RNA deep sequencing uncovers a new Sobemovirus species Sobemovirus orxatae affecting chufa Cyperus esculentus.
Cyperus esculentus is a common weed that has a special agricultural interest in the Mediterranean region of Spain for the production of the non-alcoholic beverage called orxata. In the recent years, a loss of yield was observed and may be caused by different unknown pathogens. In this study we performed a RNA High Throughput Sequencing experiment on a plant showing streaked or mottled leaves, leading to chlorosis symptoms. We obtained the complete genome sequence of a new Sobemovirus species that we propose to name Sobemovirus orxatae. We designed specific RT-PCR primers and performed a survey of different fields of the region that confirmed this new species is extended in tiger nuts crops. This study strengthen the importance of emerging pathogen vigilance and plant sanitation in tiger nut cultivation.