ABSTRACT
We present here the first complete genomic sequence of Arracacha virus A from a Peruvian arracacha sample collected in 1975 and compare it with the genomes of other nepoviruses. Its RNA1 and RNA2 both had greatest amino acid identities with those of the subgroup A nepovirus Melon mild mottle virus.
GENOME ANNOUNCEMENT
In 1975, during a virus survey of subsistence plantings containing crop mixtures at Umari, Huanuco Department, in the Peruvian Andes, a virus was isolated from arracacha plants [Peruvian parsnip (Arracaccia xanthorhiza), family Apiaceae] showing pronounced leaf mosaic symptoms. The virus was mechanically transmissible to 38 species from 10 plant families. Following characterization using electron microscopy, density centrifugation, and serology, it was identified as a member of the Nepovirus genus and named Arracacha virus A (AVA) (1, 2). In 1978, AVA-infected leaf samples were dried over calcium chloride in Peru, sealed in glass vials, and sent to the United Kingdom. They currently form part of what is now called the Fera plant virus collection.
In 2015, total RNA was extracted from the freeze-dried AVA-infected leaf material using an RNeasy kit (Qiagen, United Kingdom), including the optional DNase treatment. An indexed plant ribosome-subtracted sequencing library was then produced from the total RNA using the ScriptSeq complete plant leaf kit (Illumina, USA), according to the manufacturer’s instructions. The indexed library was then sequenced along with others on a MiSeq instrument (Illumina), using a 600-cycle V3 kit. The resulting 492,656 paired reads were trimmed on the 3′ end to a quality score of 20 using Sickle (3), assembled using Trinity (4), and the resulting contigs compared to the GenBank nr and nt databases using BLAST+ (5). Reads of viral origin were extracted using MeganN (6). Two contigs of 7,411 and 3,852 nucleotides (nt) in length were assembled and shown by similarity to other nepoviruses to represent the RNA1 and RNA2 components of the AVA genome, respectively.
The AVA RNA1 encoded a putative 266-kDa polyprotein with an amino acid identity resembling those of the subgroup A nepoviruses Melon mild mottle virus (39%) (7) and Grapevine fanleaf virus (36%) (8). The AVA RNA2 encoded a putative 127-kDa polyprotein with 32% and 30% amino acid identities to Melon mild mottle virus and Potato black ringspot virus (9), another subgroup A nepovirus, respectively. These findings, along with the absence of any significant homology between the 3′ untranslated regions (UTRs) of the RNA1 and RNA2 molecules confirm that AVA belongs to subgroup A of the Nepovirus genus.
Accession number(s).
The sequences were deposited in GenBank under accession numbers KY569301 (RNA1) and KY569302 (RNA2).
ACKNOWLEDGMENTS
This work was supported by the UK Government’s Department of the Environment Food and Rural Affairs (DEFRA) Future Proofing Plant Health project. Sequencing work was carried out with funding from DEFRA.
Footnotes
Citation Adams IP, Boonham N, Jones RAC. 2017. First complete genome sequence of Arracacha virus A isolated from a 38-year-old sample from Peru. Genome Announc 5:e00141-17. https://doi.org/10.1128/genomeA.00141-17.
REFERENCES
- 1.Jones RAC, Kenten RH. 1978. Arracacha virus A, a newly recognised virus infecting arracacha (Arracacia xanthorrhiza; Umbelliferae) in the Peruvian Andes. Ann Appl Biol 90:85–91. doi: 10.1111/j.1744-7348.1978.tb02613.x. [DOI] [Google Scholar]
- 2.Jones RAC, Kenten RH. 1980. Arracacha virus A. Descriptions of plant viruses, No 216 Association of Applied Biologists, Wellesbourne, Warwick, United Kingdom: http://www.dpvweb.net/dpv/showdpv.php?dpvno=216. [Google Scholar]
- 3.Joshi NA, Fass JN. 2011. Sickle—a windowed adaptive trimming tool for FASTQ files using quality. https://github.com/najoshi/sickle. [Google Scholar]
- 4.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, Regev A. 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]
- 5.Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL. 2009. Blast+: architecture and applications. BMC Bioinformatics 10:421. doi: 10.1186/1471-2105-10-421. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 6.Huson DH, Beier S, Flade I, Górska A, El-Hadidi M, Mitra S, Ruscheweyh HJ, Tappu R. 2016. MegaN community edition—interactive exploration and analysis of large-scale microbiome sequencing data. PLoS Comput Biol 12:e1004957. doi: 10.1371/journal.pcbi.1004957. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 7.Tomitaka Y, Usugi T, Yasuda F, Okayama H, Tsuda S. 2011. A novel member of the genus Nepovirus isolated from Cucumis melo in Japan. Phytopathology 101:316–322. doi: 10.1094/PHYTO-06-10-0150. [DOI] [PubMed] [Google Scholar]
- 8.Mekuria TA, Gutha LR, Martin RR, Naidu RA. 2009. Genome diversity and intra- and interspecies recombination events in Grapevine fanleaf virus. Phytopathology 99:1394–1402. doi: 10.1094/PHYTO-99-12-1394. [DOI] [PubMed] [Google Scholar]
- 9.Souza Richards R, Adams IP, Kreuze JF, Souza J, Cuellar W, Dullemans AM, van der Vlugt RAA, Glover R, Hany U, Dickinson M, Boonham N. 2014. The complete genome sequences of two isolates of potato black ringspot virus and their relationship to other isolates and nepoviruses. Arch Virol 159:811–815. http://link.springer.com/article/10.1007/s00705-013-1871-8. [DOI] [PubMed] [Google Scholar]