Viral diagnosis in cultivars of Ipomoea batatas (L.) Lam.
Ipomoea batatas (L.) Lam. commonly known as sweet potato, is an important staple food worldwide, mainly due to its high nutritional value and yield. However, vegetative reproduction of sweet potato makes it more susceptible to viral infections, which threatens its productivity, quality, and difficult long-term preservation in germplasm banks. Also, it can act as a virus reservoir infecting the rest of the plant accessions in the bank collections. Hence, this work aimed to screen Begomovirus, Potyvirus, and Carlavirus infections in 16 traditional sweet potato cultivars from the germplasm collection of the ISOPlexis Germplasm Bank, Madeira, Portugal. The infection prevalence by these viruses among cultivars was 81.25%, 25.00%, and 6.25%, respectively; being ISOP1011 the only accession coinfected by Potyvirus and Carlavirus. The accessions ISOP1006, ISOP1010, and ISOP1047 were also coinfected by Begomovirus and Potyvirus, highlighting their vulnerability to viral infections. The ISOP1005 and ISOP1027 accessions were the only ones not infected by any of these viruses. The analysis of the partial sequence obtained from the Carlavirus detected in the accession ISOP1011, revealed the existence of an ORF that encodes for 93 amino acids of the catalytic domain of an RNA-directed RNA polymerase related to the Tymovirus protein family, as could be confirmed by comparison with proteins stored in UniProtKB. Multiple sequence alignment with these proteins showed that Motifs A and B of the catalytic domain were conserved. The search for sequence similarity with sequences deposited in GenBank reported a high sequence identity with Sweet potato yellow mottle virus (SPYMV) and Sweet potato chlorotic fleck virus (SPCFV). However, the 9-11% discrepancy in nucleotide sequence identity and a phylogenetic analysis carried out using the maximum probability method suggests the virus isolated from ISOP1011 is a new divergent strain of the SPCFV species.
Adams MJ, Candresse T, Hammond J, Kreuze JF, Martelli GP, Namba S, …Yoshikawa N (2012). Family Betaflexiviridae. In: King AMQ, Adams MJ, Carstens EB, Lefkowitz EJ (Eds). Virus Taxonomy. Ninth Report on the International Committee on Taxonomy of Viruses. Elsevier Academic Press Cambridge pp 920-941. https://doi.org/10.1016/B978-0-12-384684-6.00078-1
Barkessa MKE (2018). A review on sweet potato (Ipomea batatas) viruses and associated diseases. International Journal of Research in Agriculture and Forestry 5(9):1-10.
Clark CA, Davis JA, Abad JA, Cuellar WJ, Fuentes S, Kreuze JF, ...Valkonen JP (2012). Sweet potato viruses: 15 years of progress on understanding and managing complex diseases. Plant Diseases 96(2):168-185. http://dx.doi.org/10.1094/PDIS-07-11-0550
Cuellar WJ, Galvez M, Fuentes S, Tugume J, Kreuze J (2015). Synergistic interactions of Begomoviruses with sweet potato chlorotic stunt virus (genus Crinivirus) in sweet potato (Ipomoea batatas L.): sweet potato Begomovirus synergism with SPCSV. Molecular Plant Pathology 16(5):459-471. https://doi.org/10.1111/mpp.12200
Da Silva EM, dos Santos TMM, Pavis C, Pinheiro de Carvalho, MAA (2020). Sweet potato chlorotic fleck virus RNA dependent RNA polymerase gene, partial cds. GenBank: MK281368 NCBI. https://www.ncbi.nlm.nih.gov/nuccore/MK281368
Desbiez C, Moury B, Lecoq H (2011). The hallmarks of ‘‘green’’ viruses: Do plant viruses evolve differently from the others? Infection, Genetics and Evolution 11(5):812-824. https://doi.org/10.1016/j.meegid.2011.02.020
Elena SF, Agudelo-Romero P, Carrasco P, Codoner FM, Martin S, Torres-Barceló C, Sanjuán R (2008). Experimental evolution of plant RNA viruses. Heredity 100(5): 478-483. https://doi.org/10.1038/sj.hdy.6801088
FAOSTAT (2012). Crop production data 2012. Retrieved 2020 July 01 from http://faostat.fao.org
Foissac X, Svanella-Dumas L, Gentit P, Dulucq MJ, Marais A, Candresse T (2005). Polyvalent degenerate oligonucleotides reverse transcription-polymerase chain reaction: a polyvalent detection and characterization tool for trichoviruses, capilloviruses, and foveaviruses. Phytopathology 95(6):617-625. https://doi.org/10.1094/PHYTO-95-0617
Gennadius P (1889). Disease of the tobacco plantations in the Trikonia. The aleurodid of tobacco. Ellenike Georgia 5:1-3.
Hansen JL, Long AM, Schultz SC (1997). Structure of the RNA dependent RNA polymerase of poliovirus. Structure 5(8):1109-1122. https://doi.org/10.1016/S0969-2126(97)00261-X
International Potato Center (2018). Sweet potato facts and figures. Retrieved 2020 March 27 from https://cipotato.org/crops/sweetpotato/sweetpotato-facts-and-figures/2018
Johansen E, Edwards MC, Hampton RO (1994). Seed transmission of viruses: current perspectives. Annual review of phytopathology 32(1):363-386.
Koonin EV (1991). The phylogeny of RNA-dependent RNA polymerases of positive-strand RNA viruses. Journal of General Virology 72(9):2197-2206.
Koonin EV, Dolja VV (1993). Evolution and taxonomy of positive-strand RNA viruses: implications of comparative analysis of amino acid sequences. Critical Reviews in Biochemistry and Molecular Biology 28(5):375-430.
Lozano G, Trenado HP, Valverde RA, Navas-Castillo J (2009). Novel Begomovirus species of recombinant nature in sweet potato (Ipomoea batatas) and Ipomoea indica: taxonomic and phylogenetic implications. Journal of General Virology 90(10):2550-2562. https://doi.org/10.1099/vir.0.012542-0
Mohanraj R, Sivasankar S (2014). Sweet potato (Ipomoea batatas [L.] Lam) a valuable medicinal food: a review. Journal of Medicinal Food 17(7):733-741. http://doi.org/10.1089/jmf.2013.2818
Ng KS, Arnold JJ, Cameron CE (2008). Structure-function relationships among RNA-dependent RNA polymerases. In: Paddison PJ, Vogt PK (Eds). RNA Interference. Current Topics in Microbiology and Immunology. vol 320. Springer, Berlin, Heidelberg pp 137-156. https://doi.org/10.1007/978-3-540-75157-1_7
Rice W (1983). Sexual reproduction: an adaptation reducing parent-offspring contagion. Evolution 37(6):1317-71320. https://doi.org/10.2307/2408851
Ooi K, Yahara T (1999). Genetic variation of geminiviruses: comparison between sexual and asexual host populations. Molecular Ecology 8(1):89-97.
Roossinck MJ, Martin DP, Roumagnac P (2015). Plant virus metagenomics: advances in virus discovery. Phytopathology 105(6):716-727. https://doi.org/10.1094/PHYTO-12-14-0356-RVW
Rosario K, Capobianco H, Ng TFF, Breitbart M, Polston JE (2014). RNA viral metagenome of whiteflies leads to the discovery and characterization of a whitefly-transmitted Carlavirus in North America. PLoS One 9(1):e86748. https://doi.org/10.1371/journal.pone.0086748
Sabanadzovic S, Aboughanem N, Gorbalenya A (2009). Permutation of the active site of putative RNA-dependent RNA polymerase in a newly identified species of plant alpha-like virus. Virology 394(1):1-7. https://doi.org/10.1016/j.virol.2009.08.006
Silva G, Bömer M, Rathnayake AI, Sewe SO, Visendi P (2019). Molecular characterization of a new virus species identified in yam (Dioscorea spp.) by high-throughput sequencing. Plants 8(6):167. https://doi.org/10.3390/plants8060167
Stewart AD, Logsdon JM, Kelley SE (2005). An empirical study of the evolution of virulence under both horizontal and vertical transmission. Evolution 59(4):730-739.
Trenado HP, Orílio AF, Márquez-Martín B, Moriones E, Navas-Castillo J (2011). Sweepoviruses cause Disease in sweet potato and related Ipomoea spp.: fulfilling koch’s postulates for a divergent group in the genus Begomovirus. PLoS One 6(11):e27329. https://doi.org/10.1371/journal.pone.0027329
Umer M, Liu J, You H (2019). Genomic, morphological and biological traits of the viruses infecting major fruit trees. Viruses 11(6):515. https://doi.org/10.3390/v11060515
Valverde RA, Clark CA, Valkonen JP (2007). Viruses and virus disease complexes of sweetpotato. Plant Viruses 1(1):116-126.
Weng Z, Barthelson R, Gowda S, Hilf ME (2007). Persistent infection and promiscuous recombination of multiple genotypes of an RNA virus within a single host generate extensive diversity. PLoS One 2(9):e917. https://doi.org/10.1371/journal.pone.0000917
Zheng L, Rodoni BC, Gibbs MJ, Gibbs A (2010). A novel pair of universal primers for the detection of Potyviruses. Plant Pathology 59(2):211-220. https://doi.org/10.1111/j.1365-3059.2009.02201.x
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