Using high‐throughput sequencing in support of a plant health outbreak reveals novel viruses in Ullucus tuberosus (Basellaceae)

Abstract

Ullucus tuberosus (ulluco) is a tuber‐forming species that has become a novel crop in highland and temperate maritime climates. Eight viruses have been previously reported infecting Ullucus, including Andean potato latent virus (APLV), a quarantine virus within the European Union. No reference sequences have been published for the viruses previously described from U. tuberosus. Plants grown in the UK for the internet trade were tested for the presence of quarantine viruses using ELISA and real‐time RT‐PCR. ELISA positive results were obtained for APLV and multiple other viruses. A similar suite of viruses was detected at a second outbreak site linked to horticultural trade. Virus identification was by high‐throughput sequencing (HTS) using a ribosomal RNA (rRNA)‐depleted total RNA approach. Analysis of viral contigs indicated the presence of several novel viruses closely related to, but not consistent with, the viruses indicated by ELISA. Further confirmatory testing by real‐time RT‐PCR indicated that two tymoviruses, tentatively named Ullucus tymovirus 1 and Ullucus tymovirus 2, were more closely related to each other (85% identity), than to APLV or Andean potato mild mosaic virus (63–66% identity). APLV could not be confirmed from either site by either HTS or PCR. A novel tobamovirus (Ullucus tobamovirus 1) was only detected at the initial outbreak site. A novel polerovirus (Ullucus polerovirus 1) and a distinct genotype of Papaya mosaic virus were detected from both outbreak sites. Deploying HTS during a plant health outbreak demonstrates the potential of this approach to give rapid, accurate diagnosis.

Historical virus isolate collections: An invaluable resource connecting plant virology’s pre‐sequencing and post‐sequencing eras

“…In addition, the Hu isolate group was more closely related to eggplant mosaic virus (EMV; genus Tymovirus) than to those of the Col isolate group (Koenig et al, 1979). In the 1990s, Lizarraga et al (1996aLizarraga et al ( , 2001 (Fox et al, 2019). Although they reacted strongly with APLV antiserum, they…”

“…Recently, several viruses were found infecting ullucu in the UK, including a potyvirus tentatively named ullucus potyvirus-1 (UPotV-1), two unknown viruses from the genus Tymovirus, and other viruses in the genera Tobamovirus, Polerovirus, and Comovirus (Fox et al, 2019). It was suggested that some of these might be the same as those identified earlier and sequencing of virus isolates obtained from an historical plant virus collection is now underway to resolve whether this is so.…”

Sequence analysis of 43‐year old samples of Plantago lanceolata show that Plantain virus X is synonymous with Actinidia virus X and is widely distributed

“…Indexed TruSeq complete plant libraries, including an RNA depletion step, were produced from the RNA and sequenced using a MiSeq v. 2 600-cycle kit (Illumina). The resulting data was then analysed as described by Fox et al (2019). Phylogenetic trees were produced using the maximumlikelihood algorithm and 500 bootstraps in MEGA 7 (Kumar et al, 2016).…”

First report of Rose spring dwarf‐associated virus in Rosa spp. in United Kingdom

“…A MiSeq instrument and a MiSeq Reagent Kit v3 (600-cycle) (Illumina Inc.) were used to run the library. The run generated 569,452 reads for the sample, and data was analysed as described by Fox et al (2019). Three fragments of rose spring dwarf-associated virus (RSDaV) were identified (234, 251 and 229 bp; GenBank Accession Nos.…”