Identification and full genome analysis of the first putative virus of sea buckthorn (Hippophae rhamnoides L.)

Abstract

The agricultural importance of sea buckthorn (Hippophae rhamnoides L.) is rapidly increasing. Several bacterial and fungal pathogens infecting sea buckthorn have been identified and characterized; however, the viral pathogens are not yet known. In this study, we identified, isolated, and sequenced a virus from a wild plantation of sea buckthorn for the first time. Sequence analysis of the obtained viral genome revealed high similarity with sequences of several viruses belonging to the genus Marafivirus, especially olive latent virus 3 (OLV-3). The genome of the new virus is 6,989 nucleotides (nt) in length according to 5' and 3' rapid amplification of cDNA ends (RACE) (without polyA-tail), with 5' and 3' untranslated regions being 133 and 109 nt long, respectively. The viral genome encoded two open reading frames (ORFs). ORF1 encoded a polyprotein of 1,954 amino acids (aa) with the characteristic marafivirus non-structural protein domains--methyltransferase, Salyut domain, papain-like cysteine protease, helicase, and RNA-dependent RNA polymerase. ORF1 was separated from ORF2 by a six nt and encoded the coat protein (CP). CP had typical signatures of minor (30.96 kDa) and major (21.18 kDa) forms. Both CP forms were cloned and expressed in a bacterial expression system, and only the major CP was able to self-assemble into 30 nm virus-like particles that resembled the native virus, thus demonstrating that minor CP is not essential for virion assembly. We suggest the newly discovered virus to be named as "Sea buckthorn marafivirus", abbreviated as "SBuMV". Author summarySea buckthorn is an exceptionally valuable plant that is currently widely cultivated as multipurpose horticultural species for food, pharmacology, cosmetics, and landscape conservation. Diseases and pests directly affect the cultivation of SBT. To date, several pests and diseases, mainly fungal and bacterial, but no viral, sea buckthorn have been reported. Identification of new pathogens would assist in the development of control strategies, and quarantine purposes and ensure sustainable sea buckthorn cultivation. Here, for the first time, we present a virus putatively infecting sea buckthorn. We had characterized its full genome, cloned and expressed minor and major forms of coat protein either individually or co-expressed. We also showed that major coat protein-derived virus-like particles self- assembled directly in the bacterial cells, and the majority of the expressed CPs were soluble. Our study suggests that the minor CP is not essential for the assembly of seemingly structurally intact viral particles, meaning that it can have other functions.