Canna yellow streak virus (Potyvirus, Potyviridae) was sequenced using the novel method of next-generation pyrosequencing. The complete genome was found to be 9,502 nucleotides excluding the poly-A tail with a predicted genome organisation typical for a member of the genus Potyvirus. As with other potyviruses that infect monocotyledons, some of the predicted cleavage sites of the polyprotein genome were unusual, such as a glutamic acid/threonine (E/T) between the CI and 6K2 proteins and a glutamic acid/aspartic acid (E/D) between the NIa and NIb proteins. Evidence of the presence of endogenous pararetroviruses in the canna genome was found from the large number of sequences obtained with this method.
The seeds were imported from Asia and samples were screened in compliance with import testing requirements. A total of 3,000 seeds were tested for Tomato mottle mosaic virus (ToMMV; genus Tobamovirus) using the RT-PCR test (F-5476 and R-6287) from Levitzky et al. (2019). A product of the expected size (811 bp) was obtained in all subsamples (12 subsamples each of 250 seeds) and subsequently sent for Sanger sequencing. Sequences from four of these samples were compared against those in GenBank, and confirmed to be ToMMV (Accession Nos. OK334226, OK334230-32), with ≥99% nucleotide and 99-100% amino acid identity compared with the exemplar strain (KF477193; YP_008492931.1). To obtain the whole genome of the isolate, the 12 subsamples were bulked and sequenced by high throughput sequencing (HTS) as described by Fox et al. (2019) and bioinformatic analysis using the Angua pipeline (Fowkes et al., 2021). The whole genome of ToMMV was obtained (6375 bp; OK334224), and confirmed after a BLAST search (99.6% identity KF477193.1; Figure 1).The genome of Tomato mosaic virus (ToMV) was also found (OK334225).
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