Exploring the virome of Vasconcellea x heilbornii: the first step towards a sustainable production program for babaco in Ecuador

Authors: CORNEJO-FRANCO, JAUN - Centro De Investigaciones Biotecnologicas Del Ecuador; FLORES, FRANCISCO - Centro De Investigaciones Biotecnologicas Del Ecuador; CHICA, EDUARDO - Centro De Investigaciones Biotecnologicas Del Ecuador; Grinstead, Sam; Mollov, Dimitre; QUITO-AVILA, DIEGO - Centro De Investigaciones Biotecnologicas Del Ecuador

Submitted to: European Journal of Plant Pathology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/11/2020
Publication Date: 6/16/2020
Citation: Cornejo-Franco, J., Flores, F., Chica, E., Grinstead, S.C., Mollov, D.S., Quito-Avila, D. 2020. Exploring the virome of Vasconcellea x heilbornii: the first step towards a sustainable production program for babaco in Ecuador. European Journal of Plant Pathology. https://doi.org/10.1007/s10658-020-02037-2.
DOI: https://doi.org/10.1007/s10658-020-02037-2

Interpretive Summary: Babaco is a natural hybrid in the family Caricaceae, related to papaya, growing in temperate areas of the Andes. Its fruits are used by native peoples for juice and jams. Fruit production in Ecuador has been declining due to babaco diseases, caused by different pathogens including babaco mosaic virus. In this study, we used high throughput sequencing to investigate whether there are other viral pathogens infecting babaco. Seven viruses, previously unreported in babaco, were identified. Three of them had low sequence identity comparisons to known viruses and will be characterized as new virus species. This report provides the basis for understanding the complexity of virus infections in babaco, and will be very useful in establishing a needed virus-free nursery certification program.

Technical Abstract: During the last decade, the low cost of high-throughput sequencing (HTS) technologies has allowed its use for the detection and discovery of new viruses. In plants, the use of HTS mostly ends up with the genomic characterization of viruses without considering applied aspects of such findings. The objective of this study was to use HTS and conventional shotgun sequencing to investigate the virome of babaco (Vasconcellea x heilbornii) —a non-traditional fruit crop native to Ecuador— and its importance in nurseries and production orchards. Seven viruses were detected, including papaya ringspot virus and two orthologues of papaya virus Q and papaya meleira virus, respectively. In addition, three RNA viruses were found with homology, albeit with low sequence identity, to Apple latent spherical virus (genus Cheravirus, 66% nt identity), Cherry leaf roll virus (genus Nepovirus, 44% nt identity) and Citrullus lanatus cryptic virus (genus Partitivirus, 68% nt identity). Pararetrovirus-like sequences with homology to Citrus endogenous pararetrovirus (51% nt identity) were also detected. Virus surveys using RT-PCR-based detection assays revealed that PRSV is the most detrimental virus, with up to 36% incidence in symptomatic plants. Partitivirus- and pararetrovirus-like sequences were detected in 100% of tested plants, perhaps suggesting their persistent nature as cryptic and integrated viruses, respectively. Considering the vegetative propagation nature of this crop, this work provides information on the incidence of babaco viruses and supports the implementation of a virus-free certification program.