Open Access Highly Accessed Research article

RNA-Seq derived identification of differential transcription in the chrysanthemum leaf following inoculation with Alternaria tenuissima

Huiyun Li12, Sumei Chen1, Aiping Song1, Haibin Wang1, Weimin Fang1, Zhiyong Guan1, Jiafu Jiang1* and Fadi Chen12*

Author Affiliations

1 College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China

2 Jiangsu Province Engineering Lab for Modern Facility Agriculture Technology and Equipment, Nanjing 210095, China

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BMC Genomics 2014, 15:9  doi:10.1186/1471-2164-15-9

Published: 4 January 2014



A major production constraint on the important ornamental species chrysanthemum is black spot which is caused by the necrotrophic fungus Alternaria tenuissima. The molecular basis of host resistance to A. tenuissima has not been studied as yet in any detail. Here, high throughput sequencing was taken to characterize the transcriptomic response of the chrysanthemum leaf to A. tenuissima inoculation.


The transcriptomic data was acquired using RNA-Seq technology, based on the Illumina HiSeqâ„¢ 2000 platform. Four different libraries derived from two sets of leaves harvested from either inoculated or mock-inoculated plants were characterized. Over seven million clean reads were generated from each library, each corresponding to a coverage of >350,000 nt. About 70% of the reads could be mapped to a set of chrysanthemum unigenes. Read frequency was used as a measure of transcript abundance and therefore as an identifier of differential transcription in the four libraries. The differentially transcribed genes identified were involved in photosynthesis, pathogen recognition, reactive oxygen species generation, cell wall modification and phytohormone signalling; in addition, a number of varied transcription factors were identified. A selection of 23 of the genes was transcription-profiled using quantitative RT-PCR to validate the RNA-Seq output.


A substantial body of chrysanthemum transcriptomic sequence was generated, which led to a number of insights into the molecular basis of the host response to A. tenuissima infection. Although most of the differentially transcribed genes were up-regulated by the presence of the pathogen, those involved in photosynthesis were down-regulated.

Ornamental plant; Alternaria tenuissima; RNA-Seq; Cell wall modification genes