HomePlant DiseaseVol. 102, No. 9A Novel Strain of the Begomovirus Tomato Leaf Curl Sudan Virus Infecting Datura stramonium in Sudan PreviousNext DISEASE NOTES OPENOpen Access licenseA Novel Strain of the Begomovirus Tomato Leaf Curl Sudan Virus Infecting Datura stramonium in SudanH. S. Mohammed, M. A. El Siddig, A. A. El Hussein, J. Navas-Castillo, and E. Fiallo-OlivéH. S. MohammedSearch for more papers by this author, M. A. El SiddigSearch for more papers by this author, A. A. El HusseinSearch for more papers by this author, J. Navas-CastilloSearch for more papers by this author, and E. Fiallo-Olivé†Corresponding author: E. Fiallo-Olivé; E-mail: E-mail Address: [email protected]http://orcid.org/0000-0002-2460-1199Search for more papers by this authorAffiliationsAuthors and Affiliations H. S. Mohammed , Botany Department, Faculty of Science, University of Khartoum, 11115 Khartoum, Sudan, and Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga – Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29750 Algarrobo-Costa, Málaga, Spain M. A. El Siddig A. A. El Hussein , Botany Department, Faculty of Science, University of Khartoum, 11115 Khartoum, Sudan J. Navas-Castillo E. Fiallo-Olivé † , IHSM-UMA-CSIC, 29750 Algarrobo-Costa, Málaga, Spain. Published Online:6 Jul 2018https://doi.org/10.1094/PDIS-01-18-0195-PDNAboutSectionsSupplemental ToolsAdd to favoritesDownload CitationsTrack Citations ShareShare onFacebookTwitterLinked InRedditEmailWechat Devil’s trumpet (Datura stramonium) plants were frequently observed showing yellowing and leaf curl symptoms in Khartoum State (Sudan) in the last few years. Leaf samples from 14 symptomatic plants were collected in Ajaily (one in 2016 and seven in 2017) and Soba Al-Hilla (six in 2017) and dried using silica gel until analysis. To investigate the presence of begomoviruses (genus Begomovirus, family Geminiviridae), total nucleic acids were extracted from all leaf samples and used as template for polymerase chain reaction (PCR) with generic primers (AV494 and AC1048) targeting a core region of the begomoviral coat protein gene (Wyatt and Brown 1996). All samples yielded the expected DNA fragment of 550 bp. All 14 PCR products were directly sequenced at Macrogen (Seoul, South Korea) and showed a nucleotide identity of 99.2 to 100% between them. Blast analysis evidenced the highest nucleotide identity (98%) with an isolate of tomato leaf curl Sudan virus (ToLCSDV) found infecting tomato in Sudan (GenBank accession no. KC763630) (Fiallo-Olivé et al. 2013), suggesting that the symptomatic plants were infected by ToLCSDV. Rolling-circle amplification (RCA) using φ29 DNA polymerase (TempliPhi kit, GE Healthcare, Little Chalfont, UK) was carried out with extracts of all samples, and subsequent digestion with HpaII yielded identical restriction patterns for all of them. RCA products were also digested with a set of six-nucleotide restriction enzymes (BamHI, HindIII, EcoRI, and SalI). BamHI yielded an amplicon of ∼2.7 kbp from all the samples, which was cloned from one of them (sample Ajaily-2016) into pBluescript II SK(+) (Stratagene, La Jolla, CA). Two selected clones were sequenced (Macrogen) and were identical (2,768 nt, one deposited in GenBank under accession no. MG868938). Sequence was aligned with those selected after BLAST analysis using MUSCLE, and identity percentages were calculated with Sequence Demarcation Tool (Muhire et al. 2014). Cloned full-length viral genome showed the highest nucleotide identity (91%) with the abovementioned ToLCSDV isolate (KC763630) (Fiallo-Olivé et al. 2013). In accordance with the current taxonomic criteria for begomovirus species (cutoff value <91%) and strain (cutoff value <94%) demarcation (Brown et al. 2015), the begomovirus isolate characterized in this investigation represents a novel strain of ToLCSDV that we name strain Datura. To our knowledge, this is the first record of a species of the genus Datura as a natural host of ToLCSDV. Tomato leaf curl disease is a major limiting factor of tomato production in Sudan, at times resulting in up to 75% yield losses (Yassin 1983). The widespread presence of D. stramonium in areas where tomato is grown in Sudan poses an additional threat to the cultivation of this important crop in the region.