish location and a previously reported isolate from the AL-Lith location in Saudi Arabia. The lowest identity was observed between the 42WMA-SA isolate and an isolate from Palestine.

Plants in nature are under the persistent intimidation of severe microbial diseases, threatening ... more Plants in nature are under the persistent intimidation of severe microbial diseases, threatening a sustainable food production system. Plant-bacterial pathogens are a major concern in the
contemporary era, resulting in reduced plant growth and productivity. Plant antibiotics and chemicalbased bactericides have been extensively used to evade plant bacterial diseases. To counteract this
pressure, bacteria have evolved an array of resistance mechanisms, including innate and adaptive
immune systems. The emergence of resistant bacteria and detrimental consequences of antimicrobial
compounds on the environment and human health, accentuates the development of an alternative
disease evacuation strategy. The phage cocktail therapy is a multidimensional approach effectively
employed for the biocontrol of diverse resistant bacterial infections without affecting the fauna
and flora. Phages engage a diverse set of counter defense strategies to undermine wide-ranging
anti-phage defense mechanisms of bacterial pathogens. Microbial ecology, evolution, and dynamics
of the interactions between phage and plant-bacterial pathogens lead to the engineering of robust
phage cocktail therapeutics for the mitigation of devastating phytobacterial diseases. In this review,
we highlight the concrete and fundamental determinants in the development and application of
phage cocktails and their underlying mechanism, combating resistant plant-bacterial pathogens.
Additionally, we provide recent advances in the use of phage cocktail therapy against phytobacteria
for the biocontrol of devastating plant diseases.

During the growing seasons of 2014 through 2016, a total of 336 leaf samples from bell pepper (sh... more During the growing seasons of 2014 through 2016, a total of 336 leaf samples from bell pepper (showing leafroll and interveinal yellowing) and arable weeds were collected from Riyadh region, Saudi Arabia. The use of a polerovirus generic reverse transcription (RT)-PCR assay confirmed their presence in the bell pepper samples. Sequencing of the generic amplicon revealed high similarity (87.6 to 98.1% in nt) with four poleroviruses; Tobacco vein distorting virus, Pepper vein yellows virus, Pepper yellows virus, and Pepper yellow leaf curl virus. To further characterize one of these isolates (105D), a larger part of the genome (~1,300 nt) spanning approximately from the 3¢ end of ORF2 to the middle of ORF3, was amplified and sequenced. Blasting the resulting sequence revealed the low amino acid and nucleotide identity percentages in †

Potato leafroll virus (PLRV) is a widespread and one of the most damaging viral pathogens causing... more Potato leafroll virus (PLRV) is a widespread and one of the most damaging viral pathogens causing significant quantitative and qualitative losses in potato worldwide. The current knowledge of the geographical distribution, standing genetic diversity and the evolutionary patterns existing among global PLRV populations is limited. Here, we employed several bioinformatics tools and comprehensively analyzed the diversity, genomic variability, and the dynamics of key evolutionary factors governing the global spread of this viral pathogen. To date, a total of 84 full-genomic sequences of PLRV isolates have been reported from 22 countries with most genomes documented from Kenya. Among all PLRV-encoded major proteins, RTD and P0 displayed the highest level of nucleotide variability. The highest percentage of mutations were associated with RTD (38.81%) and P1 (31.66%) in the coding sequences. We detected a total of 10 significantly supported recombination events while the most frequently detected ones were associated with PLRV genome sequences reported from Kenya. Notably, the distribution patterns of recombination breakpoints across different genomic regions of PLRV isolates remained variable. Further analysis revealed that with exception of a few positively selected codons, a major part of the PLRV genome is evolving under strong purifying selection. Protein disorder prediction analysis revealed that CP-RTD had the highest percentage (48%) of disordered amino acids and the majority (27%) of disordered residues were positioned at the C-terminus. These findings will extend our current knowledge of the PLRV geographical prevalence, genetic diversity, and evolutionary factors that are presumably shaping the global spread and successful adaptation of PLRV as a destructive potato pathogen to geographically isolated regions of the world.

Background Citrus plants are prone to infection by different viroids which deteriorate their vigo... more Background Citrus plants are prone to infection by different viroids which deteriorate their vigor and production. Citrus viroid V (CVd-V) is among the six citrus viroids, belongs to genus Apscaviroid (family Pospiviroidae) which induces symptoms of mild necrotic lesions on branches and cracks on trunk portion. Methods and results A survey was conducted to evaluate the prevalence of CVd-V in core and non-core citrus cultivated areas of Punjab, Pakistan. A total of 154 samples from different citrus cultivars were tested for CVd-V infection by RT-PCR. The results revealed 66.66% disease incidence of CVd-V. Citrus cultivars Palestinia Sweet lime, Roy Ruby, Olinda Valencia, Kaghzi lime, and Dancy were identified as new citrus hosts of CVd-V for the first time from Pakistan. The viroid infection was confirmed by biological indexing on indicator host Etrog citron. The reported primers used for the detection of CVd-V did not amplify, rather showed non-specific amplification, which led to the designing of new primers. Whereas, new back-to-back designed primers (CVd-V AF1/CVd-V AR1) detected CVd-V successfully and obtained an expected amplified product of CVd-V with 294 bp. Sequencing analysis confirmed the new host of CVd-V showing 98-100% nucleotide sequence homology with those reported previously from other countries while 100% sequence homology to the isolates reported from Pakistan. Based on phylogenetic analysis using all CVd-V sequences in GenBank, two main CVd-V groups (I and II) were identified, and newly identified isolates during this study fall in the group I. Conclusion The study revealed that there are some changes in the nucleotide sequences of CVd-V which made difficult for their detection using reported primers. All isolates of Pakistan showed high sequence homology with other isolates of CVd-V from Iran and USA whereas; the isolates from China, Japan, Tunisia, and Africa are distantly related. It is evident that CVd-V is spreading in all citrus cultivars in Pakistan.

Biochemical studies were made to monitor the relationship of chemical components and development ... more Biochemical studies were made to monitor the relationship of chemical components and development of resistance in cucumber plants against Cucumber mosaic virus (CMV). Total soluble phenols, soluble sugars, chlorophyll and mineral nutrients; Potassium, Magnesium, Sodium and Lead were compared among resistant and susceptible varieties. Different metabolites showed different trends among diseased and healthy plants from resistant and susceptible groups of varieties. The phenolic and Magnesium contents increased in the inoculated plants of both susceptible and resistant genotypes. In resistant variety, rise in magnesium concentration in inoculated plants was less as compared to that of inoculated plants of the susceptible varieties. However, the chlorophyll, sugars, potassium were reduced in the inoculated plants of both reaction resistant and susceptible reaction groups. Plants from susceptible group presented a lower of level of nutrients as compared to uninoculated ones whereas; the changes in sodium contents were not showing any relation to resistance mechanism.

Citrus Canker—Distribution, Taxonomy, Epidemiology, Disease Cycle, Pathogen Biology, Detection, and Management: A Critical Review and Future Research Agenda

Bacillus thuringiensis CHGP12 uses a multifaceted approach for the suppression of Fusarium oxysporum f. sp. ciceris and to enhance the biomass of chickpea plants, 2022

BACKGROUND: Bacillus species synthesize antifungal lipopeptides (LPs) making them a sustainable a... more BACKGROUND: Bacillus species synthesize antifungal lipopeptides (LPs) making them a sustainable and eco-friendly management option to combat Fusarium wilt of chickpea. RESULTS: In this study, 18 endophytic Bacillus strains were assessed for their antifungal activity against Fusarium oxysporum f. sp. ciceris (FOC) associated with Fusarium wilt of chickpea. Among them, 13 strains produced significant inhibition zones in a direct antifungal assay while five strains failed to produce the inhibition of FOC. Bacillus thuringiensis CHGP12 exhibited the highest inhibition 3.45 cm of FOC. The LPs extracted from CHGP12 showed significant inhibition of the pathogen. Liquid chromatography-mass spectrometry (LC-MS) analysis confirmed that CHGP12 possessed the ability to produce fengycin, surfactin, iturin, bacillaene, bacillibactin, plantazolicin, and bacilysin. In an in vitro qualitative assay CHGP12 exhibited the ability to produce lipase, amylase, cellulase, protease, siderophores, and indole 3-acetic acid (IAA). IAA and gibberellic acid (GA) were quantified using ultra-performance liquid chromatography (UPLC) with 370 and 770 ng mL −1 concentrations of IAA and GA respectively. Furthermore, the disease severity showed a 40% decrease over control in CHGP12 treated plants compared to the control in a glasshouse experiment. Moreover, CHGP12 also exhibited a significant increase in total biomass of the plants namely, root and shoot growth parameters, stomatal conductance, and photosynthesis rate. CONCLUSION: In conclusion, our findings suggest that B. thuringiensis CHGP12 is a promising strain with high antagonistic and growth-promoting potential against Fusarium wilt of chickpea.

New Disease Reports, 2015

International Journal of Agriculture and Biology, 2018

Whitefly samples were collected from several greenhouses and identified as Bemisia tabaci by poly... more Whitefly samples were collected from several greenhouses and identified as Bemisia tabaci by polymerase chain reaction (PCR), followed by sequencing of mtCOI gene that revealed their identity as biotype B MEAM1. Transmission of Cucurbit chlorotic yellows virus (CCYV) by the identified whitefly biotype was estimated by conducting several experiments. The results showed that a single whitefly was sufficient to transmit the virus to healthy seedlings. It was also found that the vector required a 90-min acquisition and inoculation access period to successfully transfer the virus. Moreover, vector was found to be able to retain the virus for 6 days' post acquisition. Efficiency of cucumber and D. stramonium, plants was compared as a source of CCYV inoculum for virus acquisition by B. tabaci and obtained results revealed that cucumber was a more efficient source of virus infection than D. stramonium. Using cucumber as source of infection, 90% of the inoculated plants (from each species i.e. cucumber and D. stramonium), were infected while using D. stramonium, as a source, the percentage of infection in cucumber plants dropped to 60% (cucumber) and to 50% in D. stramonium. These results showed that D. stramonium, is a relatively less efficient source of virus for whitefly acquisition as compared to cucumber. Host range experiments for CCYV showed that all the cucurbit plants were infected and had different levels of symptoms. Cucumis sativus, C. melo, C. amaranticolor and D. stramonium showed interveinal chlorosis, whereas general yellowing and reduced growth were observed in all positively tested hosts.

To cite this paper: AL-Saleh, M.A., M.A. Amer, I.M. AL-Shahwan, O.A. Abdalla and M.T. Shakeel, 20... more To cite this paper: AL-Saleh, M.A., M.A. Amer, I.M. AL-Shahwan, O.A. Abdalla and M.T. Shakeel, 2014. Molecular characterization of two alfalfa mosaic virus isolates infecting potato crop in central region of Saudi Arabia. Int. J. Agric. Biol.,

Citrus Canker—Distribution, Taxonomy, Epidemiology, Disease Cycle, Pathogen Biology, Detection, and Management: A Critical Review and Future Research Agenda

Bacillus thuringiensis CHGP12 uses a multifaceted approach for the suppression of Fusarium oxysporum f. sp. ciceris and to enhance the biomass of chickpea plants, 2022

New Disease Reports, 2015

International Journal of Agriculture and Biology, 2018