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First glimpse into the tomato and pepper viromes of Croatia

Tomato is important crop, hosting at least 312 viruses, satellites or viroids, and a pivotal research species in the Croatian-Slovenian project “Nanopore high throughput sequencing for the resolution of problems in the plant pathogen epidemiology and diagnostics“. Main sampling sites are greenhouses in the continental Croatia (Vidovec, Sedlarica). In 2021, tomatoes from the coastal region (Turanj) and symptomatic peppers neighboring tomatoes were also collected. Leaves were used for lateral flow tests (LFT) and nucleic acids extraction. For nanopore high throughput sequencing (HTS) library preparation, representative tomato DNase treated CTAB-extracts were pooled, rRNA depleted and polyA tailed. Based on HTS and LFT results, tomato (31) and pepper (3) samples were individually tested by RT-PCR with primers for pospiviroids, potato virus S (PVS), potato virus Y (PVY), tomato spotted wilt virus (TSWV), cucumber mosaic virus (CMV) and CMV satellite. PVS consensus genome from a tomato in Vidovec (ON468562) was highly similar to a potato isolate from the Netherlands (MF418030) belonging to the ordinary (PVSO) strain. That tomato was also infected with PVY (ON505007), as were others from Vidovec and Sedlarica (ON505008). Their genomes were most similar to a Slovakian tomato isolate (MW685827) clustering with PVY-NTN strains. A severely diseased tomato from Turanj harbored only TSWV with segments S and M highly similar to isolates from Italy (DQ376178 and MH756624, respectively) and L to a Spanish isolate (KP008130). Peppers were either infected by CMV (two from Vidovec) or by potyviruses (positive in LFT for potyvirus group, Agdia, species pending identification) and a pospiviroid (one from Sedlarica and Vidovec). A pospiviroid amplicon was also obtained for one of the Sedlarica PVY+ tomatoes. Partial sequences suggest citrus exocortis viroid (CEVd) is distributed in tomatoes and peppers but this needs to be confirmed. This first glimpse into the Croatian tomato and pepper viromes suggests PVY was predominant in the continental tomatoes with a virus or a viroid occasionally in coinfections. A few peppers tested so far had viromes constituting of CMV, potyviruses and pospiviroids.

high throughput sequencing, nanopore, PVY, PVS, TSWV, pospiviroids, pepper, tomato

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