scholarly journals Secuenciación del genoma completo del Potato yellow vein virus (PYVV) en tomate (Solanum lycopersicum) en Colombia

2017 ◽  
Vol 22 (1) ◽  
pp. 5 ◽  
Author(s):  
Laura Muñoz Baena ◽  
Pablo Andrés Gutiérrez Sánchez ◽  
Mauricio Marín Montoya
Keyword(s):  
Solanum Lycopersicum ◽  
Yellow Vein ◽  
Rt Pcr ◽  
Potato Yellow Vein Virus

Potato yellow vein virus (PYVV), es uno de los fitopatógenos más limitantes para la producción de papa en la región de Los Andes. A pesar que se le ha detectado infectando tomate en Colombia, el conocimiento de las características biológicas de las cepas presentes en este hospedante es muy limitado. En este estudio, utilizando secuenciación masiva de nueva generación (NGS), se obtuvo la secuencia completa de los tres segmentos genómicos del PYVV en plantas de tomate en Marinilla (Antioquia) y se evalúo la utilidad de tres juegos de cebadores para su detección mediante pruebas de RT-PCR convencional y en tiempo real (RT-qPCR). El genoma de la secuencia consenso presentó tamaños de 8043 nt (ARN1), 5346 nt (ARN2) y 3896 nt (ARN3) y se identificaron los diez ORF previamente reportados en este virus, aunque, en general, éstos presentaron menores| niveles de identidad que los registrados entre cepas de PYVV de papa. Análisis de variación y de selección identificaron dos regiones en los ORF MET/HEL y CPm que presentan selección positiva, lo que podría estar asociado a la adaptación por hospedante. Los tres juegos de cebadores amplificaron las regiones esperadas de la cápside de PYVV, siendo posible identificar, por diferencias en valores de temperatura de fusión (Tm) y por secuenciación Sanger, la ocurrencia de al menos dos variantes principales de este virus en el Oriente Antioqueño, lo que concuerda con los niveles moderados de polimorfismos encontrados en las secuencias obtenidas por NGS.

scholarly journals Potato Virus Y (PVY) y Potato Yellow Vein Virus (PYVV) en Infecciones Mixtas No Causan Síntomas Atípicos en Plantas de Papa

2016 ◽  
Vol 11 (2) ◽  
pp. 26 ◽  
Author(s):  
Jenny Paola Alfaro García ◽  
Liliana Franco-Lara
Keyword(s):  
Solanum Tuberosum ◽  
Potato Virus ◽  
Potato Virus Y ◽  
Yellow Vein ◽  
Solanum Phureja ◽  
Rt Pcr ◽  
Potato Yellow Vein Virus

Observaciones anteriores en cultivos de papa (<em>Solanum tuberosum</em> y <em>Solanum phureja</em>) mostraron síntomas llamados atípicos en este trabajo, que consistían en hojas con manchas irregulares verde oscuro sobre un fondo amarillo intenso, que sugieren la presencia de virus. Estos síntomas no correlacionan con ningún virus descrito para papa en Colombia. En plantas, existen reportes de infecciones virales con dos o más virus que llevan a interacciones como sinergismo o antagonismo. En este trabajo se evaluó la hipótesis de que los síntomas atípicos podrían ser resultado de infecciones mixtas entre PYVV (<em>Potato yellow vein virus) (Crinivirus) </em>y PVY (<em>Potato virus Y</em>) (<em>Potyirus)</em>, pues ambos virus son comunes en cultivos de papa en Colombia. Se reportan resultados de RT-PCR (reacción en cadena de la polimerasa mediada por retrotranscripción) para la detección de PYVV y PVY, y de ELISA para PVX, PVS, PVM y PRLV en 57 plantas con y sin síntomas atípicos provenientes de campo. Los resultados no apoyan la hipótesis planteada, pues de 10 plantas con síntomas atípicos evaluadas solo una estaba infectada con los dos virus.  Por otro lado, coinfecciones de PVY y PYVV se observaron en plantas sin síntomas aparentes (4 plantas de 5 evaluadas) y en plantas con síntomas característicos de PYVV (17 plantas de 37 evaluadas). Del total de 20 plantas evaluadas por ELISA, 18 presentaban infección por PVX aunque no se observaron síntomas asociados a este virus. Ocho de estas plantas, además de PVX estaban infectadas también con PVY y PYVV, pero mostraban síntomas de característicos de PYVV, lo que sugiere que PVX tampoco correlaciona con los síntomas atípicos. Se sugiere la presencia de un virus no reportado infectando el cultivo de papa en Colombia.

scholarly journals Variability of P26 and P10 genes in Colombian isolates of Potato yellow vein virus (PYVV)

2019 ◽  
Vol 37 (2) ◽  
pp. 129-143
Author(s):  
Jhon Calderón ◽  
Teresa Mosquera Vásquez ◽  
Ángela María Vargas
Keyword(s):  
Negative Selection ◽  
Pcr Amplification ◽  
Potato Production ◽  
Diversity Indices ◽  
Trialeurodes Vaporariorum ◽  
Yellow Vein ◽  
Rt Pcr ◽  
Pathogenic Factors ◽  
Vein Disease ◽  
Potato Yellow Vein Virus

Potato yellow vein virus (PYVV) is the causal agent of the potato yellow vein disease and can reduce potato production up to 50%. This virus also infects tomatoes and can remain asymptomatic in plants. PYVV transmission is mediated by vegetative seed, the vector Trialeurodes vaporariorum, and grafts. Its genome has the P26 and P10 genes that are orthologues in the Crinivirus genus, which have been characterized as pathogenic factors and have not been studied in PYVV. We analyzed the variability of P26 and P10 from 45 and 48 sequences, which were obtained by RT-PCR amplification of the total RNA of symptomatic potato leaves from the provinces of Nariño, Cundinamarca, and Boyaca (Colombia). We included sequences of each gene of the PYVV genome of potato and tomato isolates from GenBank. The variability in these genes is influenced by the flow and uncontrolled use of vegetative seed between different provinces, that favor the dispersion of viral variants. In addition, the variability analysis based on maximum likelihood trees, haplotypes, and diversity indices showed that P26 is more variable than P10 and both are more variable in Andigena than in Phureja potatoes. The Tajima and Fu and Li tests revealedthat these genes are subject to negative selection.

scholarly journals Molecular insights on potato yellow vein crinivirus infections in the highlands of Colombia

2021 ◽  
Vol 102 (6) ◽  
Author(s):  
Ángela Niño ◽  
Francisco J. del Toro ◽  
Francisco Tenllado ◽  
Tomás Canto ◽  
Liliana Franco-Lara
Keyword(s):  
High Throughput Sequencing ◽  
Asymptomatic Infection ◽  
Yellow Vein ◽  
Rt Pcr ◽  
Genomic Rnas ◽  
Complete Sequences ◽  
Genomic Regions ◽  
Potato Yellow Vein Virus ◽  
Geographical Locations ◽  
Viral Isolates

Potato yellow vein virus (PYVV) was detected in potatoes grown in the Central highlands, north of Bogotá (~3000 m altitude), Colombia. At this altitude viral whitefly vectors are largely absent, but infection persists because of the use of uncertified tubers. Plants with typical PYVV-induced yellowing symptoms, as well as with atypical yellowing or non-symptomatic symptoms were sampled at three separate geographical locations. PYVV presence was assessed by RT-PCR, and several plants were subjected to high-throughput sequencing (HTS) of their small RNA (sRNA) populations. Complete or almost complete sequences of four PYVV isolates were thus reconstructed, all from symptomatic plants. Three viral isolates infected plants singly, while the fourth co-infected the plant together with a potyvirus. Relative proportions of sRNAs to each of the three crinivirus genomic RNAs were found to remain comparable among the four infections. Genomic regions were identified as hotspots of sRNA formation, or as regions that poorly induced sRNAs. Furthermore, PYVV titres in the mixed versus single infections remained comparable, indicating an absence of synergistic/antagonistic effects of the potyvirus on the accumulation of PYVV. Daughter plants raised in the greenhouse from tubers of the infected, field-sampled plants displayed mild PYVV infection symptoms that disappeared with time, demonstrating the occurrence of recovery and asymptomatic infection phenotypes in this pathosystem.

scholarly journals Identificación y caracterización molecular del genoma completo de tres virus en cultivos de lulo (Solanum quitoense) de Antioquia (Colombia)

2018 ◽  
Vol 12 (2) ◽  
pp. 281-292 ◽  
Author(s):  
Yuliana Gallo ◽  
Luisa Fernanda Toro ◽  
Helena Jaramillo ◽  
Pablo Andrés Gutiérrez ◽  
Mauricio Marín
Keyword(s):  
Cucumber Mosaic Virus ◽  
Mosaic Virus ◽  
Yellow Vein ◽  
Streak Virus ◽  
Rt Pcr ◽  
Potato Yellow Vein Virus

El lulo es uno de los renglones agrícolas más promisorios para la región andina de Colombia, gracias a sus excelentes características organolépticas y a su potencial para el procesamiento industrial. En Antioquia, se ha observado en los últimos años la presencia de plantas con síntomas de enfermedades virales, que incluyen amarillamientos intervenales, mosaicos y deformación de brotes. En este trabajo, se evaluó dicha situación en un grupo (bulk) de muestras foliares de plantas sintomáticas de lulo obtenidas en municipios del Oriente Antioqueño, utilizando la metodología molecular de secuenciación de nueva generación (NGS), y la confirmación posterior por RT-PCR. Los análisis bioinformáticos de las secuencias obtenidas (10.777.822 de reads) indicaron la presencia de tres virus de RNA en el transcriptoma evaluado; el Cucumber mosaic virus (CMV) se encontró en mayores niveles de infección (40,4% del total de reads), mientras que los otros virus correspondieron al Potato yellow vein virus (PYVV) (0,09%) y Alstroemeria necrotic streak virus (ANSV) (0,06%), siendo posible obtener sus genomas completos. La ocurrencia de los tres virus fue confirmada en plantas individuales de lulo mediante pruebas de RT-PCR/secuenciación Sanger con cebadores específicos diseñados a partir de los datos de NGS (ANSV y CMV), o con cebadores reportados previamente (PYVV). En el futuro será necesario evaluar los efectos de estos virus sobre los rendimientos, longevidad de plantas y calidad de semilla en los cultivos de lulo en el país, así como sus métodos de transmisión, rango de hospedantes y sintomatología específica.

scholarly journals First Report of Mosaic Disease Caused by Colombian datura virus on Solanum lycopersicum Plants Commercially Cultivated in Japan

Plant Disease ◽  
2014 ◽  
Vol 98 (5) ◽  
pp. 698-698 ◽  
Author(s):  
Y. Tomitaka ◽  
T. Usugi ◽  
R. Kozuka ◽  
S. Tsuda
Keyword(s):  
Nucleotide Sequence ◽  
Solanum Lycopersicum ◽  
Mosaic Disease ◽  
Causal Agent ◽  
Cultivated Plants ◽  
Rt Pcr ◽  
Degenerate Primers ◽  
Specific Primers ◽  
Tomato Plants ◽  
First Report

In 2009, some commercially grown tomato (Solanum lycopersicum) plants in Chiba Prefecture, Japan, exhibited mosaic symptoms. Ten plants from a total of about 72,000 cultivated plants in the greenhouses showed such symptoms. To identify the causal agent, sap from leaves of the diseased plants was inoculated into Chenopodium quinoa and Nicotiana benthamiana plants. Local necrotic lesions appeared on inoculated leaves of C. quinoa, but no systemic infection was observed. Systemic mosaic symptoms were observed on the N. benthamiana plants inoculated. Single local lesion isolation was performed three times using C. quinoa to obtain a reference isolate for further characterization. N. benthamiana was used for propagation of the isolate. Sap from infected leaves of N. benthamiana was mechanically inoculated into three individual S. lycopersicum cv. Momotaro. Symptoms appearing on inoculated tomatoes were indistinguishable from those of diseased tomato plants found initially in the greenhouse. Flexuous, filamentous particles, ~750 nm long, were observed by electron microscopy in the sap of the tomato plants inoculated with the isolate, indicating that the infecting virus may belong to the family Potyviridae. To determine genomic sequence of the virus, RT-PCR was performed. Total RNA was extracted from the tomato leaves experimentally infected with the isolate using an RNeasy Plant Mini kit (QIAGEN, Hilden, Germany). RT-PCR was performed by using a set of universal, degenerate primers for Potyviruses as previously reported (2). Amplicons (~1,500 bp) generated by RT-PCR were extracted from the gels using the QIAquick Gel Extraction kit (QIAGEN) and cloned into pCR-BluntII TOPO (Invitrogen, San Diego, CA). DNA sequences of three individual clones were determined using a combination of plasmid and virus-specific primers, showing that identity among three clones was 99.8%. A consensus nucleotide sequence of the isolate was deposited in GenBank (AB823816). BLASTn analysis of the nucleotide sequence determined showed 99% identity with a partial sequence in the NIb/coat protein (CP) region of Colombian datura virus (CDV) tobacco isolate (JQ801448). Comparison of the amino acid sequence predicted for the CP with previously reported sequences for CDV (AY621656, AJ237923, EU571230, AM113759, AM113754, and AM113761) showed 97 to 100% identity range. Subsequently, CDV infection in both the original and experimentally inoculated plants was confirmed by RT-PCR using CDV-specific primers (CDVv and CDVvc; [1]), and, hence, the causal agent of the tomato disease observed in greenhouse tomatoes was proved to be CDV. The first case of CDV on tomato was reported in Netherlands (3), indicating that CDV was transmitted by aphids from CDV-infected Brugmansia plants cultivated in the same greenhouse. We carefully investigated whether Brugmansia plants naturally grew around the greenhouses, but we could not find them inside or in proximity to the greenhouses. Therefore, sources of CDV inoculum in Japan are still unclear. This is the first report of a mosaic disease caused by CDV on commercially cultivated S. lycopersicum in Japan. References: (1) D. O. Chellemi et al. Plant Dis. 95:755, 2011. (2) J. Chen et al. Arch. Virol. 146:757, 2001. (3) J. Th. J. Verhoeven et al. Eur. J. Plant. Pathol. 102:895, 1996.

scholarly journals Nuevos registros de aislamientos del Cucumber mosaic virus y su RNA satélite en Colima, México

2019 ◽  
Vol 37 (2) ◽  
Author(s):  
Pedro Valadez-Ramírez ◽  
Javier Paz-Román ◽  
Salvador Guzmán-González ◽  
Marco Tulio Buenrostro-Nava ◽  
Daniel Leobardo Ochoa-Martínez
Keyword(s):  
Cucumber Mosaic Virus ◽  
Mosaic Virus ◽  
Solanum Lycopersicum ◽  
Capsicum Annuum ◽  
Catharanthus Roseus ◽  
Cucumis Melo ◽  
Rt Pcr ◽  
Impacto Económico

El <em>Cucumber mosaic virus</em> (CMV) ocasiona una de las enfermedades virales más importantes a nivel mundial en plantas silvestres y cultivadas. En México son pocos los estudios que se han abordado con este virus, y dada su amplia gama de hospedantes e impacto económico, es necesario contar con mayor información de su presencia y distribución en zonas de importancia agrícola como las del estado de Colima. En este trabajo, se reportan nuevos aislamientos del CMV identificados por RT-PCR, secuenciación de DNA y su análisis filogenético: CMV-Vin en vinca (<em>Catharanthus roseus</em>), CMV-Chi en chile jalapeño (<em>Capsicum annuum</em>) y CMV-Tom en tomate saladette (<em>Solanum lycopersicum</em>). Se confirmó, además, la presencia del CMV en melón cantaloupe (<em>Cucumis melo</em>) (CMV-Mel). Los aislamientos CMV-Vin, CMV-Chi y CMV-Mel agruparon en el subgrupo IB, mientras que CMV-Tom agrupó en el subgrupo IA de CMV. De estos aislamientos, sólo CMV-Vin evidenció la presencia de un RNA satélite (satRNA Vin) sin dominio necrogénico. Este es el primer reporte de la presencia del CMV en vinca, chile y tomate y de un RNA satélite en vinca en Colima, México.

scholarly journals First Report of Tomato Brown Rugose Fruit Virus Infecting Tomato Crop in Saudi Arabia

Plant Disease ◽  
2021 ◽  
Author(s):  
Ahmed Sabra ◽  
Mohammed Ali Al Saleh ◽  
I. M. Alshahwan ◽  
Mahmoud A. Amer
Keyword(s):  
Saudi Arabia ◽  
Mosaic Virus ◽  
Solanum Lycopersicum ◽  
Tomato Mosaic Virus ◽  
Enzyme Linked Immunosorbent Assay ◽  
Rt Pcr ◽  
First Report ◽  
Pcr Products ◽  
Dark Green ◽  
Leaf Symptoms

Tomato (Solanum lycopersicum L.) is the most economically important member of family Solanaceae and cultivated worldwide and one of the most important crops in Saudi Arabia. The aim of this study is screening of the most common viruses in Riyadh region and identified the presence of tomato brown rugose fruit virus (ToBRFV) in Saudi Arabia. In January 2021, unusual fruit and leaf symptoms were observed in several greenhouses cultivating tomatoes commercially in Riyadh Region, Saudi Arabia. Fruit symptoms showed irregular brown spots, deformation, and yellowing spots which render the fruits non-marketable, while the leaf symptoms included mottling, mosaic with dark green wrinkled and narrowing. These plants presented the symptoms similar to those described in other studies (Salem et al., 2015, Luria et al., 2017). A total 45 Symptomatic leaf samples were collected and tested serologically against suspected important tomato viruses including: tomato chlorosis virus, tomato spotted wilt virus, tomato yellow leaf curl virus, tomato chlorotic spot virus, tomato aspermy virus, tomato bushy stunt virus, tomato black ring virus, tomato ringspot virus, tomato mosaic virus, pepino mosaic virus and ToBRFV using Enzyme linked immunosorbent assay (ELISA) test (LOEWE®, Biochemica, Germany), according to the manufacturers' instructions. The obtained results showed that 84.4% (38/45) of symptomatic tomato samples were infected with at least one of the detected viruses. The obtained results showed that 55.5% (25/45) of symptomatic tomato samples were found positive to ToBRFV, three out of 25 samples (12%) were singly infected, however 22 out of 45 (48.8%) had mixed infection between ToBRFV and with at least one of tested viruses. A sample with a single infection of ToBRFV was mechanically inoculated into different host range including: Chenopodium amaranticolor, C. quinoa, C. album, C. glaucum, Nicotiana glutinosa, N. benthamiana, N. tabacum, N. occidentalis, Gomphrena globosa, Datura stramonium, Solanum lycopersicum, S. nigrum, petunia hybrida and symptoms were observed weekly and the systemic presence of the ToBRFV was confirmed by RT-PCR and partial nucleotide sequence. A Total RNA was extracted from DAS-ELISA positive samples using Thermo Scientific GeneJET Plant RNA Purification Mini Kit. Reverse transcription-Polymerase chain reaction (RT-PCR) was carried out using specific primers F-3666 (5´-ATGGTACGAACGGCGGCAG-3´) and R-4718 (5´-CAATCCTTGATGTG TTTAGCAC-3´) which amplified a fragment of 1052 bp of Open Reading Frame (ORF) encoding the RNA-dependent RNA polymerase (RdRp). (Luria et al. 2017). RT-PCR products were analyzed using 1.5 % agarose gel electrophoresis. RT-PCR products were sequenced in both directions by Macrogen Inc. Seoul, South Korea. Partial nucleotide sequences obtained from selected samples were submitted to GenBank and assigned the following accession numbers: MZ130501, MZ130502, and MZ130503. BLAST analysis of Saudi isolates of ToBRFV showed that the sequence shared nucleotide identities ranged between 98.99 % to 99.50 % among them and 98.87-99.87 % identity with ToBRFV isolates from Palestine (MK881101 and MN013187), Turkey (MK888980, MT118666, MN065184, and MT107885), United Kingdom (MN182533), Egypt (MN882030 and MN882031), Jordan (KT383474), USA (MT002973), Mexico (MK273183 and MK273190), Canada (MN549395) and Netherlands (MN882017, MN882018, MN882042, MN882023, MN882024, and MN882045). To our knowledge, this is the first report of occurrence of ToBRFV infecting tomato in Saudi Arabia which suggests its likely introduction by commercial seeds from countries reported this virus and spread in greenhouses through mechanical means. The author(s) declare no conflict of interest. Keywords: Tomato brown rugose fruit virus, tomato, ELISA, RT-PCR, Saudi Arabia References: Luria N, et al., 2017. PLoS ONE 12(1): 1-19. Salem N, et al., 2015. Archives of Virology 161(2): 503-506. Fig. 1. Symptoms caused by ToBRFV showing irregular brown spots, deformation, yellowing spots on fruits (A, B, C) and bubbling and mottling, mosaic with dark green wrinkled and narrowing on leaf (D).

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