Review of Beet pseudoyellows virus genome structure built the consensus genome organization of cucumber strains and highlighted the unique feature of strawberry strain Md. Shamim Akhter 1,2 • Sachin Ashok Bhor 1 • Ngcebo Hlalele 3 • Masahiro Nao 4 • Ken-Taro Sekine 5,6 • Takashi Yaeno 1 • Naoto Yamaoka 1 • Masamichi Nishiguchi 1 • Augustine Gubba 3 • Kappei Kobayashi 1 Received: 2 May 2016 / Accepted: 19 July 2016 / Published online: 26 July 2016 Ó Springer Science+Business Media New York 2016 Abstract The complete nucleotide sequences of Beet pseudoyellows virus (BPYV)-MI (cucumber isolate; Mat- suyama, Idai) genomic RNAs 1 and 2 were determined and compared with the previously sequenced Japanese cucumber strain (BPYV-JC) and a strawberry strain (BPYV-S). The RNA 2 of BPYV-MI showed 99 % nucleotide sequence identity with both BPYV-JC and -S having highly conserved eight ORFs. In contrast, the RNA1 of BPYV-MI showed sequence identities of 98 and 86 % with BPYV-JC and -S, respectively. Phylogenetic analysis of RNA-dependent RNA polymerase (RdRp) coding sequences from three fully sequenced BPYV strains and five partially sequenced cucurbit-infecting BPYV strains from Japan and South Africa has shown that cucurbit-infecting strains are closer to each other than to BPYV-S. In addition, the strawberry strain BPYV-S has an ORF2 in the downstream of RdRp gene in RNA1, but all the cucumber strains, BPYV-JC, -MI, and those from South Africa, lacked the ORF2 of RNA1, highlighting the dif- ference between common BPYV cucumber strains and a unique strawberry strain. Keywords BPYV Á Crinivirus Á Cucumber Á Host adaptation Á Strawberry Introduction The Beet pseudoyellows virus (BPYV), belonging to family Closteroviridae genus Crinivirus and transmitted by greenhouse whitefly (Trialeurodes vaporariorum Westwood), was first documented in the United States [1]. In Japan, yellowing disease of greenhouse cucumber (Cucumis sativus L.) and muskmelon (C. melo L.) caused by BPYV cucumber strain was first described in 1979: in the field, with the disease incidence of almost 100 % of cucumber plants infected resulting in 30–40 % loss of fruit yield [2]. The virus has subsequently been reported from France, The Netherlands, Australasia, and Italy [3–5]. BPYV has a wide host range and infects agricul- tural crops as well as weeds and ornamentals. BPYV cucumber strain, isolated in Saitama Prefecture, Japan, has a broad host range and was able to infect 30 plant species from nine families following experimental trans- mission by whiteflies [6]. A high incidence of cucumber yellowing disease caused by BPYV has also been reported Edited by Thomas Hohn. Electronic supplementary material The online version of this article (doi:10.1007/s11262-016-1376-0) contains supplementary material, which is available to authorized users. & Kappei Kobayashi kappei@ehime-u.ac.jp 1 Laboratory of Plant Molecular Biology and Virology, Faculty of Agriculture, The United Graduate School of Agricultural Sciences, Ehime University, 3-5-7 Tarumi, Matsuyama, Ehime 790-8566, Japan 2 Fruit Research Station, Bangladesh Agricultural Research Institute (BARI), Rajshahi 6206, Bangladesh 3 Department of Plant Pathology, School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Private Bag X01, Scottsville, Pietermaritzburg 3209, South Africa 4 Ehime Prefecture Plant Protection Office, Matsuyama, Ehime 790-2405, Japan 5 Iwate Biotechnology Research Center, Kitakami, Iwate 024-0003, Japan 6 Present Address: Faculty of Agriculture, University of the Ryukyus, Nakagami, Okinawa 903-0213, Japan 123 Virus Genes (2016) 52:828–834 DOI 10.1007/s11262-016-1376-0