Abstract
The ryegrass mosaic virus (RgMV) is a single positive-strand RNA virus belonging to the genus Rymovirus. The major natural hosts for RgMV are members of the Gramineae species, including ryegrass. Here, we report the nearly complete genome sequence of RgMV by de novo assembly using ryegrass transcriptomes.
GENOME ANNOUNCEMENT
Ryegrass mosaic virus (RgMV), a member of the genus Rymovirus in the family Potyviridae, is a filamentous virus replicating in the host cytoplasm (1, 2). Its natural hosts are thus very limited to the members of the Gramineae species, including Lolium multiflorum, Lolium perenne, and Dactylis glomerata (3, 4). Of these species, perennial ryegrass (L. perenne) in the family Poaceae is cultivated worldwide and is an important naturalized plant utilized as pasture and forage crops in agriculture (5, 6). Infection by RgMV in Lolium spp. and Dactylis glomerata exhibits light-green to yellow mosaic symptoms, leading to serious damage to crop yields (2, 7, 8). RgMV is transmitted by both sap and eriophyid mites (Abacarus hystrix) (2, 9). RgMV has a monocistronic, positive single-stranded RNA genome encoding a polyprotein and replicates in the cytoplasm (2).
To identify viruses infecting ryegrass, several sets of transcriptome data for Lolium species have been screened. Of these species, a recent study provided a reference transcriptome for the perennial ryegrass, which was derived from six different tissues, including the stem, root, meristem, mature leaf, inflorescence, and leaf sheath (10). Six different libraries prepared using a mRNA-Seq sample prep kit (Illumina) were sequenced by the paired-end Illumina GAIIx sequencer. Raw data for all six libraries were downloaded and de novo transcriptome assembly was performed for each library using the Trinity program (v.2.0.2) (11). A BLAST search identified three contigs showing strong sequence similarity to the RgMV reference genome sequence (NC_001814.1). Of the three contigs, a contig 9,522 nucleotides (nt) long comprised the nearly complete genome of RgMV. We named the newly identified virus RgMV isolate Denmark (KR061300) according to the identified country. The 5′ and 3′ untranslated region (UTR) sequences of the Denmark RgMV isolate are 16 and 3 nt shorter, respectively, than the reference sequence (NC_001814.1). In general, the 5′ and 3′ UTR sequences for many RNA viruses are highly conserved. The genome of the Denmark RgMV isolate encodes a polyprotein that is processed by proteolytic cleavage into 10 proteins, including PI, HC-Pro, P3, 6K1, C1, 6K2, VPg, NIa, Nib, and Cp. In addition, we confirmed that all six ryegrass samples were infected by RgMV. Thus far, only two genome sequences for RgMV are available. BLASTn results showed 93% and 92% nt sequence identities to the other Danish (NC_001814.1) and Australian (AF035818.1) isolates, respectively. Altogether, our study provides the nearly complete genome sequence for the Denmark RgMV isolate, which is the third genome sequence for RgMV thus far identified. In addition, we demonstrated the successful de novo genome assembly of RNA viruses using transcriptome data.
Nucleotide sequence accession number.
The genome sequence of ryegrass mosaic virus isolate Denmark has been submitted to GenBank (accession no. KR061300).
ACKNOWLEDGMENT
This work was carried out with the support of “Cooperative Research Program for Agriculture Science & Technology Development” (project PJ00976401), Rural Development Administration, Republic of Korea.
Footnotes
Citation Jo Y, Choi H, Cho WK. 2015. De novo genome assembly of ryegrass mosaic virus from a ryegrass transcriptome. Genome Announc 3(3):e00497-15. doi:10.1128/genomeA.00497-15.
REFERENCES
- 1.Stenger DC, Hall JS, Choi I-R, French R. 1998. Phylogenetic relationships within the family Potyviridae: wheat streak mosaic virus and brome streak mosaic virus are not members of the genus Rymovirus. Phytopathology 88:782–787. doi: 10.1094/PHYTO.1998.88.8.782. [DOI] [PubMed] [Google Scholar]
- 2.Mulligan TE. 1960. The transmission by mites, host-range and properties of ryegrass mosaic virus. Ann Appl Biol 48:575–579. doi: 10.1111/j.1744-7348.1960.tb03559.x. [DOI] [Google Scholar]
- 3.Heard AJ, Brook BA, Roberts ET, Cook RJ. 1974. The incidence of ryegrass mosaic virus in crops of ryegrass grown for seed in some southern counties of England. Plant Pathol 23:119–127. doi: 10.1111/j.1365-3059.1974.tb01833.x. [DOI] [Google Scholar]
- 4.Wilkins PW, Catherall PL. 1974. The effect of some isolates of ryegrass mosaic virus on different genotypes of Lolium multiflorum. Ann Appl Biol 76:209–216. doi: 10.1111/j.1744-7348.1974.tb07974.x. [DOI] [PubMed] [Google Scholar]
- 5.Xu J, Schubert J, Altpeter F. 2001. Dissection of RNA-mediated ryegrass mosaic virus resistance in fertile transgenic perennial ryegrass (Lolium perenne L.). Plant J 26:265–274. doi: 10.1046/j.1365-313X.2001.01025.x. [DOI] [PubMed] [Google Scholar]
- 6.Redfearn DD, Venuto BC, Pitman WD, Alison MW, Ward JD. 2002. Cultivar and environment effects on annual ryegrass forage yield, yield distribution, and nutritive value. Crop Sci 42:2049–2054. doi: 10.2135/cropsci2002.2049. [DOI] [Google Scholar]
- 7.A’Brook B, Heard AJ. 1975. The effect of ryegrass mosaic virus on the yield of perennial ryegrass swards. Ann Appl Biol 80:163–168. doi: 10.1111/j.1744-7348.1975.tb01617.x. [DOI] [Google Scholar]
- 8.Holmes SJI. 1979. Effect of ryegrass mosaic virus on the quality of perennial ryegrass. Ann Appl Biol 91:75–79. doi: 10.1111/j.1744-7348.1979.tb07415.x. [DOI] [Google Scholar]
- 9.Guy PL. 1993. First record of ryegrass mosaic virus and its mite vector Abacarus hystrix (Nal.) in New Zealand. N Z J Agric Res 36:377–379. doi: 10.1080/00288233.1993.10417735. [DOI] [Google Scholar]
- 10.Farrell JD, Byrne S, Paina C, Asp T. 2014. De novo assembly of the perennial ryegrass transcriptome using an RNA-Seq strategy. PLoS One 9:e103567. doi: 10.1371/journal.pone.0103567. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 11.Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N. 2011. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 29:644–652. doi: 10.1038/nbt.1883. [DOI] [PMC free article] [PubMed] [Google Scholar]