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Comprehensive analysis of genomic variation of Hop stunt viroid

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Abstract

Hop stunt viroid (HSVd) infects a wide range of plants. In this study, we assembled de novo two HSVd genomes from the transcriptome of an apricot species. To examine HSVd variation in a single tree, we sequenced 70 HSVd genomes from unique apricot and plum trees and identified 11 HSVd variants. In addition, we analysed all known 572 HSVd sequences and identified 382 non-redundant HSVd variants. Phylogenetic analysis identified five groups of the 382 HSVd variants. Furthermore, we generated a consensus HSVd sequence by averaging across all 382 sequences. Comparative sequence analysis identified several regions showing sequence variation, while the terminal left region of the rod-like structure was highly conserved.

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Acknowledgments

This work was carried out with the support of “Next-Generation BioGreen21 Program (Project No. PJ01130902)” Rural Development Administration, Republic of Korea. This work is dedicated to the memory of my father, Tae Jin Cho (1946–2015).

Author contributions

W.K.C. and Y.J. designed the research; Y.J., H.K., H.C., J.K.C., S.L., S.M.K., S.L.K., and B.C.L. performed the research; Y.J., H.K., J.K.C., H.C., S.M.K., S.L.K., B.C.L., and W.K.C. analysed the data; and Y.J., H.K., and W.K.C. wrote the paper.

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Authors and Affiliations

  1. Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea

    Yeonhwa Jo, Hangil Kim, Hoseong Choi & Won Kyong Cho

  2. Center for Plant Aging Research, Institute for Basic Science (IBS), Daegu, 42988, Republic of Korea

    Hyosub Chu

  3. The Taejin Genome Institute, Gadam-gil 61, Hoeongseong, 25239, Republic of Korea

    Jin Kyong Cho & Won Kyong Cho

  4. College of Crop Protection and Agronomy, Qingdao Agricultural University, Qingdao, Shandong, 266109, China

    Sen Lian

  5. Crop Foundation Division, National Institute of Crop Science, RDA, Wanju, 55365, South Korea

    Sang-Min Kim, Sun-Lim Kim & Bong Choon Lee

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  1. Yeonhwa Jo
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Correspondence to Won Kyong Cho.

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Additional information

Yeonhwa Jo, Hyosub Chu and Hangil Kim contributed equally to this work.

Electronic supplementary material

Supplementary Figure 1

The phylogenetic tree for the 382 non-redundant HSVd variants generated by the Splitstree program. After alignment of 382 HSVd genome sequences using ClustalW implemented in MEGA6 program, the aligned file was converted into a nexus file. The generated nexus file was imported into Splitstree program to show phylogenetic networks for 382 non-redundant HSVd variants. Known HSVd isolates as well as HSVd variants from this study were indicated by the red color. All 11 variants in this study and nine variants from the previous study (Amari et al. 2001) were indicated by the numbers with larger font-size in bold. The 11 variants in this study are HSVd-Pl16 (3), HSVd-A2 (5), HSVd-A13 (374), HSVd-A15 (375), HSVd-A25 (376), HSVd-A32 (377), HSVd-A33 (378), HSVd-A43 (379), HSVd-Pl15 (380), HSVd-Pl20 (381), and HSVd-4-Pl2 (382); the nine variants in the previous study were HSVd.apr3 (1), HSVd.p3 (5), HSVd.apr2 (10), HSVd.apr8 (86), HSVd.apr1 (261), HSVd.apr7 (262), HSVd.apr6 (263), HSVd.apr5 (264), HSVd.apr4 (265). (PDF 73 kb)

Supplementary Table 1

The detailed information for the 382 non-redundant HSVd variants. (XLSX 90 kb)

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Jo, Y., Chu, H., Kim, H. et al. Comprehensive analysis of genomic variation of Hop stunt viroid . Eur J Plant Pathol 148, 119–127 (2017). https://doi.org/10.1007/s10658-016-1075-7

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