Correo Electrónico
DNINFOA - SIA
Bibliotecas
Convocatorias
Identidad U.N.
Published
Next generation sequence analysis of the forage peanut (Arachis pintoi) virome
Secuenciación de nueva generación del viroma del maní forrajero (Arachis pintoi)
Keywords:
Alphaflexiviridae, Polerovirus, Potyvirus, Viral genomes (en)Alphaflexiviridae, Polerovirus, Potyvirus, Genomas virales (es)
El maní forrajero (Arachis pintoi) es uno los cultivos forrajeros mejor adaptado a los agroecosistemas tropicales, donde se utiliza en mezclas con gramíneas para alimentación animal, como alternativa para la cobertura del suelo en áreas urbanas y talúdes y para la conservación de suelos en plantaciones de palma africana, café y cítricos. Aunque el maní forrajero se considera una planta tolerante a plagas y enfermedades, en los últimos años se ha observado en Colombia el aumento de síntomas asociados a enfermedades virales. Con el objeto de evaluar la ocurrencia de virus en dichos materiales sintomáticos, en el presente estudio se utilizó la metodología de Secuenciación de Nueva Generación (NGS) del transcriptoma de un grupo de muestras de A. pintoi procedentes de zonas urbanas en Medellín (Colombia). Los resultados indicaron la presencia de 3.291.089 reads asociados a genomas virales de miembros de las familias Potyviridae, Luteoviridae y Alphaflexiviridae; siendo posible obtener los genomas completos del Peanut mottle virus (9707 nt), Turnip yellows virus (5578 nt) y de dos variantes de un virus filogenéticamente relacionado con el género Allexivirus. Estas dos variantes carecen del ORF6 presente en Allexivirus, por lo que posiblemente se trata de miembros de un género hasta ahora no caracterizado en la familia Alphaflexiviridae. La ocurrencia de al menos tres virus que infectan plantas de A. pintoi en Colombia, llama la atención sobre la necesidad de emprender un trabajo de limpieza de germoplasma en el material de siembra utilizado para el establecimiento de este forraje tropical.
Downloads
References
Adams DB and Kuhn CW. 1977. Seed transmission of Peanut mottle virus in Peanuts. Phytopathology 67(9): 1126-1129.
Adams MJ, Antoniw JF and Beaudoin F. 2005. Overview and analysis of the polyprotein cleavage sites in the family Potyviridae. Molecular Plant Pathology 6(4): 471-87. doi: 10.1111/j.1364-3703. 2005.00296.x
Adams IP, Glover RH, Monger WA, Mumford R, Jackeviciene E, Navalinskiene M, Samuitiene M and Boonham N. 2009. Next-generation sequencing and metagenomic analysis: a universal diagnostic tool in plant virology. Molecular Plant Pathology 10(4): 537-545. doi: 10.1111/j.1364-3703.2009.00545.x
Beuve M, Stevens M, Liu HY, Wintermantel WM, Hauser S and Lemaire O. 2008. Biological and molecular characterization of an American sugar beet-infecting Beet western yellows virus isolate. Plant Disease 92(1): 51-60. doi: 10.1094/PDIS-92-1-0051
Bowman AM, Wilson GPM and Gogel BJ. 1988. Evaluation of perennial peanuts (Arachis spp.) as forage on the New South Wales coast. Tropical Grasslands 32: 252-258.
Edgar RC. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32(5): 1792-1797. doi: 10.1093/nar/gkh340
Gish W and States DJ. 1993. Identification of protein coding regions by database similarity search. Nature Genetics 3(3): 266-272. doi: 10.1038/ng0393-266
Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N and Regev A. 2011. Full-length transcriptome assembly from RNA-seq data without a reference genome. Nature Biotechnology 29(7): 644-652. doi: 10.1038/nbt.1883
Gutiérrez PA, Alzate JF and Marín M. 2014a. Genome sequence of a virus isolate from tamarillo (Solanum betaceum) in Colombia: evidence for a new potyvirus. Archives of Virology 160(2): 557-560. doi: 10.1007/s00705-014-2296-8
Gutiérrez PA, Alzate JF and Marín M. 2014b. Caracterización del viroma de ARN de tejido radical de Solanum phureja mediante pirosecuenciación 454 GS-FLX. Bioagro 26(2): 89-98.
Gutiérrez PA, Alzate JF and Marín M. 2015. Complete genome sequence of an isolate of Potato virus X (PVX) infecting Cape gooseberry (Physalis peruviana) in Colombia. Virus Genes 50(3): 518-522. doi: 10.1007/s11262-015-1181-1
Gutiérrez P, Mesa H and Marín M. 2016. Genome sequence of a divergent Colombian isolate of Potato virus V (PVV) infecting Solanum phureja. Acta Virologica 60(1):49-54. doi: 10.4149/av_2016_01_49
Hasegawa M, Kishino H and Yano T. 1985. Dating the human-ape split by a molecular clock of mitochondrial DNA. Journal of Molecular Evolution 22(2): 160-174. doi: 10.1007/BF02101694
Hauser S, Stevens M, Beuve M and Lemaire O. 2002. Biological properties and molecular characterization of Beet chlorosis virus (BChV). Archives of Virology 147(4): 745-762. doi: 10.1007/s007050200023
Jones RM. 1993. Persistence of Arachis pintoi cv. Amarillo on three soil types at Samford, South-Eastern Queensland. Tropical Grasslands 27:11-15.
King AMQ, Adams MJ, Carstens EB and Lefkowitz EJ. 2012. Ninth Report of the International Committee on Taxonomy of Viruses. Elsevier Academic Press, San Diego, EEUU. 1338 p.
Krapovickas A and Gregory WC. 1994. Taxonomía del género Arachis (Leguminosae). Bonplandia 8(1): 1-186.
Kreuze J, Koenig R, De Souza J, Vetten HJ, Muller G, Flores B, Ziebell H and Cuellar W. 2013. The complete genome sequences of a Peruvian and a Colombian isolate of Andean potato latent virus and partial sequences of further isolates suggest the existence of two distinct potato-infecting tymovirus species. Virus Research 173(2): 431-435. doi: 10.1016/j.virusres.2013.01.014
Kuhn CW. 1965. Symptomatology, host range and effect on yield of seed transmitted peanut virus. Phytopathology 55(8): 880-884.
Langmead B, Trapnell C, Pop M and Salzberg SL. 2009. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 10(3): R25. doi: 10.1186/gb-2009-10-3-r25
Lascano CE and Thomas D. 1988. Forage quality and animal selection of Arachis pintoi in association with tropical grasses in the eastern plains of Colombia. Grass and Forage Science 43(4): 433-439. doi: 10.1111/j.1365-2494.1988.tb01900.x
Lavia GI, Ortiz AM, Robledo G, Fernández A and Seijo G. 2011. Origin of triploid Arachis pintoi (Leguminosae) by autopolyploidy evidenced by FISH and meiotic behavior Annals of Botany 108(1): 103-111. doi: 10.1093/aob/mcr108
Le SQ and Gascuel O. 2008. An improved general amino acid replacement matrix. Molecular Biology and Evolution 25(7): 1307-1320. doi: 10.1093/molbev/msn067
Lim S, Lee YH, Igori D, Zhao F, Yoo RH, Lee SH, Baek IY and Moon JS. 2014. First Report of Peanut mottle virus infecting soybean in South Korea. Plant Disease 98(9): 1285. doi: 10.1094/PDIS-04-14-0356-PDN
Martelli GP, Adams MJ, Kreuze JF and Dolja VV. 2007. Family Flexiviridae: a case study in virion and genome plasticity. Annual Review of Phytopathology 45(1): 73-100. doi: 10.1146/annurev.phyto.45.062806.094401
Morales FJ, Castano M, Velasco AC and Arroyave J. 1991. Natural infection of tropical forage legume species of Arachis and Stylosanthes by potyviruses related to Peanut mottle virus. Plant Disease 75(11): 1090-1093. doi: 10.1094/PD-75-1090
Nickel H, Kawchuk L, Twyman RM, Zimmermann S, Junghans H, Winter S, Fischer R and Prüfer D. 2008. Plantibody-mediated inhibition of the Potato leafroll virus P1 protein reduces virus accumulation. Virus Research 136(1-2): 140-145. doi: 10.1016/j.virusres.2008.05.001
Nischwitz C, Maas AL, Mullis RM, Culbreath AK and Gitaitis RD. 2007. First report of Peanut mottle virus in forage peanut (Arachis glabrata) in North America. Plant Disease 91(5): 632. doi: 10.1094/PDIS-91-5-0632A
Olspert A, Chung BY, Atkins JF, Carr JP and Firth AE. 2015. Transcriptional slippage in the positive-sense RNA virus family Potyviridae. EMBO Reports 16(8): 995-1004. doi: 10.15252/embr.201540509
Palmieri DA, Bechara MD, Curi RA, Monteiro JP, Valente SES, Gimenes MA and Lopes CR. 2010. Genetic diversity analysis in the section Caulorrhizae (genus Arachis) using microsatellite markers. Genetics and Molecular Biology 33(1): 109-118. doi: 10.1590/S1415-47572010005000001
Pfeffer S, Dunoyer P, Heim F, Richards KE, Jonard G and Ziegler-Graff V. 2002. P0 of Beet western yellows virus is a suppressor of posttranscriptional gene silencing. Journal of Virology 76(13): 6815-6824. doi: 10.1128/JVI.76.13.6815-6824.2002
Posada D and Crandall KA. 1998. MODELTEST: testing the model of DNA substitution. Bioinformatics 14(9): 817-818. doi: 10.1093/bioinformatics/14.9.817
Rathjen JP, Karageorgos LE, Habili N, Waterhouse PM and Symons RH. 1994. Soybean dwarf luteovirus contains the third variant genome type in the luteovirus group. Virology 198(2): 671-679. doi: doi: 10.1006/viro.1994.1079
Rincón CA, Cuesta PA, Pérez R, Lascano CE and Ferguson J. 1992. Maní forrajero perenne (Arachis pintoi Krapovickas y Gregory). Una alternativa para ganaderos y agricultores. Boletín Técnico No. 219. ICA/CIAT, Palmira. 23 p.
Rincón A. 2001. Potencial productivo de ecotipos de Arachis pintoi en el Piedemonte de los Llanos Orientales de Colombia. Pasturas Tropicales 23: 19-24.
Roossinck MJ, Martin DP and Roumagnac P. 2015. Plant virus metagenomics: Advances in virus discovery. Phytopathology 105(6): 716-27. Doi: 10.1094/PHYTO-12-14-0356-RVW
Sabanadzovic S, Abou N and Tzanetakis IE. 2011. Blackberry virus E: an unusual flexivirus. Archives of Virology 156(9): 1665-1669. doi: 10.1007/s00705-011-1015-y
Soumya K, Yogita M, Prasanthi Y, Anitha K, Kavi-Kishor PB, Jain RK and Mandal B. 2014. Molecular characterization of Indian isolate of Peanut mottle virus and immunodiagnosis using bacterial expressed core capsid protein. Virus disease 25(3): 331-337. doi: 10.1007/s13337-014-0210-3.
Sreenivasulu P and Demski JW. 1988. Transmission of Peanut mottle and Peanut stripe viruses by Aphis craccivora and Myzus persicae. Plant Disease 72:722-723. doi: 10.1094/PD-72-0722
Sreenivasulu P, Reddy CVS, Ramesh B and Kumar PL. 2008. Groundnut viruses. pp. 47-97. En: Rao GP, Khurana SMP and Lenardon SL. Characterization, diagnosis & management of plant viruses. Volume 1: industrial crops. Studium Press, India.
Stevens M, Freeman B, Liu HY, Herrbach E and Lemaire O. 2005. Beet poleroviruses: close friends or distant relatives? Molecular Plant Pathology. 6: 1-9. doi: 10.1111/j.1364-3703.2004.00258.x
Tamura K, Stecher G, Peterson D, Filipski A and Kumar S. 2013. MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Molecular Biology and Evolution 30(12): 2725-2729. doi: 10.1093/molbev/mst197.
Teycheney PY and Dietzgen RG. 1994. Cloning and sequence analysis of the coat protein genes of an Australian strain of Peanut mottle and an Indonesian 'blotch' strain of peanut stripe potyviruses. Virus Research 31(2): 235-244. doi: 10.1016/0168-1702(94)90006-X
Valls JFM. 1996. Variability in the genus Arachis and potential forage uses. pp 15-27. En: Springer TL and Pittman RN (eds). Identifying germplasm for succesful forage legume-grass interations. Proceedings of a Symposium of the Crop Science Society of America. USDA, Washington.
Veidt I, Lot H, Leiser M, Scheidecker D, Guilley H, Richards K and Jonard G. 1988. Nucleotide sequence of Beet western yellows virus RNA. Nucleic Acids Research 16(21): 9917-9932. doi: 10.1093/nar/16.21.9917
Villamil-Garzón A, Cuellar WJ and Guzmán-Barney M. 2014. Natural co-infection of Solanum tuberosum crops by the Potato yellow vein virus and potyvirus in Colombia. Agronomía Colombiana 32(2): 213-223. doi: 10.15446/agron.colomb.v32n2.43968
Wu Q, Ding S, Zhang Y and Zhu S. 2015. Identification of viruses and viroids by Next-Generation Sequencing and homology dependent and homology independent algorithms. Annual Review of Phytopathology 53: 1-20. doi: 10.1146/annurev-phyto-080614-120030
Wylie SJ, Li H, Dixon KW, Richards H and Jones MG. 2013. Exotic and indigenous viruses infect wild populations and captive collections of temperate terrestrial orchids (Diuris species) in Australia. Virus Research 2013 171(1): 22-32. doi: 10.1016/j.virusres.2012.10.003
Xiang HY, Dong SW, Shang QX, Zhou CJ, Li DW, Yu JL and Han CG. 2011. Molecular characterization of two genotypes of a new polerovirus infecting brassicas in China. Archives of Virology 2011 156(12): 2251-2255. doi: 10.1007/s00705-011-1091-z
Zhou CJ, Xiang HY, Zhuo T, Li DW, Yu JL and Han CG. 2011. A novel strain of Beet western yellows virus infecting sugar beet with two distinct genotypes differing in the 5'-terminal half of genome. Virus Genes 42(1):141-149. doi: 10.1007/s11262-010-0553-9
License
Copyright (c) 2016 Revista Facultad Nacional de Agronomía Medellín
This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.
The journal allows the author(s) to maintain the exploitation rights (copyright) of their articles without restrictions. The author(s) accept the distribution of their articles on the web and in paper support (25 copies per issue) under open access at local, regional, and international levels. The full paper will be included and disseminated through the Portal of Journals and Institutional Repository of the Universidad Nacional de Colombia, and in all the specialized databases that the journal considers pertinent for its indexation, to provide visibility and positioning to the article. All articles must comply with Colombian and international legislation, related to copyright.
Author Commitments
The author(s) undertake to assign the rights of printing and reprinting of the material published to the journal Revista Facultad Nacional de Agronomía Medellín. Any quotation of the articles published in the journal should be made given the respective credits to the journal and its content. In case content duplication of the journal or its partial or total publication in another language, there must be written permission of the Director.
Content Responsibility
The Faculty of Agricultural Sciences and the journal are not necessarily responsible or in solidarity with the concepts issued in the published articles, whose responsibility will be entirely the author or the authors.
