A. M. Al-Subhi

A divergent isolate of Tomato yellow leaf curl virus from Oman with an associated DNAβ satellite: an evolutionary link between Asian and the Middle Eastern virus–satellite complexes

Tomato is cultivated in the coastal region of Al-Batinah, in the Sultanate of Oman, during the winter season, to meet the high demand for fresh produce in the domestic market. In order to identify the causal agent of a widespread disease associated with infestations of the whitefly Bemisia tabaci (Genn.) leaves were collected from tomato plants showing symptoms characteristic of the disease in Al-Batinah during 2004 and 2005. Total nucleic acids were isolated from the tomato leaves and used as the template for Φ29 DNA polymerase amplification of begomoviral circular DNA. Putative full unit length begomoviral DNA multimers were digested with Nco I and cloned into the plasmid vector pGEM7Zf+. The complete nucleotide (nt) sequence was determined as 2,765 bases, indicative of a monopartite begomoviral genome. A comparison of the genome sequence for the seven field isolates examined, indicated that they shared 99% nt identity. The virus from Oman was most closely related to TYLCV-IR at 91% nt identity, a monopartite begomoviral species described previously from Iran. Based on the guidelines of the ICTV the Oman isolate has been designated TYLCV-Om and is considered an isolate of TYLCV-IR. A satellite DNA (satDNA β), was amplified by polymerase chain reaction using degenerate primers and cloned, and the DNA sequence was determined. Analysis of the complete nt sequence of 1,371 bases indicated that the satDNA shared 88.5% similarity with its closest relatives, which are DNAβ molecules from tomato in Pakistan. This is the first report of a satDNA β associated with the TYLCV species. The TYLCV-Om and associated satDNA, thus represent a begomovirus-complex at the Asian-Middle East crossroads that quiet uniquely share geographical and genetic hallmarks of both.

Indigenous grass species with potential for maintaining rangeland and livestock feeding in Oman

Abstract This study aimed at identifying plant species with potential for rangeland conservation and to provide livestock feed in Oman. A survey was carried out in Al-Khod region near Muscat (Oman) to identify potential grass species. Samples were collected from various sites during the rainy season (November–April) to study the morphology and chemical composition of selected grasses. Cenchrus and Pennisetum species were the most promising grasses in terms of livestock feeding. The yield of pasture dominated by Cenchrus was higher than that reported for the species in other countries with a similar arid environment and comparable to grasses grown in Oman under irrigation. Relevant meteorological records indicated that the grasses had good potential to withstand shortage of water. The germination test on burs and seeds showed high dormancy reflecting ability to survive under uncertain rainfall and potential for survival under rangeland conditions. Storage of seeds for a period of 1 year improved their germination up to 66%. Variation in morphological traits indicated the suitability of grasses to develop varieties for commercial use under farm or rangeland conditions.

DNA based characterization of Ceratocystis fimbriata isolates associated with mango decline in Oman

Abstract.A serious mango decline disease has recently been reported from the Sultanate of Oman. Based on morphological characteristics, the pathogen responsible for the disease was previously identified as Ceratocystis fimbriata. C. fimbriata is one of the most important pathogens of mango in Brazil and its appearance in Oman is of great concern. Recent phylogenetic studies have shown that C. fimbriata most likely represents a species complex. The aim of this study was to confirm the identity of the mango pathogen in Oman based on DNA sequences. Sequence data were obtained for the internal transcribed spacer 1 and 2 regions and the 5.8S rRNA gene regions and these were compared with sequence data of C. fimbriata from several hosts and geographic areas. The isolates from Oman where shown to represent C. fimbriata sensu lato and also to be most closely related to an isolate from mango in Brazil. This provides some evidence that the mango pathogen in Oman might have originated in Brazil.

Molecular Characterization of the 16S rRNA Gene of Phytoplasmas Detected in Two Leafhopper Species Associated with Alfalfa Plants Infected with Witches' Broom in Oman

Two leafhopper species, Austroagallia avicula and Empoasca sp., were consistently found in alfalfa fields infected with witches’ broom phytoplasma (OmanAlfWB) in the Al-Batinah, Dakhliya, North and South Sharqiya, Muscat, and Al-Bureimi regions of the Sultanate of Oman. Phytoplasmas from both leafhoppers were detected by specific polymerase chain reaction (PCR) amplification of the 16S rRNA gene and the spacer region in direct PCR using P1/P7 primer pairs. Comparative RFLP profiles of the amplified rRNA gene and the spacer region from leafhopper phytoplasmas and from 20 phytoplasma controls yielded patterns referable to phytoplasmas belonging to the peanut witches’ broom group (16SrII group). In particular, extensive RFLP analyses with the endonucleases HpaII, Tru9I, Tsp509I, and RsaI indicated that the phytoplasmas in A. avicula and Empoasca sp. were identical but showed some differences from OmanAlfWB; however, RFLP patterns obtained with TaqI showed the OmanAlfWB and the phytoplasmas from the two leafhoppers to be identical. Direct PCR products amplified from phytoplasma leafhopper DNA using the P1/P7 primer pair were cloned and sequenced yielding 1758 bp and 1755 bp products from A. avicula and Empoasca sp. respectively; the homology of these sequences with OmanAlfWB and papaya yellow crinkle phytoplasmas was more than 98%. A phylogenetic tree based on the 16S rRNA gene and spacer region sequences from 44 phytoplasmas revealed that the phytoplasmas from the leafhoppers clustered with OmanAlfWB, papaya yellow crinkle, and gerbera phyllody phytoplasmas, all belonging to 16SrII group, but were distinct from lime witches’ broom phytoplasma, the most commonly found phytoplasma in the Sultanate of Oman.

Classification of a new phytoplasmas subgroup 16SrII-W associated with Crotalaria witches’ broom diseases in Oman based on multigene sequence analysis

BackgroundCrotalaria aegyptiaca, a low shrub is commonly observed in the sandy soils of wadis desert and is found throughout all regions in Oman. A survey for phytoplasma diseases was conducted. During a survey in a wild area in the northern regions of Oman in 2015, typical symptoms of phytoplasma infection were observed on C. aegyptiaca plants. The infected plants showed an excessive proliferation of their shoots and small leaves.ResultsThe presence of phytoplasma in the phloem tissue of symptomatic C. aegyptiaca leaf samples was confirmed by using Transmission Electron Microscopy (TEM). In addition the extracted DNA from symptomatic C. aegyptiaca leaf samples and Orosius sp. leafhoppers were tested by PCR using phytoplasma specific primers for the 16S rDNA, secA, tuf and imp, and SAP11 genes. The PCR amplifications from all samples yielded the expected products, but not from asymptomatic plant samples. Sequence similarity and phylogenetic tree analyses of four genes (16S rDNA, secA, tuf and imp) showed that Crotalaria witches’ broom phytoplasmas from Oman is placed with the clade of Peanut WB (16SrII) close to Fava bean phyllody (16SrII-C), Cotton phyllody and phytoplasmas (16SrII-F), and Candidatus Phytoplasma aurantifolia’ (16SrII-B). However, the Crotalaria’s phytoplasma was in a separate sub-clade from all the other phytoplasmas belonging to Peanut WB group. The combination of specific primers for the SAP11 gene of 16SrII-A, −B, and -D subgroup pytoplasmas were tested against Crotalaria witches’ broom phytoplasmas and no PCR product was amplified, which suggests that the SAP11 of Crotalaria phytoplasma is different from the SAP11 of the other phytoplasmas.ConclusionWe propose to assign the Crotalaria witches’ broom from Oman in a new lineage 16SrII-W subgroup depending on the sequences analysis of 16S rRNA, secA, imp, tuf, and SAP11 genes. To our knowledge, this is the first report of phytoplasmas of the 16SrII group infecting C. aegyptiaca worldwide.

Evaluation of indigenous Omani legumes for their nutritional quality, phytochemical composition and antioxidant properties

Four indigenous Omani legumes (faba bean, cowpeas, chickpeas and lentils), collected from three different regions of Oman, were evaluated for their proximate composition, phytochemical contents and antioxidant properties. The proximate composition varied significantly. Regional variability however, did not affect the proximate composition, except crude protein content of cowpea and chickpea. The average values for moisture, protein, fat, fibre and ash ranged from 8.5% to 9.6%, 22.5% to 23.9%, 1.1% to 1.8%, 4.5% to 7.6% and 3.1 to 3.5% respectively. Both variety and regional variability affected the phytochemical contents. The average total phenol contents, tannins, and flavonoids ranged from 15.1 to 131.8 mg GAE/100 g, 13.2 to 100.8 mg CAE/100 g and 1.7 to 19.9 mg CAE/100g respectively, whereas the oxalates and saponins contents ranged from 56.1 to 197.8 and 2,699.1 to 3,598.1 mg/100 g respectively. A significant correlation was observed between the total phenol contents and the reducing power of legumes.

Genetic analysis of ‘Candidatus Phytoplasma aurantifolia’ associated with witches’ broom on acid lime trees

“Candidatus Phytoplasma aurantifolia” is associated with witches’ broom disease of lime in Oman and the UAE. A previous study showed that an infection by phytoplasma may not necessarily result in the physical appearance of witches’ broom symptoms in some locations in Oman and the UAE. This study investigated whether phytoplasma strains belonging to “Ca. P. aurantifolia” (based on the 16S rRNA gene analysis) in locations where disease symptoms are expressed are different from phytoplasma in locations where disease symptoms are not expressed. About 21 phytoplasma strains (15 from areas and trees with disease symptoms and six from areas and trees without disease symptoms) were included in the analysis. The study utilized sequences of the imp and SAP11 genes to characterize the 21 strains. Phylogenetic analysis of both genes showed that the 21 strains are similar to each other and to reference strains in GenBank. The study shows that there is a low level of diversity among all phytoplasma strains. In addition, it shows that phytoplasma in places where witches’ broom symptoms are not expressed are similar to phytoplasma in places where disease symptoms are expressed. This may suggest that disease expression is not linked to the presence of different phytoplasma strains, but may be due to other factors such as weather conditions.