The dynamic transcriptome reveals response patterns to black shank disease in tobacco (Nicotiana tabacum L.)
Zhijun Tong,
Zuoqian Fan,
Tianyu Du,
Dunhuang Fang,
Xueyi Sui,
Chuyu Ye,
Qian-Hao Zhu,
Longjiang Fan,
Bingguang Xiao,
Enhui Shen
Affiliations
Zhijun Tong
Key Laboratory of Tobacco Biotechnological Breeding, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, China
Zuoqian Fan
Institute of Crop Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
Tianyu Du
Institute of Crop Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
Dunhuang Fang
Key Laboratory of Tobacco Biotechnological Breeding, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, China
Xueyi Sui
Key Laboratory of Tobacco Biotechnological Breeding, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, China
Chuyu Ye
Institute of Crop Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
Qian-Hao Zhu
CSIRO Agriculture and Food, GPO Box 1700, Canberra 2601, Australia
Longjiang Fan
Institute of Crop Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
Bingguang Xiao
Key Laboratory of Tobacco Biotechnological Breeding, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, China; Corresponding authors at: Key Laboratory of Tobacco Biotechnological Breeding, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, China; Institute of Crop Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China.
Enhui Shen
Institute of Crop Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China; The Rural Development Academy, Zhejiang University, Hangzhou, China; Corresponding authors at: Key Laboratory of Tobacco Biotechnological Breeding, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, China; Institute of Crop Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China.
Black shank disease, caused by Phytophthora nicotianae, is one of the major causes of yield loss in tobacco production. The present study aimed to explore the dynamic transcriptome in tobacco genotypes resistant or susceptible to black shank disease and to understand the defense response of tobacco to P. nicotianae infection. Roots and stems were sampled from two resistant and two susceptible materials at 0, 12, 24, 48, and 72 h post infection and used in RNA-sequencing. Conventional approaches that identify differentially expressed genes are not the best way for handling the complex datasets, so a new method that calculates the standard deviation among samples was applied to identify transcripts with variable expression levels in roots and stems of the four materials at different time points. Of the total of 229,501 transcripts, 7,261 were found to be variable transcripts, with many of them annotated to be related to defense responses against pathogen infection. These variable transcripts showed expression patterns that varied significantly between roots and stems as well as between the resistant and the susceptible materials. Several transcripts were identified to be potential candidates for further functional characterization. Our findings provide invaluable insights into the dynamic transcriptome in defense responses of tobacco against P. nicotianae infection.
