Detection and genome characterization of Potato virus Y isolates infecting potato ( Solanum tuberosum L.) in La Union (Antioquia, Colombia)
S Pablo Andrés Gutiérrez,M Mauricio Marín,E Daniel Muñoz +2 more
- 01 Sep 2016
- Vol. 34, Iss: 3, pp 317-328
TL;DR: Detailed molecular analysis using nextgeneration sequencing, IC-RT-qPCR and RT-PCR on the PVY isolates infecting seed-tubers and foliage of potato plants cv.
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Abstract: Potato virus Y (PVY) is one of the most severe viruses affecting the production of potato ( Solanum tuberosum ) in the world. This study presents a detailed molecular analysis using nextgeneration sequencing (NGS), IC-RT-qPCR and RT-PCR on the PVY isolates infecting seed-tubers and foliage of potato plants cv. Diacol-Capiro in La Union (Antioquia, Colombia). Analysis of incidence by IC-RT-qPCR in 15 random leaf samples of three cultivation plots and fifteen sprouting tuber eye-buds reveal infection levels between 13.4 and 80%; a higher incidence of 86.7% was observed in seed-tuber samples with threshold cycle (Ct) values as low as 24.3. Genome assembly from a bulk of foliage samples resulted in a consensus PVY genome (PVY_LaUnionF) of 9,702 nt and 399 polymorphic sites within the polyprotein ORF; while the assembled genome from sprouts of tubers has 9,704 nt (PVY_LaUnionT) and contained only six polymorphic nucleotide sites. Phylogenetic analysis demonstrates that the PVY isolates from leaf samples are in the recombinant PVYNTN group (sequence identity >99%); while those from tuber sprouts are in the PVYN/NTN group with identities above 95%. Sanger sequencing of viral capsid suggests the presence of a third variant related to PVYO, a prevalent strain reported in potato fields worldwide.
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Citations
PVDP: A portable open source pipeline for detection of plant viruses in RNAseq data. A case study on potato viruses in Antioquia (Colombia)
Pablo A. Gutiérrez,Ary Rivillas,Daniel Tejada,Susana Giraldo,Andrea Restrepo,Maria Alejandra Ospina,Susana Cadavid,Yuliana Gallo,Mauricio Marín +8 more
TL;DR: This work presents a stand-alone plant virus detection pipeline (PVDP) optimized for the surveillance of potato viruses but also useful in other plant hosts, and includes a curated database of plant viruses in addition to an R script for presenting results as a user-friendly html report.
24
Molecular characterization of Potato virus Y (PVY) and Potato virus V (PVV) isolates naturally infecting cape gooseberry (Physalis peruviana) in Antioquia, Colombia
Natalia del Pilar Lara Álvarez,Helena Jaramillo,Yuliana Gallo,Pablo A. Gutiérrez,Mauricio Marín +4 more
- 01 Jan 2018
TL;DR: It is suggested that cape gooseberry could be an alternate host to viruses of other economically important solanaceous crops in the Andean region of South America.
Prevalence of RNA viruses in seeds, plantlets, and adult plants of cape gooseberry (Physalis peruviana) in Antioquia (Colombia)
Erika Corrales-Cabra,Mónica Higuita,Rodrigo Hoyos,Yuliana Gallo,Mauricio Marín,Pablo A. Gutiérrez +5 more
TL;DR: The results reveal that the P. peruviana virome is largely unexplored, and urgent measures should be implemented to certify the health status of planting material, and crops.
6
Next generation sequencing and proteomics in plant virology: how is colombia doing?
Leidy Johana Madroñero,Zayda-Lorena Corredor-Rozo,Javier Escobar-Perez,Myriam L. Velandia-Romero +3 more
TL;DR: In this review, advancements in ‘omic’ technologies and their different applications in plant virology in Colombia are discussed and bioinformatics pipelines and resources for omics data analyses are presented.
Detección molecular de seis virus de ARN en brotes de tubérculos de papa criolla (Solanum phureja) en Antioquía , Colombia
Andrea Sierra Mejía,Yuliana Gallo García,Meike Estrada Arteaga,Pablo Gutiérrez-Sánchez,Mauricio Marín Montoya +4 more
- 01 Jan 2020
TL;DR: The incidence of six RNA viruses (PLRV, PVS, PVV, PVX, PVY and PYVV) in sprouts from the tuber-seeds used by farmers to start their new crop cycles were investigated and complete genome sequences were obtained for all viruses under study.
5
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