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Transcriptome Analysis of Sugarcane Response to the Infection by Sugarcane Steak Mosaic Virus (SCSMV)

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Abstract

Sugarcane streak mosaic virus (SCSMV) is one of the pathogens causing sugarcane mosaic disease (SMD). Transcriptome of a susceptible sugarcane cultivar challenged by SCSMV was studied by high-throughput, paired-end RNA sequencing. Overall, we obtained 63,025 unigenes, including 14,384 unigenes measuring more than 1 kb each. We annotated 38,505 unigenes with COG, GO, KEGG, KOG, Pfam, Swiss-Prot and Nr. We screened 4982 differently expressed genes (DEGs) including 3841 annotated DEGs, of which 3791 were up-regulated, and 50 were down-regulated. The expression of DEGs in the three KEGG pathways, unbiquitin proteolytic system, proteasome and translational pathways in endoplasmic reticulum (ER) was investigated in response to stress and unfolded protein response (UPR). Interestingly, the DEGs in the 3 pathways were up-regulated. We tested eight DEGs encoding proteins in response to ER stress and UPR. We found that these genes were up-regulated in sugarcane challenged by SCSMV. This study presented the first report of the sugarcane transcriptome following SCSMV infection. It sheds light on the genetic mechanisms in sugarcane in response to SCSMV infection.

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Acknowledgements

We are grateful to the financial support by National High-tech R&D Program of China (863 Program) (2013AA102604), National Natural Science Foundation (31371688) and the earmarked fund for the Modern Agriculture Technology of China (CARS-20-1-1).

Author Contributions

MD and JX designed the research, analyze data and wrote the paper; GC, LP and QX performed the research; YY analyzed the data.

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Authors and Affiliations

  1. Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China

    Meng Dong, Guangyuan Cheng, Lei Peng, Qian Xu, Yongqing Yang & Jingsheng Xu

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  1. Meng Dong
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  2. Guangyuan Cheng
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  3. Lei Peng
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  4. Qian Xu
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  5. Yongqing Yang
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Correspondence to Jingsheng Xu.

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Communicated by: Sithichoke Tangphatsornruang

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Fig. S1

A. Virus detection of the tissue cultured sugarcane plantlets by RT-PCR. Lane 1, negative control. Lane 2–11 in up row, samples negative for SCMV and SrMV, respectively. Lane 2–11 in down row, in which lane 2–5 showing samples negative for SCSMV, while lane 2–5 showing samples positive for SCSMV. B. Sugarcane samples for qRT-PCR. Samples negative for SCMV in the up row. Samples negative for SrMV in the middle row. Samples positive for SCSMV in the basal row. (JPEG 495 kb)

Fig. S2

A. MA plot of DEGs. B. Volcano plot of gene expression between control and virus-infected sugarcane. (JPEG 434 kb)

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Dong, M., Cheng, G., Peng, L. et al. Transcriptome Analysis of Sugarcane Response to the Infection by Sugarcane Steak Mosaic Virus (SCSMV). Tropical Plant Biol. 10, 45–55 (2017). https://doi.org/10.1007/s12042-016-9183-2

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