| Sumario: | There are some graft-transmissible citrus diseases such as incompatibility of varieties grafted on trifoliate rootstocks, impietratura and
cristacortis that, although they have been described for many years in many citrus growing areas, their causal agent is still unknown
and rapid detection methods could not be developed. Diagnosis can only be made by means of infectivity assays on indicator pl ants,
resulting slow, expensive and non-specific and pose a limitation for the analysis of a large number of samples. These diseases are
present in Spain and their diagnosis is mandatory in Sanitation and Certification Programs. To identify the causal agent asso ciated to
such diseases and develop specific molecular detection methods, the small RNAs (sRNAs) fraction, extracted from Etrog citron plants
infected with each of the above diseases, was analyzed by deep sequencing. The assembly of the sRNAs derived from each sample
allowed the obtaining of several sequence fragments that were present in infected plants and not in healthy ones. In the case of
incompatibility on trifoliate rootstocks disease, we determined the complete genome sequence of a new virus provisionally nam ed
Trifoliate citrus bud union associated virus (TCBUaV), that showed homology with species of th e genus Cytorhabdovirus, whereas for
impietratura and cristacortis diseases we obtained partial sequences of individual viral genomes that had no homology with an y virus
available in the databases. Obtaining specific sequences of each pathogen has allowed us to develop specific and rapid molecular
detection methods thereof by RT-PCR
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