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Small RNA-Seq to characterise viruses responsible of Lettuce big-vein disease

Miguel Aranda: CEBAS-CSIC

<div>Lettuce big-vein disease (LBVD) is an emerging disease causing losses ranging from 30 to 70% in lettuce production worldwide. Several studies have associated this disease with <em data-mce-fragment="1">M</em><em data-mce-fragment="1">irafiori lettuce big-vein virus</em> (MiLBVV; genus <em data-mce-fragment="1">Ophiovirus</em>), alone or in mixed infection with <em data-mce-fragment="1">Lettuce</em><em data-mce-fragment="1"> big-vein associated virus</em> (LBVaV; genus <em data-mce-fragment="1">Varicosavirus</em>). We used Illumina small RNA sequencing (sRNA-seq) to detect viruses present in symptomatic lettuce plants from commercial fields in Southern Spain. Data analysis showed the presence of MiLBVV and LBVaV in samples from different plant tissues. Additionally, <em data-mce-fragment="1">Ranunculus white mottle virus</em> (RWMV; genus <em data-mce-fragment="1">Ophiovirus</em>) was also identified in these samples. Sequences of the coat protein genes were used to infer MiLBVV and LBVaV nucleotide diversities within the analysed samples and to differentiate potential strains. Comparison of the sequences determined in this work with those available in databases allowed the design of universal primers to detect and quantify the accumulation of both MiLBVV and LBVaV. Subsequent analysis of multiple samples from symptomatic lettuce plants of several plots located in Southern Spain showed high rates of MiLBVV and LBVaV mixed infections, with 58% of the positive samples infected with both viruses, but also significant proportions of single infections, which were more frequent for LBVaV (21%). Moreover, the presence of one or both viruses was detected in 6 out of 10 commercial seed lots obtained from different providers, suggesting the possibility of their seed transmission.</div>