The Cretan Carob Virome

Carob (Ceratonia siliqua) is an important yet often underestimated Mediterranean tree species. Historically used as a sweetener by ancient Greeks and Arabs, it also supported populations during periods of famine. Beyond its cultural value, carob exhibits notable agronomic traits, including drought and temperature tolerance, soil erosion prevention, and potential contributions to rural development. Although a Cretan carob genome assembly has recently become available, little is known about pathogens associated with this species, particularly viruses. Here, we characterized the virome of carob trees in Crete using high throughput sequencing (HTS) and targeted molecular validation. We collected 134 leaf samples from 34 growers across the island four prefectures. HTS analysis revealed novel isolates of two Secoviridae members (Artichoke yellow ringspot virus - AYRSV) and Strawberry latent ringspot virus - SLRSV), as well as Soybean ilarvirus 1 (SolV1), a putative and incompletely characterized jivivirus, and a previously undescribed coguvirus of the family Phenuiviridae, all confirmed by PCR screening. Phylogenetic and sequence analyses support the classification of the coguvirus as a distinct viral species, for which we propose the name Carob coguvirus 1 (CaCoV1). To our knowledge, this study provides the first comprehensive characterization of the carob virome. These findings expand current knowledge of viral diversity in carob and establish a foundation for future epidemiological studies, certification of propagation material, and the sustainable expansion of carob cultivation in Crete and other Mediterranean regions.