Abstract
BackgroundA disease of unknown etiology in water chestnut plants (Eleocharis dulcis) was reported in China between 2012 and 2014. High throughput sequencing of small RNA (sRNA) combined with bioinformatics, and molecular identification based on PCR detection with virus-specific primers and DNA sequencing is a desirable approach to identify an unknown infectious agent. In this study, we employed this approach to identify viral sequences in water chestnut plants and to explore the molecular interaction of the identified viral pathogen and its natural plant host.ResultsBased on high throughput sequencing of virus-derived small RNAs (vsRNA), we identified the sequence a new-to-science double-strand DNA virus isolated from water chestnut cv. ‘Tuanfeng’ samples, a widely grown cultivar in Hubei province, China, and analyzed its genomic organization. The complete genomic sequence is 7535 base-pairs in length, and shares 42–52% nucleotide sequence identity with viruses in the Caulimoviridae family. The virus contains nine predicated open reading frames (ORFs) encoding nine hypothetical proteins, with conserved domains characteristic of caulimoviruses. Phylogenetic analyses at the nucleotide and amino acid levels indicated that the virus belongs to the genus Soymovirus. The virus is tentatively named Water chestnut soymovirus-1 (WCSV-1). Phylogenetic analysis of the putative viral polymerase protein suggested that WCSV-1 is distinct to other well established species in the Soymovirus genus. This conclusion was supported by phylogenetic analyses of the amino acid sequences encoded by ORFs I, IV, VI, or VII. The sRNA bioinformatics showed that the majority of the vsRNAs are 22-nt in length with a preference for U at the 5′-terminal nucleotide. The vsRNAs are unevenly distributed over both strands of the entire WCSV-1 circular genome, and are clustered into small defined regions. In addition, we detected WCSV-1 in asymptomatic and symptomatic water chestnut samples collected from different regions of China by using PCR. RNA-seq assays further confirmed the presence of WCSV-1-derived viral RNA in infected plants.ConclusionsThis is the first discovery of a dsDNA virus in the genus Soymovirus infecting water chestnuts. Data presented also add new information towards a better understanding of the co-evolutionary mechanisms between the virus and its natural plant host.
Highlights
A disease of unknown etiology in water chestnut plants (Eleocharis dulcis) was reported in China between 2012 and 2014
Identification of a novel soymovirus in water chestnut samples by deep sequencing and subsequent bioinformatics analyses To identify the unknown virus associated with disease in water chestnut plants, a deep sequencing approach was used to identify small RNA (sRNA) sequences including those that may be produced by a virus in samples from symptomatic water chestnut plants
Bioinformatics analysis of sequences from Water chestnut soymovirus-1 (WCSV-1) indicated the presence of conserved viral features shared with the movement protein (MP), CP, Aspartic proteinase (AP), RNA-dependent DNA polymerase (RT), and RNaseH proteins in Caulimoviridae viruses (Fig. 6), suggesting that WCSV-1 is a novel member of Caulimoviridae family distinct from other well characterized viruses in the genus Soymovirus (Figs. 3 and 4) [3]
Summary
A disease of unknown etiology in water chestnut plants (Eleocharis dulcis) was reported in China between 2012 and 2014. Members of the Caulimoviridae family are plant pararetroviruses that contain a double-strand DNA (dsDNA) genome and replicate through an RNA intermediate. As the plant is usually clonally propagated via vegetative bulbs, viral agents can be transmitted to generation and be spread worldwide by germplasm exchange. Such transmission of viral agents may cause significant economic losses as bulb quality and yield are often reduced in virally infected plants. The etiology of the viral disease in water chestnut plants remains unclear
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