Abstract
While whitefly-transmitted begomoviruses are economically important constraints to tomato production in Kuwait, little is known about genomic features of these viruses from Kuwait. A begomovirus isolated from severely diseased tomatoes, collected over a two-year period in the main tomato-growing areas of Kuwait, was characterized at the molecular level. The complete genomic sequence of the begomovirus was determined, and phlylogeographic studies were conducted to better understand genetic diversity of the virus in the region. Based on genome properties and phylogenetic analysis, the begomovirus was found to be a strain of tomato yellow leaf curl virus (TYLCV). The virus genome was monopartite, as neither DNA B nor satellite DNA molecules were detected. Two isolates characterized in this study shared 97 % and 95 % nucleotide sequence identity with a previously characterized Kuwaiti isolate, TYLCV-KISR. Among TYLCV isolates with known genome sequences, the Kuwaiti isolates shared highest sequence identity (95 %) with TYLCV-Almeria (Spain). Genetic diversity and phylogenetic analysis showed that the three Kuwaiti isolates formed a distinct clade that was separate from those of known TYLCV sequences. One Kuwaiti isolate (KW 1-3) could be a novel variant of TYLCV. Two recombination events were detected in the genome sequence of KW 1-3, which appeared to be a recombinant derived from TYLCV parents from Oman and Kuwait.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410
Converse R, Omar R, Alsdirawi F, AboEl-Nil M: The status of crop pests and pest control in Kuwait: development study for the agricultural sector (plant and animals) in Kuwait, Appendix IV. Kuwait Institute for Scientific Research, Report 1995, No. KISR 4615, Kuwait
Khan AJ, Idris AM, Al-Saady NA, Al-Mahruki MS, Al-Subhi AM, Brown JK (2008) A divergent isolate of tomato yellow leaf curl virus from Oman with an associated DNA beta satellite: an evolutionary link between Asian and the Middle Eastern virus-satellite complexes. Virus Genes 36:169–176
Martin DP, Lemey P, Lott M, Moulton V, Posada D, Lefeuvre P (2010) RDP3: a flexible and fast computer program for analysing recombination. Bioinformatics 26:2462–2463
Porebski S, Bailey LG, Baum BR (1997) Modification of a CTAB DNA extraction protocol for plants containing high polysaccharides and polyphenol component. Plant Mol Biol Report 15:8–15
Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2007) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729
Varma A, Malathi VG (2003) Emerging geminivirus problems: a serious threat to crop production. Ann Appl Biol 142:145–164
Acknowledgments
The authors are grateful to the Kuwait Foundation for Advancement of Science (KFAS) for partial funding and continued support of the project. The support of the management of the Kuwait Institute for Scientific Research (KISR) is gratefully acknowledged.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Al-Ali, E.H.M., Al-Hashash, H.K., Ben-Hejji, A.H. et al. First complete genomic characterization and phylogeny of a new recombinant of tomato yellow leaf curl virus (genus Begomovirus, family Geminiviridae) from Kuwait. Arch Virol 160, 1823–1826 (2015). https://doi.org/10.1007/s00705-015-2427-x
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00705-015-2427-x