Abstract
The chrysanthemum is one of popular flowers in the world and a host for several viruses. So far, molecular interaction studies between the chrysanthemum and viruses are limited. In this study, we carried out a transcriptome analysis of chrysanthemum in response to three different viruses including Cucumber mosaic virus (CMV), Tomato spotted wilt virus (TSWV) and Potato virus X (PVX). A chrysanthemum 135K microarray derived from expressed sequence tags was successfully applied for the expression profiles of the chrysanthemum at early stage of virus infection. Finally, we identified a total of 125, 70 and 124 differentially expressed genes (DEGs) for CMV, TSWV and PVX, respectively. Many DEGs were virus specific; however, 33 DEGs were commonly regulated by three viruses. Gene ontology (GO) enrichment analysis identified a total of 132 GO terms, and of them, six GO terms related stress response and MCM complex were commonly identified for three viruses. Several genes functioning in stress response such as chitin response and ethylene mediated signaling pathway were up-regulated indicating their involvement in establishment of host immune system. In particular, TSWV infection significantly down-regulated genes related to DNA metabolic process including DNA replication, chromatin organization, histone modification and cytokinesis, and they are mostly targeted to nucleosome and MCM complex. Taken together, our comparative transcriptome analysis revealed several genes related to hormone mediated viral stress response and DNA modification. The identified chrysanthemums genes could be good candidates for further functional study associated with resistant to various plant viruses.
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This work was carried out with the support of “Next-Generation BioGreen21 Program (Project No. PJ01130902)” Rural Development Administration, Republic of Korea.
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Hoseong Choi and Yeonhwa Jo have contributed equally to this work.
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Supplementary Fig. 1
RT-PCR results displaying viral replication in each virus inoculated leaves. Mock, PVX, CMV and TSWV on the upper part indicate samples which were treated by buffer (Mock), PVX, CMV and TSWV saps, respectively. PVX, CMV, TSWV and ACTIN on the left side indicate the names of primer-pairs used for RT-PCR. PVX, CMV and TSWV specific primers amplify PVX coat protein gene (711 bp), CMV coat protein gene (657 bp) and TSWV nucleocapsid protein gene (777 bp), respectively. Actin gene (480 bp) was used as a reference gene and PC indicates positive controls which were cloned vectors containing partial viral sequence for PVX, CMV and TSWV. (TIFF 180 kb)
Supplementary Fig. 2
The directed acyclic graph (DAG) illustrating the relationships of the enriched GO terms according to biological process in response to TSWV and PVX infection. DAG showing the relationship of the enriched GO terms identified from up-regulated genes by TSWV (A), down-regulated genes by TSWV (B) and up-regulated genes by PVX (C). Red colored box identified enriched GO terms in each gene set. To simplify hierarchical clusters, GO terms with FDRs less than 0.001 were used. (TIFF 891 kb)
Supplementary Fig. 3
Direct comparison of DEGs between this and a previous study. Venn diagram displays the number of overlapped DEGs among four different conditions. For the direct comparison, all chrysanthemum DEGs were converted to corresponding Arabidopsis loci based on sequence similarity. All non-redundant DEGs in each condition were subjected for the comparison. (TIFF 439 kb)
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Choi, H., Jo, Y., Lian, S. et al. Comparative analysis of chrysanthemum transcriptome in response to three RNA viruses: Cucumber mosaic virus, Tomato spotted wilt virus and Potato virus X . Plant Mol Biol 88, 233–248 (2015). https://doi.org/10.1007/s11103-015-0317-y
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DOI: https://doi.org/10.1007/s11103-015-0317-y