ARIETA-SOSA, J. G.

LAMAS, N. S.

MELO, F. L.

REIS, M. B. A.

RIBEIRO, S. G.

ROMANO, E.

SANCHES, M. M.

English

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Genome Assembly of Schlumbergera Virus X Infecting Prickly Pear(Opuntia cochenillifera) in BrazilMárcio Martinello Sanches,a Natalia Silva Lamas,a Marcelo Banho A. Reis,a Juan Gabriel Arieta-Sosa,a Eduardo Romano,aFernando Lucas Melo,b Simone Graça RibeiroaEmbrapa Recursos Genéticos e Biotecnologia, Brasilia, Brazila; Universidade de Brasília, Brasília, BrazilbPotexviruses frequently infect plants from the family Cactaceae. We report the complete genome sequence of a new Schlum-bergera virus X (SchVX) isolate. The genome has 6,615 nucleotides and shares 94% nucleotide identity with SchVX-K11 fromSchlumbergera. This is the first sequence of an isolate of SchVX from the genus Opuntia.Received 3 February 2015 Accepted 4 February 2015 Published 19 March 2015Citation Sanches MM, Lamas NS, Reis MBA, Arieta-Sosa JG, Romano E, Melo FL, Ribeiro SG. 2015. Genome assembly of Schlumbergera virus X infecting prickly pear (Opuntiacochenillifera) in Brazil. Genome Announc 3(2):e00133-15. doi:10.1128/genomeA.00133-15.Copyright © 2015 Sanches et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license.Address correspondence to Simone Graça Ribeiro, simone.ribeiro@embrapa.br.Prickly pear (Opuntia cochenillifera) (family Cactaceae) is avaluable forage for livestock feeding during the dry season inthe semiarid northeast region of Brazil. It contains about 90%water and is a liquid supplement, especially for dairy cattle, goats,and sheep (1, 2). Because of their vegetative propagation, cacta-ceous plants are often infected by viruses, especially potexviruses.The potexviruses (family Alphaflexiviridae, genus Potexvirus)are rod-shaped, nonenveloped, single-stranded, positive-senseRNA viruses (3). Four potexviruses infecting cactaceous plantswere described in Brazil. Cactus virus X was reported from differ-ent cacti and is widely spread in the country (4). Three virusesinfecting Opuntia tuna (Zygocactus virus X [ZyVX]), Hylocereusundatus (ZyVX and Schlumbergera virus X [SchVX]), andSchlumbergera truncata (Opuntia virus X [OpVX], ZyVX, andSchVX) were more recently identified based on partial nucleotidesequences of the RdRp gene in Sao Paulo State (5). We identified anew SchVX isolate from prickly pear (SchVX-Palma-PE) in Brazil.Plants collected in Pernambuco State were propagated and culti-vated in the greenhouse. Total RNA from symptomless plants wasextracted with an RNeasy Plant minikit and used for whole-transcriptome shotgun sequencing, using an Illumina HiSeq 2000platform at Fasteris (Switzerland), aiming to study water-stress-related genes. De novo assembly was performed with the VELVETprogram (6) and in an initial BLAST search, several contigs werefound to be potexvirus-derived. To further characterize these vi-rus sequences, we used Geneious software to perform BLASTnand BLASTx searches against a viral reference sequence database.Comparisons of the nucleotide (nt) and the predicted amino acids(aa) sequences with other potexviruses were made with the SDT(7) and MUSCLE (8) programs. A contig of 6,615 nucleotides wasidentified as Schlumbergera virus X with an identity of 94% for theentire genome sequence with SchVX-K11 (GenBank accession no.AY366207). SchVX-K11 was first described infecting Schlum-bergera bridgesii from a botanical garden in Croatia (former Yu-goslavia) during the 1960s (9), but only in 2004 was it classified asa distinct Potexvirus member based on its nucleotide sequence(10).The annotation of this contig rendered five complete openreading frames (ORFs). ORF1 (4,638 nt) encodes the RNA-polymerase (RdRp) with 1,545 amino acids. The triple gene block(TGB) is formed by ORF2 (690 nt) with 229 amino acids, ORF3(333 nt) encoding a 110-aa protein, and ORF4 (183 nt) with60 amino acids. The TGB proteins are involved in cell-to-cellmovement of viral RNA. ORF5 (678 nt) encodes the coat protein(CP) with 225 amino acids. The 5= untranslated region (UTR) is83 nt long, and the 3= UTR has 102 nt, excluding the poly(A) tail.A phylogenetic analysis using the six complete potexvirus ge-nomes from cactaceous hosts available in GenBank confirmedthat the potexvirus isolated from prickly pear is an SchVX isolate.The comparison of the partial sequence of the RdRp gene with thesequences of SchVX previously identified in Brazil (5) revealed anidentity of 94% with the isolate from H. undatus and 86% with theisolate from S. truncate.Nucleotide sequence accession number. The nucleotide se-quence of SchVX-Palma-PE has been deposited in GenBank un-der the accession number KP090203.ACKNOWLEDGMENTSThis research was sponsored by Embrapa, INCTIPP, CNPq, and FAP-DF.REFERENCES1. Santos D, Farias I, Lira M, Santos M, Arruda G, Coelho R, Dias F, MeloJ. 2006. Manejo e utilização da palma forrageira (opuntia e nopalea) emPernambuco. IPA, Recife, Brazil.2. Almeida R. 2012. Palma forrageira na alimentação de ovinos e caprinosno semiarido brasileiro. Revista Verde de Agroecologia e Desenvolvi-mento Sustentável 7:8 –14.3. Adams M, Candresse T, Hammond J, Kreuze J, Martelli G, Namba S,Pearson M, Ryu K, Vaira A. 2012. Family Alphaflexiviridae, p 904 –919.In Andrew MQ, King M, Carstens EB, Lefkowitz EJ (ed), Virus taxonomy:ninth report of the International Committee on Taxonomy of Viruses.Elsevier, Amsterdam, the Netherlands.4. Aragão F, Marinho V, Kitajima E. 1993. Cactus virus X in Cactaceaein Brazil and a novel method to purify it directly from cactus tissues.Fitopatologia Brasileira 18:112–117.5. Duarte L, Alexandre M, Rivas E, Harakava R, Galleti S, Barradas M.crossmarkGenome AnnouncementsMarch/April 2015 Volume 3 Issue 2 e00133-15 genomea.asm.org 12008. Potexvirus diversity in Cactaceae from Sao Paulo state in Brazil. JPlant Pathol 90:545–551.6. Zerbino DR, Birney E. 2008. Velvet: algorithms for de novo short readassembly using de Bruijn graphs. Genome Res 18:821– 829. http://dx.doi.org/10.1101/gr.074492.107.7. Muhire B, Martin DP, Brown JK, Navas-Castillo J, Moriones E, ZerbiniFM, Rivera-Bustamante R, Malathi VG, Briddon RW, Varsani A. 2013.A genome-wide pairwise-identity-based proposal for the classification ofviruses in the genus Mastrevirus (family Geminiviridae). Arch Virol 158:1411–1424. http://dx.doi.org/10.1007/s00705-012-1601-7.8. Edgar RC. 2004. MUSCLE: multiple sequence alignment with high accu-racy and high throughput. Nucleic Acids Res 32:1792–1797. http://dx.doi.org/10.1093/nar/gkh340.9. PlešE N, Milii D. 1966. Vergleichende Untersuchungen an Isolaten desKakteen-X-Virus mit Testpflanzen. J Phytopathol 55:197–210. http://dx.doi.org/10.1111/j.1439-0434.1966.tb02226.x.10. Koenig R, Pleij CW, Loss S, Burgermeister W, Aust H, Schiemann J.2004. Molecular characterisation of potexviruses isolated from three dif-ferent genera in the family Cactaceae. Arch Virol 149:903–914. http://dx.doi.org/10.1007/s00705-003-0268-5.Sanches et al.Genome Announcements2 genomea.asm.org March/April 2015 Volume 3 Issue 2 e00133-15

Genome assembly of schlumbergera virus x infecting prickly pear (Opuntia cochenillifera) in Brazil.

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Genome assembly of schlumbergera virus x infecting prickly pear (Opuntia cochenillifera) in Brazil.

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