The agent causing bud blight disease (BBD) of sweet cherry (Prunus avium), first reported in Yamagata Prefecture, Japan, in the 1990s is graft-transmissible. Previously, little cherry virus 1 (LChV-1), little cherry virus-2 (LChV-2), cherry necrotic rusty mottle virus (CNRMV), cherry green ring mottle virus (CGRMV), and/or cherry virus A (CVA) were all detected from sweet cherry trees with BBD. Here, RNA viruses in sweet cherry trees with BBD were reinvestigated by high-throughput sequencing. Illumina RNA-sequencing of double-stranded RNAs from leaves of diseased cherry trees (S1, S2, S3, and S4) indicated that all trees were infected with at least six known viruses, LChV-1, LChV-2, CNRMV, CGRMV, CVA, prune dwarf virus (PDV), and/or apple chlorotic leaf spot virus. Thus, cherry trees with BBD are all infected with multiple viruses. Moreover, we found an undescribed novel virus of the family Betaflexiviridae (tentatively named cherry virus B, ChVB) in tree S3. The complete genome sequence of ChVB comprises 8806 nt, in which five open reading frames were found similar to the viruses of the genus Foveavirus. Homology search and phylogenetic analysis indicated that ChVB is a new species of the genus Foveavirus.
This is a preview of subscription content, log in to check access.
This study was supported by JSPS KAKENHI grant number 24380027.
Compliance with ethical standards
Conflict of interest
The authors declare that they have no conflict of interest.
Human and animal rights
This article does not contain any studies with human participants or animals.
Candresse T, Lanneau M, Revers F, Grasseau N, Macquaire G, German S, Malinowsky T, Dunez J (1995) An immunocapture PCR assay adapted to the detection and the analysis of the molecular variability of apple chlorotic leaf spot virus. Acta Hortic 386:136–147CrossRefGoogle Scholar
Coetzee B, Freeborough MJ, Maree HJ, Celton JM, Rees DJ, Burger JT (2010) Deep sequencing analysis of viruses infecting grapevines: virome of a vineyard. Virology 400:157–163CrossRefGoogle Scholar
Eastwell KC, Bernardy MG (2001) Partial characterization of a closterovirus associated with apple mealybug-transmitted little cherry disease in North America. Phytopathology 91:268–273CrossRefGoogle Scholar
Gu YH, Tao X, Lai XJ, Wang HY, Zhang YZ (2014) Exploring the polyadenylated RNA virome of sweet potato through high-throughput sequencing. PLoS One 9:e98884CrossRefGoogle Scholar
Isogai M, Uyeda I, Kimura I (1995) The genomic diversity of field isolates of rice black-streaked dwarf fijivirus. Ann Phytopathol Soc Jpn 61:575–577CrossRefGoogle Scholar
Isogai M, Aoyagi J, Nakagawa M, Kubodera Y, Satoh K, Katoh T, Inamori M, Yamashita K, Yoshikawa N (2004) Molecular detection of five cherry viruses from sweet cherry trees in Japan. J Gen Plant Pathol 70:288–291CrossRefGoogle Scholar
Ito T, Suzaki K, Nakano M (2013) Genetic characterization of novel putative rhabdovirus and dsRNA virus from Japanese persimmon. J Gen Virol 94:1917–1921CrossRefGoogle Scholar
Jelkmann W (1995) Cherry virus A: cDNA cloning of dsRNA, nucleotide sequence analysis and serology reveal a new plant capillovirus in sweet cherry. J Gen Virol 76:2015–2024CrossRefGoogle Scholar
Jelkmann W, Fechtner B, Agranovsky AA (1997) Complete genome structure and phylogenetic analysis of little cherry virus, a mealybug-transmissible closterovirus. J Gen Virol 78:2067–2071CrossRefGoogle Scholar
Jo Y, Choi H, Cho JK, Yoon JY, Choi SK, Cho WK (2015) In silico approach to reveal viral populations in grapevine cultivar Tannat using transcriptome data. Sci Rep 5:15841CrossRefGoogle Scholar
Keim-Konrad R, Jelkman W (1996) Genome analysis of the 3′-terminal part of the little cherry disease associated dsRNA reveals a monopartite clostero-like virus. Arch Virol 141:1437–1451CrossRefGoogle Scholar
Kikuchi S, Toshida K, Sato Y, Ishiguro M (2001) Studies on cherry bud blight 1. Research on actual condition and cause of sweet cherry bud blight. Bull Yamagata Hortic Exp Stn 13:11–22Google Scholar
Kummert J, Malice M, Marbot S, Lepoivre P, Steyer S, Oger R (2004) Sampling protocols and risk of error significance in molecular detection tests for fruit trees certification. Acta Hortic 657:541–546CrossRefGoogle Scholar
Liang P, Navarro B, Zhang Z, Wang H, Lu M, Xiao H, Wu Q, Zhou X, Di Serio F, Li S (2015) Identification and characterization of a novel geminivirus with a monopartite genome infecting apple trees. J Gen Virol 96:2411–2420CrossRefGoogle Scholar
Marais A, Svanella-Dumas L, Foissac X, Gentit P, Candresse T (2006) Asian prunus viruses: new related members of the family Flexiviridae in Prunus germplasm of Asian origin. Virus Res 120:176–183CrossRefGoogle Scholar
Marini DB, Gibson PG, Scott SW (2009) The complete nucleotide sequence of an isolate of Asian prunus virus 1 from peach [Prunus persica (L. Batch]. Arch Virol 154:1375–1377CrossRefGoogle Scholar
Martelli GP, Flores R, Schneider B (2011) Classification of pome and stone fruit viruses, viroids, and phytoplasmas. In: Hadidi A, Barba M, Candresse T, Jelkmann W (eds) Virus and virus-like diseases of pome and stone fruits. APS Press, St. Paul, pp 13–16CrossRefGoogle Scholar
Massart S, Olmos A, Jijakli H, Candresse T (2014) Current impact and future directions of high-throughput sequencing in plant virus diagnostics. Virus Res 188:90–96CrossRefGoogle Scholar
Roossinck MJ, Martin DP, Roumagnac P (2015) Plant virus metagenomics: advances in virus discovery. Phytopathology 105:716–727CrossRefGoogle Scholar
Rott ME, Jelkmann W (2001a) Detection and partial characterization of a second closterovirus associated with little cherry disease, little cherry virus-2. Phytopathology 91:261–267CrossRefGoogle Scholar
Rott ME, Jelkmann W (2001b) Complete nucleotide sequence of cherry necrotic rusty mottle virus. Arch Virol 146:395–401CrossRefGoogle Scholar
Rott ME, Jelkmann W (2011) Cherry necrotic rusty mottle and cherry rusty mottle viruses. In: Hadidi A, Barba M, Candresse T, Jelkmann W (eds) Virus and virus-like diseases of pome and stone fruits. APS Press, St. Paul, pp 133–136CrossRefGoogle Scholar
Sasaki S, Yamagishi N, Yoshikawa N (2011) Efficient virus-induced gene silencing in apple, pear and Japanese pear using apple latent spherical virus vectors. Plant Methods 7:15CrossRefGoogle Scholar
Takahashi T, Sugawara T, Yamatsuta T, Isogai M, Natsuaki T, Yoshikawa N (2007) Analysis of the spatial distribution of identical and two distinct virus populations differently labeled with cyan and yellow fluorescent proteins in coinfected plants. Phytopathology 97:1200–1206CrossRefGoogle Scholar
Thompson D, Howell WE, Kolber M (2011) Biological indexing. In: Hadidi A, Barba M, Candresse T, Jelkmann W (eds) Virus and virus-like diseases of pome and stone fruits. APS Press, St. Paul, pp 133–136Google Scholar
Villamor DE, Eastwell KC (2013) Viruses associated with rusty mottle and twisted leaf diseases of sweet cherry are distinct species. Phytopathology 103:1287–1295CrossRefGoogle Scholar
Villamor DE, Susaimuthu J, Eastwell KC (2015) Genomic analyses of cherry rusty mottle group and cherry twisted leaf-associated viruses reveal a possible new genus within the family betaflexiviridae. Phytopathology 105:399–408CrossRefGoogle Scholar
Wylie SJ, Luo H, Li H, Jones MG (2012) Multiple polyadenylated RNA viruses detected in pooled cultivated and wild plant samples. Arch Virol 157:271–284CrossRefGoogle Scholar
Wylie SJ, Li H, Saqib M, Jones MG (2014) The global trade in fresh produce and the vagility of plant viruses: a case study in garlic. PLoS One 9:e105044CrossRefGoogle Scholar
Zerbino DR, Birney E (2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18:821–829CrossRefGoogle Scholar
Zhang YP, Kirkpatrick BC, Smart CD, Uyemoto JK (1998) cDNA cloning and molecular characterization of cherry green ring mottle virus. J Gen Virol 79:2275–2281CrossRefGoogle Scholar