Sattar Muhammad Naeem, Almaghasla Mostafa I, Tahir Muhammad Nouman, El-Ganainy Sherif M, Chellappan Biju Vadakkemukadiyil, Arshad Muhammad, Drou Nizar
Central Laboratories, King Faisal University, Al-Ahsa, Saudi Arabia.
Department of Arid Land Agriculture, College of Agricultural and Food Sciences, King Faisal University, Al-Ahsa, Saudi Arabia.
Front Plant Sci. 2024 Oct 10;15:1375405. doi: 10.3389/fpls.2024.1375405. eCollection 2024.
Limited research in Saudi Arabia has devolved into the prevalence and genetic diversity of begomoviruses. Utilizing Illumina MiSeq sequencing, we obtained 21 full-length begomovirus sequences (2.7-2.8 kb) from eight cucumber plants grown in fields and greenhouses. We found that two complete begomovirus genomes were variants of the Boushehr strain of tomato yellow leaf curl virus (TYLCV) with nucleotide (nt) sequence identities of 94.7-95.9%. Another full-length genome was a variant of TYLCV-Iran with 94.6% identity. Five full-length sequences closely matched the DNA-A of watermelon chlorotic stunt virus (WmCSV) isolates with 97.9-98.7% nt sequence identities, while five sequences had their highest nt sequence identities (95.8-96.3%) with the DNA-B of WmCSV isolates. Simultaneously, four sequences were 99.1-99.6% identical to the DNA-A of tomato leaf curl Palampur virus (ToLCPalV). Four sequences matched the DNA-B of ToLCPalV reported from Iran and Saudi Arabia with identities ranging from 96.2-100%. Four plants showed a mixed infection of these begomoviruses. Most ORFs showed evidence of negative selection pressure, suggesting that purifying selection plays a crucial role in shaping the diversity of these begomoviruses. Additionally, potential intra- and interspecies recombination events were detected in the TYLCV and WmCSV DNA-B genomic regions. The ToLCPalV isolates identified in this study formed a cluster with the other ToLCPalV isolates reported from Saudi Arabia, Iran and Iraq, representing a unique lineage distinct from ToLCPalV reported from Southeast Asia. High mutation rate and robust selection facilitated the independent evolution of ToLCPalV without recombination. Overall, this study offers valuable insights into the diversity and evolutionary dynamics of begomoviruses infecting cucumber crops in Al-Ahsa, Saudi Arabia.
沙特阿拉伯针对番茄黄化曲叶病毒属病毒的流行情况及基因多样性开展的研究有限。我们利用Illumina MiSeq测序技术，从田间和温室种植的8株黄瓜植株中获得了21条番茄黄化曲叶病毒属病毒的全长序列（2.7 - 2.8 kb）。我们发现，两个完整的番茄黄化曲叶病毒属病毒基因组是番茄黄化曲叶病毒（TYLCV）布歇赫尔株系的变体，核苷酸（nt）序列同一性为94.7 - 95.9%。另一个全长基因组是TYLCV - 伊朗株系的变体，同一性为94.6%。5条全长序列与西瓜褪绿矮缩病毒（WmCSV）分离株的DNA - A紧密匹配，核苷酸序列同一性为97.9 - 98.7%，而5条序列与WmCSV分离株的DNA - B的核苷酸序列同一性最高（95.8 - 96.3%）。同时，4条序列与番茄卷叶帕拉姆布尔病毒（ToLCPalV）的DNA - A同一性为99.1 - 99.6%。4条序列与伊朗和沙特阿拉伯报道的ToLCPalV的DNA - B匹配，同一性范围为96.2 - 100%。4株植株表现出这些番茄黄化曲叶病毒属病毒的混合感染。大多数开放阅读框显示出负选择压力的证据，这表明纯化选择在塑造这些番茄黄化曲叶病毒属病毒的多样性方面起着关键作用。此外，在TYLCV和WmCSV的DNA - B基因组区域检测到了潜在的种内和种间重组事件。本研究中鉴定出的ToLCPalV分离株与沙特阿拉伯、伊朗和伊拉克报道的其他ToLCPalV分离株形成一个簇，代表了一个不同于东南亚报道的ToLCPalV的独特谱系。高突变率和强大的选择促进了ToLCPalV在无重组情况下的独立进化。总体而言，本研究为沙特阿拉伯艾卜哈地区感染黄瓜作物的番茄黄化曲叶病毒属病毒的多样性和进化动态提供了有价值的见解。
