High throughput sequencing for the detection and characterization of new virus found in arracacha (Arracacia xanthorrhiza)

Joao  De Souza; Segundo  Fuentes; Giovanna  Müller; Heidy  Gamarra; Mónica  Guzmán; Wilmer  Cuellar; Jan  Kreuze

doi:10.17268/sci.agropecu.2021.051

Authors

Joao De Souza Escuela de Posgrado, Programa Doctoral de Ciencias e Ingeniería Biológica, Universidad Nacional Agraria La Molina, Lima https://orcid.org/0000-0002-3739-3122
Segundo Fuentes International Potato Center (CIP), Apartado 1558, Lima https://orcid.org/0000-0001-8433-809X
Giovanna Müller International Potato Center (CIP), Apartado 1558, Lima https://orcid.org/0000-0003-0865-2946
Heidy Gamarra International Potato Center (CIP), Apartado 1558, Lima https://orcid.org/0000-0003-2746-2849
Mónica Guzmán Instituto de Biotecnología (IBUN), Universidad Nacional de Colombia, Bogota https://orcid.org/0000-0002-2541-2031
Wilmer Cuellar International Center for Tropical Agriculture (CIAT), Apartado Aéreo 6713, Cali https://orcid.org/0000-0003-4702-3237
Jan Kreuze International Potato Center (CIP), Apartado 1558, Lima https://orcid.org/0000-0002-6116-9200

DOI:

https://doi.org/10.17268/sci.agropecu.2021.051

Keywords:

Arracacha, siRNA sequencing, crinivirus, vitivirus, enamovirus

Abstract

Arracacha is a root crop cultivated in several countries of South America. The commercial product, which is the storage root, has multiple nutritional properties: its fine starch makes it easily digestible, and it contains high levels of calcium and vitamin A. High throughput sequencing (HTS) technology has been applied successfully for virus discovery in different agricultural crops, and it has been proposed to apply it in routine pathogen detection. Using HTS, novel sequences related to crinivirus and vitivirus were identified in apparently symptomeless arracacha, which were assembled into contigs located in different positions of the genome. Based on those sequences’ primers were designed to amplify corresponding sequences from further arracacha accessions and potato plant samples collected from farmers’ fields in Colombia and Peru. It was possible to determine the near complete genomes of these viruses. In addition, sequences related to an enamovirus and ST9-like RNA were also identified in arracacha plants using HTS.

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