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Genome sequencing of two Bell pepper endornavirus (BPEV) variants infecting Capsicum annuum in Colombia
Secuenciación del genoma de dos variantes de Bell pepper endornavirus (BPEV) que infectan Capsicum annuum en Colombia
DOI:
https://doi.org/10.15446/agron.colomb.v35n1.60626Keywords:
Genomics, molecular biology, Solanaceae, virus diseases. (en)Genómica, biología molecular, Solanaceae, enfermedades virales (es)
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Transcriptome analysis of chili and bell pepper samples from commercial plots in the municipalities of Santa Fe de Antioquia and El Peñol in the province of Antioquia revealed the presence of viral sequences with significant similarity to genomes of members of the genus Endornavirus. Assembly of the chili and bell pepper transcriptomes resulted in consensus sequences of 14,727 nt and 14,714 nt that were identified as Bell pepper endornavirus (BPEV). Both sequences were nearly identical by 99.9 % at both nucleotide and amino acid levels. The presence of BPEV was confirmed by RT-qPCR, RT-PCR and Sanger sequencing using RdRp-specific primers designed from the assembled sequences in ten independent random samples taken from the investigated bell pepper stands. The phylogenetic analysis of both BPEV variants and their affiliation within the genus Endornavirus is discussed. For our knowledge, this is the first study on this group of viruses in Colombia.
References
Chen, B., M. Bernards, and A. Wang. 2015. Complete genome sequence of a Bell pepper endornavirus isolate from Canada. Genome Announc. 3(4), pii:e00905-15. Doi: 10.1128/genomeA.00905-15
Coutts, R.H. 2005. First report of an endornavirus in the Cucurbitaceae. Virus Genes 31(3), 361-362. Doi: 10.1007/s11262-005-3255-y.
Das, S., R.E. Falloon, A. Stewart, and A.R. Pitman. 2014. Molecular characterisation of an endornavirus from Rhizoctonia solani AG-3PT infecting potato. Fungal Biol. 118(11), 924-934. Doi:10.1016/j.funbio.2014.08.003.
Debat, H.J., M. Grabiele, P.M. Aguilera, R. Bubillo, P.D. Zapata, D.A. Marti, and D.A. Ducasse. 2014. The complete genome of a putative endornavirus identified in yerba mate (Ilex paraguariensis St. Hil.). Virus Genes 49(2), 348-350. Doi: 10.1007/s11262-014-1096-2
Du, Z., W. Lin, P. Qiu, X. Liu, L. Guo, K. Wu, S. Zhang, and Z. Wu. 2016. Complete sequence of a double-stranded RNA from the phytopathogenic fungus Erysiphe cichoracearum that might represent a novel endornavirus. Arch. Virol. 161(8), 2343-2346. Doi: 10.1007/s00705-016-2911-y.
Espach, Y., H.J. Maree, and J.T. Burger. 2012. Complete genome of a novel endornavirus assembled from next-generation sequencedata. J. Virol. 86(23), 13142. Doi: 10.1128/JVI.02538-12.
Fukuhara, T, R. Koga, N. Aoki, C. Yuki, N. Yamamoto, N. Oyama, T. Udagawa, H. Horiuchi, S. Miyazaki, Y. Higashi, M. Takeshita, K. Ikeda, M. Arakawa, N. Matsumoto, and H. Moriyama. 2006. The wide distribution of endornaviruses, large doublestranded RNA replicons with plasmid-like properties. Arch. Virol. 151(5), 995-1002. Doi: 10.1007/s00705-005-0688-5
Fukuhara, T. and H. Moriyama. 2008. Endornaviruses. 109-116. Mahy, B.W.J. and M.H.V. van Regenmortel (eds.). Encyclopedia of virology 3rd ed. Elsevier, Oxford, UK.
Gibbs, M.J., R. Ryuichi, H. Moriyama, P. Pfeiffer, and T. Fukuhara. 2000. Phylogenetic analysis of some large double-stranded RNA replicons from plants suggests they evolved from a defective single-stranded RNA virus. J. Gen. Virol. 81(1), 227-233. Doi: 10.1099/0022-1317-81-1-227.
Grabherr, M.G., B.J. Haas, M. Yassour, J.Z. Levin, D.A. Thompson, I. Amit, X. Adiconis, L. Fan, R. Raychowdhury, Q. Zeng, Z. Chen, E. Mauceli, N. Hacohen, A. Gnirke, N. Rhind, F. di Palma, BW. Birren, C. Nusbaum, K. Lindblad-Toh, N. Friedman, and A. Regev. 2011. Full-length transcriptome assembly from RNAseq data without a reference genome. Nat. Biotechnol. 29(7), 644-652. Doi: 10.1038/nbt.1883
Grill, L.K. and S.J. Garger. 1981. Identification and characterization of double-stranded RNA associated with cytoplasmic male sterility in Vicia faba. Proc. Natl. Acad. Sci. USA. 78(11), 7043-7046. Doi: 10.1073/pnas.78.11.7043
Hacker, C.V., C.M. Brasier, and K.W. Buck. 2005. A double-stranded RNA from a Phytophthora species is related to the plant endornaviruses and contains a putative UDP glycosyltransferase gene. J. Gen. Virol. 86(5),1561-1570. Doi: 10.1099/vir.0.80808-0
Jo, Y., H. Choi, and W.K. Cho. 2015. De novo assembly of a Bell pepper endornavirus genome sequence using RNA sequencing data. Genome Announc. 3(2), pii: e00061-15. Doi: 10.1128/genomeA.00061-1
Jo, Y., H. Choi, J.Y. Yoon, S.K. Choi, and W.K. Cho. 2016. In silico identification of Bell pepper endornavirus from pepper transcriptomes and their phylogenetic and recombination analyses. Gene 575(2), 712-717. Doi: 10.1016/j.gene.2015.09.051
Jones, D.T., W.R. Taylor, and J.M. Thornton. 1992. The rapid generation of mutation data matrices from protein sequences. Comput. Appl. Biosci. 8(3), 275-282. Doi: 10.1093/bioinformatics/8.3.275
Khalifa, M.E. and M.N. Pearson. 2014. Molecular characterization of an endornavirus infecting the phytopathogen Sclerotinia sclerotiorum. Virus Res. 189, 303-309. Doi: 10.1016/j.virusres.2014.06.010
King, A.M.Q., E. Lefkowitz, M.J. Adams, and E.B. Cartens. 2012. Virus taxonomy: ninth report of the International Committee on Taxonomy of Viruses. Elsevier, San Diego, CA, USA. Doi: 10.1016/B978-0-12-384684-6.00048-3
Kozlakidis, Z., N.A. Brown, A. Jamal, X. Phoon, and R.H. Coutts. 2010. Incidence of endornaviruses in Phytophthora taxon douglasfir and Phytophthora ramorum. Virus Genes 40(1), 130-134. Doi: 10.1007/s11262-009-0421-7
Kumar, S., G. Stecher, and K. Tamura. 2016. MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. Mol. Biol. Evol. 33(7), 1870-1874. Doi: 10.1093/molbev/msw054
Langmead, B. and S. Salzberg. 2012. Fast gapped-read alignment with Bowtie 2. Nat. Methods. 9(4), 357-359. Doi: 10.1038/nmeth.1923
Li, W., T. Zhang, H. Sun, Y. Deng, A. Zhang, H. Chen, and K. Wang. 2014. Complete genome sequence of a novel endornavirus in the wheat sharp eyespot pathogen Rhizoctonia cerealis. Arch. Virol. 159(5), 1213-1216. Doi: 10.1007/s00705-013-1893-2
Lim, S., K.H. Kim, F. Zhao, R.H. Yoo, D. Igori, S.H. Lee, and J.S. Moon. 2015. Complete genome sequence of a novel endornavirus isolated from hot pepper. Arch. Virol. 160(12), 3153-3156. Doi: 10.1007/s00705-015-2616-7
Marchler-Bauer, A., M.K. Derbyshire, N.R. Gonzales, S. Lu, F. Chitsaz, L.Y. Geer, R.C. Geer, J. He, M. Gwadz, D.I. Hurwitz, C.J. Lanczycki, F. Lu, G.H. Marchler, J.S. Song, N. Thanki, Z. Wang, R.A. Yamashita, D. Zhang, C. Zheng, and S.H. Bryant. 2015. CDD: NCBI’s conserved domain database. Nucleic Acids Res. 43(Database issue):D222-226. Doi: 10.1093/nar/gku1221
Milne, I., M. Bayer, L. Cardle, P. Shaw, G. Stephen, F. Wright, and D. Marshall. 2010. Tablet-next generation sequence assembly visualization. Bioinformatics 26(3), 401-402. Doi: 10.1093/bioinformatics/btp666
Moriyama, H., T. Nitta, and T. Fukuhara. 1995. Double-stranded RNA in rice: a novel RNA replicon in plants. Mol. Gen. Genet. 248, 364-369. Doi: 10.1007/BF02191603
Moriyama, H., K. Kanaya, J.Z. Wang, T. Nitta, and T. Fukuhara. 1996. Stringently and developmentally regulated levels of a cytoplasmic double-stranded RNA and its high-efficiency transmission via egg and pollen in rice. Plant Mol. Biol. 31, 713-719. Doi: 10.1007/BF00019459
Moriyama, H., H. Horiuchi, T. Nitta, and T. Fukuhara. 1999. Unusual inheritance of evolutionarily-related double-stranded RNAs in interspecific hybrid between rice plants Oryza sativa and Oryza rufipogon. Plant Mol. Biol. 39(6), 1127-1136. Doi: 10.1023/A:1006118304093
Okada, R., E. Kiyota, S. Sabanadzovic, H. Moriyama, T. Fukuhara, P. Saha, M.J. Roossinck, A. Severin, and R.A. Valverde. 2011. Bell pepper endornavirus: molecular and biological properties, and occurrence in the genus Capsicum. J. Gen. Virol. 92(11), 2664-2273. Doi: 10.1099/vir.0.034686-0
Okada, R., C.K. Yong, R.A. Valverde, S. Sabanadzovic, N. Aoki, S. Hotate, E. Kiyota, H. Moriyama, and T. Fukuhara. 2013. Molecular characterization of two evolutionarily distinct endornaviruses co-infecting common bean (Phaseolus vulgaris). J. Gen. Virol. 94(1), 220-229. Doi: 10.1099/vir.0.044487-0
Okada, R., E. Kiyota, H. Moriyama, F. Toshiyuki, and R.A. Valverde. 2014. A new endornavirus species infecting Malabar spinach (Basella alba L.). Arch. Virol. 159(4), 807-809. Doi: 10.1007/s00705-013-1875-4
Osaki, H., H. Nakamura, A. Sasaki, N. Matsumoto, and K. Yoshida. 2006. An endornavirus from a hypovirulent strain of the violet root rot fungus, Helicobasidium mompa. Virus Res. 118(1-2),143-149. Doi: 10.1016/j.virusres.2005.12.004
Pfeiffer, P. 1998. Nucleotide sequence, genetic organization and expression strategy of the double-stranded RNA associated with the ‘447’ cytoplasmic male sterility trait in Vicia faba. J. Gen. Virol. 79 (Pt 10), 2349-2358. Doi: 10.1099/0022-1317-79-10-2349
Roossinck, M.J., S. Sabanadzovic, R. Okada, and R.A. Valverde. 2011. The remarkable evolutionary history of endornaviruses. J. Gen. Virol. 92(11), 2674-2678. Doi: 10.1099/vir.0.034702-0
Schena, L., F. Nigro, A. Ippolito, and D. Gallitelli. 2004. Real-time quantitative PCR: a new technology to detect and study phytopathogenic and antagonistic fungi. Eur. J. Plant Pathol. 110, 893-908. Doi: 10.1007/s10658-004-4842-9
Sela, N., N. Luria, and A. Dombrovsky. 2012. Genome assembly of bell pepper endornavirus from small RNA. J. Virol. 86(14), 7721. Doi: 10.1128/JVI.00983-12
Shang, H.H., J. Zhong, R.J. Zhang, C.Y. Chen, B.D. Gao, and H.J. Zhu. 2015. Genome sequence of a novel endornavirus from the phytopathogenic fungus Alternaria brassicicola. Arch. Virol. 160(7), 1827-1830. Doi: 10.1007/s00705-015-2426-y
Song, D., W.K. Cho, S.H. Park, Y. Jo, and K.H. Kim. 2013. Evolution of and horizontal gene transfer in the Endornavirus genus. PLoS One 8(5):e64270. Doi: 10.1371/journal.pone.0064270
Stielow, B., H.P. Klenk, and W. Menzel. 2011. Complete genome sequence of the first endornavirus from the ascocarp of the ectomycorrhizal fungus Tuber aestivum Vittad. Arch. Virol. 156(2), 343-345. Doi: 10.1007/s00705-010-0875-x
Tuomivirta, T.T., J. Kaitera, and J. Hantula. 2009. A novel putative virus of Gremmeniella abietina type B (Ascomycota: Helotiaceae) has a composite genome with endornavirus affinities. J. Gen. Virol. 90(9), 2299-2305. Doi: 10.1099/vir.0.011973-.
Valverde, R.A., S. Nameth, O. Abdalla, O. Al-Musa, P.R. Desjardins, and Dodds J.A. 1990. Indigenous double-stranded RNA from pepper (Capsicum annuum). Plant Sci. 67(2), 195-201. Doi: doi:10.1016/0168-9452(90)90243-H
Valverde, R.A. and D.L. Gutierrez. 2007. Transmission of a dsRNA in bell pepper and evidence that it consists of the genome of an endornavirus. Virus Genes 35(2), 399-403. Doi: 10.1007/s11262-007-0092-1
Villanueva, F., S. Sabanadzovic, R.A. Valverde, and J. Navas-Castillo. 2012. Complete genome sequence of a double-stranded RNA virus from avocado. J. Virol. 86(2), 1282-1283. Doi: 10.1128/JVI.06572-11
Wakarchuk, D.A. and R.I. Hamilton. 1990. Partial nucleotide sequence from enigmatic dsRNAs in Phaseolus vulgaris. Plant Mol. Biol. 14(4), 637-639. Doi: 10.1007/BF00027512
Yaegashi, H. and S. Kanematsu. 2016. Natural infection of the soilborne fungus Rosellinia necatrix with novel mycoviruses under greenhouse conditions. Virus Res. 219, 83-91. Doi: 10.1016/j.virusres.2015.11.004
Ye, J., G. Coulouris, I. Zaretskaya, I. Cutcutache, S. Rozen, and T. Madden. 2012. Primer-BLAST: A tool to design target-specific primers for polymerase chain reaction. BMC Bioinformatics 13, 134. Doi: 10.1186/1471-2105-13-134
Zabalgogeazcoa, I.A. and F.E. Gildow. 1992. Double-stranded ribonucleic acid in Barsoy barley. Plant Sci. 83, 187-194.
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