Abstract
The complete genomic sequence of a novel ilarvirus from Eleocharis dulcis, tentatively named "water chestnut virus A" (WCVA), was determined using next-generation sequencing (NGS) combined with reverse transcription polymerase chain reaction (RT-PCR) and rapid amplification of cDNA ends (RACE) PCR. The three genomic RNA components of WCVA were 3578 (RNA1), 2873 (RNA2), and 2073 (RNA3) nucleotides long, with four predicted open reading frames containing conserved domains and motifs typical of ilarviruses. Phylogenetic analysis of each predicted protein consistently placed WCVA in subgroup 4 of the genus Ilarvirus, together with prune dwarf virus, viola white distortion associated virus, Fragaria chiloensis latent virus, and potato yellowing virus. The genetic distances and lack of serological reaction to antisera against other ilarviruses suggest that WCVA is a novel member of the genus.
Highlights
Water chestnut (Eleocharis dulcis (Burm. f.) Trin. is a perennial aquatic plant of the genus Eleocharis (Cyperaceae) that occurs naturally in China, Japan, Ryukyu Islands, Nanyang Island and India [1]
Total RNA was extracted from the infected water chestnut sample using the EASYspin RNA Plant Mini Kit (Aidlab Biotechnologies Co., Ltd, China)
In all ORFs, water chestnut virus A (WCVA) clustered in subgroup 4 with prune dwarf virus (PDV), viola white distortion associated virus (VWDAV), fragaria chiloensis latent virus (FCILV) and potato yellowing virus (PYV), but the exact clustering pattern among these viruses differed slightly (Fig.2)
Summary
Water chestnut (Eleocharis dulcis (Burm. f.) Trin. is a perennial aquatic plant of the genus Eleocharis (Cyperaceae) that occurs naturally in China, Japan, Ryukyu Islands, Nanyang Island and India [1]. The complete genomic sequence of a novel ilarvirus from Eleocharis dulcis, tentatively named water chestnut virus A (WCVA), was determined using generation sequencing (NGS) combined with reverse transcription polymerase chain reaction (RT-PCR) and rapid amplification of cDNA ends (RACE) PCR.
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