Cucurbit is a generic term used to denote all species within the Family Cucurbitaceae also know as the gourd family . Numerous cucurbit crops are economically important worldwide. Cucurbits are consumed in different ways as fruits or vegetables, providing essential nutrients and dietary fibre . In Zimbabwe, Some of the cultivated cucurbits include the cucumber (Cucumis melo L.), the watermelon (Citrullus lanatus (Thunb.) Matsum. & Nakai), the melon (Cucumis melo L.), the pumpkin (Cucurbita maxima Duch.), the butternut (Cucurbita moschata Duch.) and the baby marrow (Cucurbita pepo L.). They are widely grown by both commercial and smallholder farmers as food and cash crops. Virus diseases on cucurbits produce diverse symptoms that result in yield reduction and in severe instances compromised fruit quality [3-4]. The negative effects of plant-infecting viruses on crops are more prominent especially in countries where their studies are underdeveloped.
High-throughput sequencing (HTS), also called next-generation sequencing (NGS) describes a series of technologies whereby millions or billions of DNA molecules are sequenced simultaneously . The application of these ever-growing sequencing technologies and bioinformatics data analysis to the studies of plant-infecting viruses, which started in 2009 , have revolutionized the fields of virus discovery and diagnostics, resulting in unprecedented virus discoveries from any host and environment . Unlike other popular techniques such as the enzyme-linked immunosorbent assay, molecular hybridization and polymerase chain reaction that mainly work on known pathogens, HTS data analysis has made possible the identification of sequences of known or unknown viruses from any host without any prior knowledge of the disease aetiology [7-8].
Zucchini shoestring virus (ZSSV) was discovered among other known cucurbit-infecting viruses in 2015 in South Africa when the RNA from severely distorted Baby marrow leaves were subjected to HTS [9-10]. Genomics and taxonomic studies revealed that ZSSV is a new species in the genus Potyvirus . The International Committee TV subsequently ratified these findings . The genus Potyvirus is one of the 8 genera that composed the family Potyviridae. Members in that family, also known as potyvirids, are differentiated by the host range, genomic features and phylogeny, with a species demarcation criterion set to a nucleotide and amino sequence identity less than 76% and 82% respectively for the large open reading frame (ORF) or its protein product. In instances where the complete ORF sequence is not available, similar criteria can be used for the coat protein (CP) coding region .
Viruses that belong to the genus Potyvirus have non-enveloped, flexuous and filamentous virions of 680–900 nm in length and 11-20 nm in diameter. The genome of potyviruses is a positive-sense ssRNA molecule with its 5’ terminus covalently linked to the viral protein genome linked (VPg) and its 3’ end polyadenylated. The 10 000 bp genome harbours two ORFs that encode eleven multifunctional proteins. A large ORF is translated into a single polyprotein that is cleaved at semi-conserved sites by three self-encoded proteases into ten mature proteins namely the protein 1 protease (P1-Pro), the helper component protease (HC-Pro), Protein 3 (P3), six kilodalton peptide 1 (6K1), the 6K2, the cytoplasmic inclusion (CI), the nuclear inclusion A protease (NIa-Pro), the nuclear inclusion B RNA-dependent RNA polymerase (NIb), the VPg and the CP . A smaller ORF, named the pretty interesting Potyviridae ORF (PIPO), is generated by a polymerase slippage mechanism and is expressed as the trans-frame protein P3N-PIPO [13-15].
In this note, we described and studied the genome sequences of three ZSSV isolates obtained through HTS of infected baby marrow leaves collected in Zimbabwe.