Virus Genes

, Volume 52, Issue 6, pp 828–834 | Cite as

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
  • Sachin Ashok Bhor
  • Ngcebo Hlalele
  • Masahiro Nao
  • Ken-Taro Sekine
  • Takashi Yaeno
  • Naoto Yamaoka
  • Masamichi Nishiguchi
  • Augustine Gubba
  • Kappei KobayashiEmail author


The complete nucleotide sequences of Beet pseudoyellows virus (BPYV)-MI (cucumber isolate; Matsuyama, 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 difference between common BPYV cucumber strains and a unique strawberry strain.


BPYV Crinivirus Cucumber Host adaptation Strawberry 



The authors are grateful to Reiko Tomita and Kazue Obara for technical assistance, and Dennis Murphy for English editing. This study was supported in part by the United Graduate School of Agricultural Sciences, Ehime University (MSA and KK), JSPS KAKENHI Grant Number 26292026 and 15K14664 (KK), the Program for Promotion of Basic and Applied Researches in Bio-oriented Industry (MNi), JSPS KAKENHI Grant Number 24580065 (MNi), and Ehime Prefecture (MNa). MSA is supported by the Ministry of Education, Culture, Sports, Science and Technology, Japan (MEXT).


This study was funded by the National University Corporation Ehime University; Japan Society for the Promotion of Science (Grant Numbers 26292026 and 15K14664 to KK, and 24580065 to MNi), National Agriculture and Food Research Organization, and Ehime Prefecture government.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical approval

This article does not contain any studies with human participants or animals performed by any of the authors.

Supplementary material

11262_2016_1376_MOESM1_ESM.pdf (518 kb)
Supplementary material 1 (PDF 519 kb)


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Copyright information

© Springer Science+Business Media New York 2016

Authors and Affiliations

  • 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
    Email author
  1. 1.Laboratory of Plant Molecular Biology and Virology, Faculty of Agriculture, The United Graduate School of Agricultural SciencesEhime UniversityMatsuyamaJapan
  2. 2.Fruit Research StationBangladesh Agricultural Research Institute (BARI)RajshahiBangladesh
  3. 3.Department of Plant Pathology, School of Agricultural, Earth and Environmental SciencesUniversity of KwaZulu-NatalScottsvilleSouth Africa
  4. 4.Ehime Prefecture Plant Protection OfficeMatsuyamaJapan
  5. 5.Iwate Biotechnology Research CenterKitakamiJapan
  6. 6.Faculty of AgricultureUniversity of the RyukyusNakagamiJapan

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